3VM8

Crystal structure of the human APOBEC3C having HIV-1 Vif-binding interface

• PDB DOI: https://doi.org/10.2210/pdb3VM8/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-12-09 Released: 2012-10-03 
• Deposition Author(s): Kitamura, S., Suzuki, A., Watanabe, N., Iwatani, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.302 
• R-Value Work: 0.228 
• R-Value Observed: 0.232 

Literature

Crystal structure of the human APOBEC3C having HIV-1 Vif-binding interface

Kitamura, S., Ode, H., Nakashima, M., Imahashi, M., Naganawa, Y., Ibe, S., Yokomaku, Y., Watanabe, N., Suzuki, A., Sugiura, W., Iwatani, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.83 kDa 
• Atom Count: 3,176 
• Modelled Residue Count: 374 
• Deposited Residue Count: 380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable DNA dC->dU-editing enzyme APOBEC-3C	A, B	190	Homo sapiens	Mutation(s): 0  Gene Names: APOBEC3C, APOBEC1L, PBI EC: 3.5.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRW3 (Homo sapiens) Explore Q9NRW3  Go to UniProtKB:  Q9NRW3
PHAROS:  Q9NRW3 GTEx:  ENSG00000244509

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.302 
• R-Value Work: 0.228 
• R-Value Observed: 0.232 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.419	α = 90
b = 104.419	β = 90
c = 74.502	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Kitamura, S., Suzuki, A., Watanabe, N., Iwatani, Y.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description