1OKI

Crystal structure of truncated human beta-B1-crystallin

• PDB DOI: https://doi.org/10.2210/pdb1OKI/pdb

• Classification: EYE LENS PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-07-25 Released: 2004-01-22 
• Deposition Author(s): van Montfort, R.L.M., Bateman, O.A., Lubsen, N.H., Slingsby, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.201 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

Starting Model: experimental

Literature

Crystal Structure of Truncated Human Beta-B1-Crystallin

Van Montfort, R.L.M., Bateman, O.A., Lubsen, N.H., Slingsby, C.

(2003) Protein Sci 12: 2606

• PubMed: 14573871 
• DOI: https://doi.org/10.1110/ps.03265903
• Primary Citation of Related Structures:  
  1OKI


• PubMed Abstract: 
  

  Crystallins are long-lived proteins packed inside eye lens fiber cells that are essential in maintaining the transparency and refractive power of the eye lens. Members of the two-domain betagamma-crystallin family assemble into an array of oligomer sizes, forming intricate higher-order networks in the lens cell. Here we describe the 1.4 angstroms resolution crystal structure of a truncated version of human betaB1 that resembles an in vivo age-related truncation. The structure shows that unlike its close homolog, betaB2-crystallin, the homodimer is not domain swapped, but its domains are paired intramolecularly, as in more distantly related monomeric gamma-crystallins. However, the four-domain dimer resembles one half of the crystallographic bovine betaB2 tetramer and is similar to the engineered circular permuted rat betaB2. The crystal structure shows that the truncated betaB1 dimer is extremely well suited to form higher-order lattice interactions using its hydrophobic surface patches, linker regions, and sequence extensions.

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Organizational Affiliation: 

Department of Crystallography, Birkbeck College, London WC1E 7HX, UK.

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 PQS (software)

Macromolecule Content

• Total Structure Weight: 48.5 kDa 
• Atom Count: 3,476 
• Modelled Residue Count: 367 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA CRYSTALLIN B1	A, B	210	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P53674 (Homo sapiens) Explore P53674  Go to UniProtKB:  P53674
PHAROS:  P53674 GTEx:  ENSG00000100122

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.201 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.04	α = 90
b = 45.04	β = 90
c = 171.111	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-01-22 
Deposition Author(s): van Montfort, R.L.M., Bateman, O.A., Lubsen, N.H., Slingsby, C.

Revision History  

• Version 1.0: 2004-01-22
  Type: Initial release
  
• Version 1.1: 2014-11-05
  Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
• Version 1.2: 2018-03-28
  Changes: Source and taxonomy, Structure summary
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary