8ZKC | pdb_00008zkc

iron-sulfur cluster transfer protein ApbC

• PDB DOI: https://doi.org/10.2210/pdb8ZKC/pdb

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-16 Released: 2024-06-12 
• Deposition Author(s): Yang, J., Liu, L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of the iron-sulfur cluster transfer protein ApbC from Escherichia coli.

Yang, J., Duan, Y.F., Liu, L.

(2024) Biochem Biophys Res Commun 722: 150167-150167

• PubMed: 38797154 
• DOI: https://doi.org/10.1016/j.bbrc.2024.150167
• Primary Citation Related Structures: 
  8ZKC


• PubMed Abstract: 
  

  Iron-sulfur (Fe-S) clusters are ubiquitous and are necessary to sustain basic life processes. The intracellular Fe-S clusters do not form spontaneously and many proteins are required for their biosynthesis and delivery. The bacterial P-loop NTPase family protein ApbC participates in Fe-S cluster assembly and transfers the cluster into apoproteins, with the Walker A motif and CxxC motif being essential for functionality of ApbC in Fe-S protein biogenesis. However, the structural basis underlying the ApbC activity and the motifs' role remains unclear. Here, we report the crystal structure of Escherichia coli ApbC at 2.8 Å resolution. The dimeric structure is in a W shape and the active site is located in the 2-fold center. The function of the motifs can be annotated by structural analyses. ApbC has an additional N-terminal domain that differs from other P-loop NTPases, possibly conferring its inherent specificity in vivo.

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Organizational Affiliation: 
• School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China. Electronic address: [e-mail].
School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.32 kDa 
• Atom Count: 2,588 
• Modeled Residue Count: 346 
• Deposited Residue Count: 408 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-sulfur cluster carrier protein	A	408	Escherichia coli	Mutation(s): 0  Gene Names: mrp, b2113, JW2100
UniProt
Find proteins for P0AF08 (Escherichia coli (strain K12)) Explore P0AF08  Go to UniProtKB:  P0AF08

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.27	α = 90
b = 74.27	β = 90
c = 167.11	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Yang, J., Liu, L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release