7PH3 | pdb_00007ph3

AMP-PNP bound nanodisc reconstituted MsbA with nanobodies, spin-labeled at position A60C

PDB DOI: https://doi.org/10.2210/pdb7PH3/pdb
EM Map EMD-13405: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli K-12, Vicugna pacos
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM mpstruc

Deposited: 2021-08-16 Released: 2022-08-24
Deposition Author(s): Parey, K., Januliene, D., Galazzo, L., Meier, G., Vecchis, D., Striednig, B., Hilbi, H., Schaefer, L.V., Kuprov, I., Bordignon, E., Seeger, M.A., Moeller, A.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The ABC transporter MsbA adopts the wide inward-open conformation in E. coli cells.

Galazzo, L., Meier, G., Januliene, D., Parey, K., De Vecchis, D., Striednig, B., Hilbi, H., Schafer, L.V., Kuprov, I., Moeller, A., Bordignon, E., Seeger, M.A.

(2022) Sci Adv 8: eabn6845-eabn6845

PubMed: 36223470 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.abn6845
Primary Citation Related Structures:
7NDF, 7PH2, 7PH3, 7PH4, 7PH7

PubMed Abstract:
Membrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their physiological environment. However, to truly understand the biophysical properties of membrane proteins in a physiological environment, they must be investigated within living cells. Here, we used a spin-labeled nanobody to interrogate the conformational cycle of the ABC transporter MsbA by double electron-electron resonance. Unexpectedly, the wide inward-open conformation of MsbA, commonly considered a nonphysiological state, was found to be prominently populated in Escherichia coli cells. Molecular dynamics simulations revealed that extensive lateral portal opening is essential to provide access of its large natural substrate core lipid A to the binding cavity. Our work paves the way to investigate the conformational landscape of membrane proteins in cells.

Organizational Affiliation

Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany.

Macromolecule Content

Total Structure Weight: 161.35 kDa
Atom Count: 10,968
Modeled Residue Count: 1,380
Deposited Residue Count: 1,420
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent lipid A-core flippase	A, B	593	Escherichia coli K-12	Mutation(s): 0 Gene Names: msbA, b0914, JW0897 EC: 7.5.2.6 Membrane Entity: Yes
UniProt
Find proteins for P60752 (Escherichia coli (strain K12)) Explore P60752 Go to UniProtKB: P60752
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60752
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody Nb_MsbA#1	C, D	117	Vicugna pacos	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3PE Query on 3PE Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A], K [auth B]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B]
88T (Subject of Investigation/LOI) Query on 88T Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C]	M [auth C], O [auth D]	(1~{R},4~{R},11~{S},14~{S},19~{Z})-19-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylimino]-7,8,17,18-tetraoxa-1,4,11,14-tetrazatricyclo[12.6.2.2^{4,11}]tetracosane-6,9,16-trione C₂₂ H₃₂ N₆ O₉ KCVYYVOXIBCERI-QJOMJCCJSA-N		Interactions Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain M [auth C] Focus chain O [auth D]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
GD (Subject of Investigation/LOI) Query on GD Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C]	N [auth C], P [auth D]	GADOLINIUM ATOM Gd UIWYJDYFSGRHKR-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Focus chain P [auth D] Interactions & Density Focus chain N [auth C] Focus chain P [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v3.0.1

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	CRC944
German Research Foundation (DFG)	Germany	SCHA 1574/6-1
German Research Foundation (DFG)	Germany	EXC 2033 - 390677874 - RESOLV