2EK1 | pdb_00002ek1

Crystal structure of RNA-binding motif of human rna-binding protein 12

• PDB DOI: https://doi.org/10.2210/pdb2EK1/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2007-03-22 Released: 2008-04-01 
• Deposition Author(s): Ihsanawati, Bessho, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.274 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Crystal structure of RNA-binding motif of human rna-binding protein 12

Ihsanawati, Bessho, Y., Shirouzu, M., Yokoyama, S.

To be published.

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 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 80.54 kDa 
• Atom Count: 5,266 
• Modeled Residue Count: 629 
• Deposited Residue Count: 760 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein 12	A, B, C, D, E, F, G, H	95	Homo sapiens	Mutation(s): 0  Gene Names: RBM12, KIAA0765
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTZ6 (Homo sapiens) Explore Q9NTZ6  Go to UniProtKB:  Q9NTZ6
PHAROS:  Q9NTZ6 GTEx:  ENSG00000244462

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.274 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.879	α = 90
b = 103.227	β = 91.5
c = 62.189	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-01 
Deposition Author(s): Ihsanawati, Bessho, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-04-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary