6LCP

Cryo-EM structure of Dnf1 from Chaetomium thermophilum in the E2P state

PDB DOI: https://doi.org/10.2210/pdb6LCP/pdb
EM Map EMD-0872: EMDB EMDataResource

Classification: LIPID TRANSPORT
Organism(s): Thermochaetoides thermophila DSM 1495
Expression System: Saccharomyces cerevisiae
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2019-11-19 Released: 2020-04-29
Deposition Author(s): He, Y., Xu, J., Wu, X., Li, L.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.48 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Structures of a P4-ATPase lipid flippase in lipid bilayers.

He, Y., Xu, J., Wu, X., Li, L.

(2020) Protein Cell 11: 458-463

PubMed: 32303992 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1007/s13238-020-00712-y
Primary Citation of Related Structures:
6LCP, 6LCR

Organizational Affiliation

State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China.

Macromolecule Content

Total Structure Weight: 226.78 kDa
Atom Count: 12,421
Modelled Residue Count: 1,516
Deposited Residue Count: 1,962
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipid-transporting ATPase	A	1,555	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0012810 EC: 7.6.2.1 Membrane Entity: Yes
UniProt
Find proteins for G0S196 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S196 Go to UniProtKB: G0S196
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0S196
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cdc50	B	407	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0052360 Membrane Entity: Yes
UniProt
Find proteins for G0SDN0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SDN0 Go to UniProtKB: G0SDN0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0SDN0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose	C	2		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G00891MP GlyCosmos: G00891MP GlyGen: G00891MP

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	4		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	2		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P5S Query on P5S Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A]	K [auth A]	O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine C₄₂ H₈₂ N O₁₀ P TZCPCKNHXULUIY-RGULYWFUSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
POV Query on POV Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	I [auth A], J [auth A]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B]	L [auth B], M [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain L [auth B] Focus chain M [auth B]
BEF Query on BEF Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900112 Query on PRD_900112	C	3alpha-alpha-mannobiose	Oligosaccharide / Metabolism		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.48 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-04-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31870835

Revision History (Full details and data files)

Version 1.0: 2020-04-29
Type: Initial release
Version 1.1: 2020-06-10
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary