4CDG

Crystal structure of the Bloom's syndrome helicase BLM in complex with Nanobody

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d4cdgc1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	LLAMA (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
C	d4cdgc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	LLAMA (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
D	d4cdgd1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	LLAMA (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
D	d4cdgd2	Artifacts	Tags	Tags	Tags	C-terminal Tags	LLAMA (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	HRDC-like	8055805	3000132	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecQ zinc finger-like	8055801	3002316	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8055797	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8055803	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8055796	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HRDC-like	8055805	3000132	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecQ zinc finger-like	8055801	3002316	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8055803	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8055797	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8055796	3002019	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF09382	e4cdgA9	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF09382	ECOD (1.6)
A	PF00570	e4cdgA10	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF00570	ECOD (1.6)
A	PF00270	e4cdgA12	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00270	ECOD (1.6)
A	PF00271,PF16124	e4cdgA11	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00271,PF16124	ECOD (1.6)
B	PF09382	e4cdgB9	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF09382	ECOD (1.6)
B	PF00570	e4cdgB10	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF00570	ECOD (1.6)
B	PF00270	e4cdgB12	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00270	ECOD (1.6)
B	PF00271,PF16124	e4cdgB11	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00271,PF16124	ECOD (1.6)
C	PF07686	e4cdgC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
D	PF07686	e4cdgD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
A	1.10.150.80	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
B	1.10.150.80	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, D	Heavy Chain	IGHV1	-	bloom syndrome protein	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00270	DEAD/DEAH box helicase (DEAD)	DEAD/DEAH box helicase	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ...	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.	Domain
A, B	PF00271	Helicase conserved C-terminal domain (Helicase_C)	Helicase conserved C-terminal domain	The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.	Domain
A, B	PF00570	HRDC domain (HRDC)	HRDC domain	The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains ...	The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains [4].	Domain
A, B	PF16124	RecQ zinc-binding (RecQ_Zn_bind)	RecQ zinc-binding	This domain is the zinc-binding domain of ATP-dependent DNA helicase RecQ [1-2].	Domain
A, B	PF09382	RQC domain (RQC)	RQC domain	This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure. The RQC domain, found only in RecQ family enzymes, is a high affinity G4 DNA binding domain [1].	Domain
A, B	PF16204	BDHCT-box associated domain on Bloom syndrome protein (BDHCT_assoc)	BDHCT-box associated domain on Bloom syndrome protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	BLOOM SYNDROME PROTEIN	DNA binding DNA/DNA annealing activity binding annealing activity organic cyclic compound binding single-stranded DNA binding nucleic acid binding ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity ATP-dependent activity forked DNA-dependent helicase activity DNA helicase activity DNA binding DNA/DNA annealing activity binding annealing activity organic cyclic compound binding single-stranded DNA binding nucleic acid binding ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity ATP-dependent activity forked DNA-dependent helicase activity DNA helicase activity helicase activity telomeric G-quadruplex DNA binding sequence-specific DNA binding G-quadruplex DNA binding telomeric DNA binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA secondary structure binding four-way junction DNA binding 3'-5' DNA helicase activity bubble DNA binding identical protein binding protein binding p53 binding Y-form DNA binding protein homodimerization activity protein dimerization activity oxidized DNA binding oxidized purine DNA binding damaged DNA binding 8-hydroxy-2'-deoxyguanosine DNA binding telomeric D-loop binding D-loop DNA binding four-way junction helicase activity molecular function activator activity molecular function regulator activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides cation binding transition metal ion binding zinc ion binding metal ion binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular component organization or biogenesis double-strand break repair cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular component organization or biogenesis double-strand break repair DNA double-strand break processing primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process metabolic process macromolecule metabolic process DNA repair DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity DNA replication replication fork processing cellular response to nitrogen compound response to organic substance response to alkaloid cellular response to endogenous stimulus cellular response to camptothecin cellular response to organic substance cellular response to alkaloid response to organic cyclic compound response to alcohol response to organonitrogen compound response to endogenous stimulus cellular response to organic cyclic compound response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to alcohol cellular response to organonitrogen compound response to camptothecin response to chemical response to X-ray response to ionizing radiation response to radiation response to abiotic stimulus cellular response to ionizing radiation cellular response to radiation cellular response to abiotic stimulus cellular response to environmental stimulus G-quadruplex DNA unwinding organelle organization DNA geometric change chromosome organization DNA conformation change regulation of DNA recombination negative regulation of biological process regulation of primary metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of biological process negative regulation of metabolic process DNA recombination biological regulation regulation of macromolecule metabolic process negative regulation of DNA recombination negative regulation of DNA metabolic process regulation of metabolic process regulation of DNA metabolic process formation of extrachromosomal circular DNA telomere organization telomere maintenance telomere maintenance via telomere trimming t-circle formation DNA duplex unwinding resolution of DNA recombination intermediates regulation of cellular process regulation of protein modification process regulation of catalytic activity regulation of protein phosphorylation regulation of cyclin-dependent protein kinase activity regulation of transferase activity regulation of cyclin-dependent protein serine/threonine kinase activity regulation of phosphate metabolic process phosphate-containing compound metabolic process protein metabolic process cell cycle phosphorus metabolic process protein modification process regulation of cell cycle organonitrogen compound metabolic process protein phosphorylation phosphorylation cellular metabolic process regulation of protein metabolic process regulation of cellular metabolic process regulation of protein kinase activity regulation of molecular function regulation of kinase activity macromolecule modification regulation of protein serine/threonine kinase activity regulation of phosphorylation regulation of phosphorus metabolic process negative regulation of cell division negative regulation of cellular process cell division regulation of cell division regulation of DNA-templated DNA replication regulation of DNA replication telomeric loop disassembly telomeric D-loop disassembly regulation of cell cycle phase transition DNA damage checkpoint signaling signaling G2/M transition of mitotic cell cycle mitotic G2 DNA damage checkpoint signaling negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle mitotic G2/M transition checkpoint cell communication regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling negative regulation of cell cycle phase transition signal transduction cell cycle process cell cycle G2/M phase transition negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process DNA integrity checkpoint signaling regulation of cell cycle G2/M phase transition negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic cell cycle process negative regulation of cell cycle G2/M phase transition signal transduction in response to DNA damage negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition recombinational repair double-strand break repair via homologous recombination nuclear DNA replication cell cycle DNA replication telomere maintenance via semi-conservative replication positive regulation of macromolecule biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process cellular response to inorganic substance response to inorganic substance cellular response to hydroxyurea response to hydroxyurea protein homooligomerization DNA unwinding involved in DNA replication	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle nuclear periphery nuclear matrix nucleolus protein-containing complex catalytic complex RecQ family helicase-topoisomerase III complex nucleoplasm replication fork condensed nuclear chromosome lateral element synaptonemal structure synaptonemal complex condensed chromosome nuclear body PML body
C, D	NANOBODY	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002121	HRDC domain	Domain
A, B	IPR032437	RecQ-like DNA helicase BLM, N-terminal domain	Domain
A, B	IPR032439	RecQ-like DNA helicase BLM, BDHCT-box associated domain	Domain
A, B	IPR012532	BDHCT	Domain
A, B	IPR011545	DEAD/DEAH box helicase domain	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR010997	HRDC-like superfamily	Homologous Superfamily
A, B	IPR001650	Helicase, C-terminal domain-like	Domain
A, B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR004589	DNA helicase, ATP-dependent, RecQ type	Family
A, B	IPR032284	ATP-dependent DNA helicase RecQ, zinc-binding domain	Domain
A, B	IPR002464	DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site	Conserved Site
A, B	IPR018982	RQC domain	Domain
A, B	IPR044876	HRDC domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P54132	Bloom syndrome lung adenocarcinoma malignant colon neoplasm myocardial infarction osteosarcoma attention deficit hyperactivity disorder, inattentive type pancreatic intraductal papillary-mucinous neoplasm Primary microcephaly colorectal cancer Werner syndrome endogenous depression hematopoietic and lymphoid system neoplasm intellectual disability large cell medulloblastoma lung cancer Bloom syndrome lung adenocarcinoma malignant colon neoplasm myocardial infarction osteosarcoma attention deficit hyperactivity disorder, inattentive type pancreatic intraductal papillary-mucinous neoplasm Primary microcephaly colorectal cancer Werner syndrome endogenous depression hematopoietic and lymphoid system neoplasm intellectual disability large cell medulloblastoma lung cancer malignant glioma non-small cell lung carcinoma ovarian cancer autism spectrum disorder pilocytic astrocytoma breast cancer psoriasis cutaneous lupus erythematosus glioblastoma hypertensive disorder interstitial cystitis leukemia lymphoma malignant mesothelioma osteogenesis imperfecta pancreatic intraductal papillary-mucinous carcinoma bipolar disorder pituitary cancer cancer squamous cell carcinoma ductal breast carcinoma in situ heart disease inflammatory bowel disease invasive ductal breast carcinoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.