8TSO

KDL bound, nucleotide-free MsbA in open, outward-facing conformation

PDB DOI: https://doi.org/10.2210/pdb8TSO/pdb
EM Map EMD-41596: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTMmpstruc

Deposited: 2023-08-11 Released: 2024-06-19
Deposition Author(s): Yang, B., Zhang, T., Lyu, J., Laganowsky, A.D., Zhao, M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.68 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Native mass spectrometry captures snapshots of the MsbA transport cycle

Zhang, T., Lyu, J., Yang, B., Zhao, M., Laganowsky, A.D.

To be published.

Macromolecule Content

Total Structure Weight: 135.08 kDa
Atom Count: 9,298
Modelled Residue Count: 1,146
Deposited Residue Count: 1,166
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-binding transport protein MsbA	A, B	583	Escherichia coli	Mutation(s): 0 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KDL (Subject of Investigation/LOI) Query on KDL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B]	E [auth A], F [auth B]	(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]-5-oxidanyl-oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid C₁₁₀ H₂₀₂ N₂ O₃₉ P₂ DIXUKJUHGLIZGU-OIPVZEHTSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]
CXE Query on CXE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B]	C [auth A], D [auth A], G [auth B], H [auth B]	PENTAETHYLENE GLYCOL MONODECYL ETHER C₂₀ H₄₂ O₆ QAXPOSPGRHYIHE-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.68 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM121751
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM139876
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM138863
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM145416
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM143052