5TV4

3D cryo-EM reconstruction of nucleotide-free MsbA in lipid nanodisc

PDB DOI: https://doi.org/10.2210/pdb5TV4/pdb
EM Map EMD-8469: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Escherichia coli O157:H7
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2016-11-08 Released: 2017-09-20
Deposition Author(s): Mi, W., Walz, T., Liao, M.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.20 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.

Macromolecule Content

Total Structure Weight: 137.76 kDa
Atom Count: 6,548
Modelled Residue Count: 1,140
Deposited Residue Count: 1,210
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipid A export ATP-binding/permease protein MsbA	A, B	605	Escherichia coli O157:H7	Mutation(s): 0 Gene Names: msbA, Z1260, ECs0997 EC: 3.6.3 Membrane Entity: Yes
UniProt
Find proteins for P60752 (Escherichia coli (strain K12)) Explore P60752 Go to UniProtKB: P60752
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60752
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
L-glycero-alpha-D-manno-heptopyranose-(1-7)-L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-alpha-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose	C	7		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G75876QI GlyCosmos: G75876QI

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FTT Query on FTT Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B]	H [auth B], J [auth B], L [auth B], M [auth B]	3-HYDROXY-TETRADECANOIC ACID C₁₄ H₂₈ O₃ ATRNZOYKSNPPBF-CYBMUJFWSA-N		Interactions Focus chain H [auth B] Focus chain J [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain H [auth B] Focus chain J [auth B] Focus chain L [auth B] Focus chain M [auth B]
MYR Query on MYR Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
DAO Query on DAO Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B]	K [auth B]	LAURIC ACID C₁₂ H₂₄ O₂ POULHZVOKOAJMA-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B]	D [auth A], E [auth A], F [auth A], G [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	1.4

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-09-20

Deposition Author(s):

Mi, W.

Walz, T.

Liao, M.

Revision History (Full details and data files)

Version 1.0: 2017-09-20
Type: Initial release
Version 1.1: 2017-09-27
Changes: Database references
Version 1.2: 2017-11-08
Changes: Derived calculations
Version 1.3: 2019-11-06
Changes: Data collection, Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary

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Deposit Data

Help and Resources

5TV4

3D cryo-EM reconstruction of nucleotide-free MsbA in lipid nanodisc

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)