1VMO | pdb_00001vmo

CRYSTAL STRUCTURE OF VITELLINE MEMBRANE OUTER LAYER PROTEIN I (VMO-I): A FOLDING MOTIF WITH HOMOLOGOUS GREEK KEY STRUCTURES RELATED BY AN INTERNAL THREE-FOLD SYMMETRY

• PDB DOI: https://doi.org/10.2210/pdb1VMO/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Gallus gallus
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 1994-01-06 Released: 1994-05-31 
• Deposition Author(s): Shimizu, T., Vassylyev, D.G., Kido, S., Doi, Y., Morikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 
  0.188 (Depositor) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Crystal structure of vitelline membrane outer layer protein I (VMO-I): a folding motif with homologous Greek key structures related by an internal three-fold symmetry.

Shimizu, T., Vassylyev, D.G., Kido, S., Doi, Y., Morikawa, K.

(1994) EMBO J 13: 1003-1010

• PubMed: 8131734 
• DOI: https://doi.org/10.1002/j.1460-2075.1994.tb06348.x
• Primary Citation Related Structures: 
  1VMO


• PubMed Abstract: 
  

  The crystal structure of vitelline membrane outer layer protein I (VMO-I), which is isolated from the vitelline membrane outer layer of hen's eggs, has been determined by the multiple isomorphous replacement method and refined to an R-factor of 18.8% at 2.2 A resolution. The main chain folds into an unusual structure that consists of three beta-sheets forming Greek key motifs, which are related by an internal pseudo three-fold symmetry. The internal portion surrounded by these three beta-sheets is filled with hydrophobic side chains. This conformational feature coincides with three internal repeats in the sequence. Although a similar fold exists in the second domain of delta-endotoxin, there are significant structural differences between the two proteins, with the three-fold symmetry being most regular in VMO-I.

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Organizational Affiliation: 
• Protein Engineering Research Institute, Osaka, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 36 kDa 
• Atom Count: 2,674 
• Modeled Residue Count: 326 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VITELLINE MEMBRANE OUTER LAYER PROTEIN I	A, B	163	Gallus gallus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P41366 (Gallus gallus) Explore P41366  Go to UniProtKB:  P41366

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work:  0.188 (Depositor) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.42	α = 90
b = 110.51	β = 90
c = 44.15	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-05-31 
Deposition Author(s): Shimizu, T., Vassylyev, D.G., Kido, S., Doi, Y., Morikawa, K.

Revision History  

• Version 1.0: 1994-05-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Other
• Version 1.4: 2024-10-30
  Changes: Structure summary