7D08 | pdb_00007d08

Acinetobacter MlaFEDB complex in ATP-bound Vtrans1 conformation

• PDB DOI: https://doi.org/10.2210/pdb7D08/pdb
• EM Map EMD-30526: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli K-12
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2020-09-09 Released: 2020-12-16 
• Deposition Author(s): Zhang, Y.Y., Fan, Q.X., Chi, X.M., Zhou, Q., Li, Y.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structures of Acinetobacter baumannii glycerophospholipid transporter.

Zhang, Y., Fan, Q., Chi, X., Zhou, Q., Li, Y.

(2020) Cell Discov 6: 86-86

• PubMed: 33298869 
• DOI: https://doi.org/10.1038/s41421-020-00230-5
• Primary Citation of Related Structures:  
  7D06, 7D08, 7D09, 7D0A

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Organizational Affiliation: 
• Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, Zhejiang, 310024, China.
Key Laboratory of Structural Biology of Zhejiang Province, Westlake University, Hangzhou, Zhejiang, 310024, China.
Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China.
Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, Zhejiang, 310024, China. [e-mail].
Key Laboratory of Structural Biology of Zhejiang Province, Westlake University, Hangzhou, Zhejiang, 310024, China. [e-mail].
Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China. [e-mail].
Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, Zhejiang, 310024, China. [e-mail].
Key Laboratory of Structural Biology of Zhejiang Province, Westlake University, Hangzhou, Zhejiang, 310024, China. [e-mail].
Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B2C2D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 281.66 kDa 
• Atom Count: 17,802 
• Modeled Residue Count: 2,374 
• Deposited Residue Count: 2,600 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intermembrane phospholipid transport system permease protein MlaE	A, D	258	Acinetobacter baumannii	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for V5V9F4 (Acinetobacter baumannii) Explore V5V9F4  Go to UniProtKB:  V5V9F4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter ATP-binding protein	B, E	273	Acinetobacter baumannii	Mutation(s): 0
UniProt
Find proteins for A0A086HZU3 (Acinetobacter baumannii) Explore A0A086HZU3  Go to UniProtKB:  A0A086HZU3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-sigma factor antagonist	C, F	103	Acinetobacter baumannii	Mutation(s): 0
UniProt
Find proteins for V5V9K5 (Acinetobacter baumannii) Explore V5V9K5  Go to UniProtKB:  V5V9K5

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
MCE family protein	G, H, I, J, K, L	222	Acinetobacter baumannii	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for V5V921 (Acinetobacter baumannii) Explore V5V921  Go to UniProtKB:  V5V921

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	M [auth B], N [auth E]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0.6

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Zhang, Y.Y., Fan, Q.X., Chi, X.M., Zhou, Q., Li, Y.Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31930059

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2020-12-23
  Changes: Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references