9FHC | pdb_00009fhc

Crystallographic structure of AcrB V612F with bound minocycline

• PDB DOI: https://doi.org/10.2210/pdb9FHC/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli K-12, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2024-05-27 Released: 2025-06-11 
• Deposition Author(s): Lazarova, M., Diederichs, K., Pos, K.M.
• Funding Organization(s): Swiss National Science Foundation, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.238 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.208 (DCC) 

Starting Model: experimental

Literature

Crystallographic structure of AcrB V612F with bound minocycline

Lazarova, M., Diederichs, K., Pos, K.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 133.56 kDa 
• Atom Count: 9,428 
• Modeled Residue Count: 1,199 
• Deposited Residue Count: 1,226 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux pump subunit AcrB	A	1,057	Escherichia coli K-12	Mutation(s): 1  Gene Names: acrB, acrE, b0462, JW0451 Membrane Entity: Yes
UniProt
Find proteins for P31224 (Escherichia coli (strain K12)) Explore P31224  Go to UniProtKB:  P31224

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPIN	B	169	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MIY (Subject of Investigation/LOI)	C [auth A]	(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE C23 H27 N3 O7 DYKFCLLONBREIL-KVUCHLLUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.238 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.208 (DCC) 

Diffraction Data: https://doi.org/10.5281/zenodo.11472085

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 227.46	α = 90
b = 227.46	β = 90
c = 227.46	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Lazarova, M., Diederichs, K., Pos, K.M.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	3100A0_118402
German Research Foundation (DFG)	Germany	SFB807-P18
German Research Foundation (DFG)	Germany	SFB1507-P3
German Research Foundation (DFG)	Germany	DFG-EXC115

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release