4IVE

Crystal structure of a polyadenylate-binding protein 3 (PABPC3) from Homo sapiens at 2.30 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4IVE/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-01-22 Released: 2013-02-06 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.212 
• R-Value Work: 0.201 
• R-Value Observed: 0.201 

Literature

Crystal structure of a polyadenylate-binding protein 3 (PABPC3) from Homo sapiens at 2.30 A resolution

Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Biological Assembly 7  

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

Biological assembly 7 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.91 kDa 
• Atom Count: 2,514 
• Modelled Residue Count: 305 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyadenylate-binding protein 3	A, B, C, D	98	Homo sapiens	Mutation(s): 0  Gene Names: BC027617, PABP3, PABPC3, PABPL3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H361 (Homo sapiens) Explore Q9H361  Go to UniProtKB:  Q9H361
PHAROS:  Q9H361 GTEx:  ENSG00000151846

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A], F [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.212 
• R-Value Work: 0.201 
• R-Value Observed: 0.201 
• Space Group: P 4₃
• Diffraction Data: https://doi.org/10.18430/M34IVE

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.395	α = 90
b = 67.395	β = 90
c = 101.38	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-06 
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

Revision History  

• Version 1.0: 2013-02-06
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-02-01
  Changes: Database references, Derived calculations