3GF5 | pdb_00003gf5

Crystal structure of the P21 R1-R7 N-terminal domain of murine MVP

• PDB DOI: https://doi.org/10.2210/pdb3GF5/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-26 Released: 2009-11-10 
• Deposition Author(s): Querol-Audi, J., Casanas, A., Luque, D., Caston, J.R., Fita, I., Verdaguer, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.267 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

The mechanism of vault opening from the high resolution structure of the N-terminal repeats of MVP

Querol-Audi, J., Casanas, A., Uson, I., Luque, D., Caston, J.R., Fita, I., Verdaguer, N.

(2009) EMBO J 28: 3450-3457

• PubMed: 19779459 
• DOI: https://doi.org/10.1038/emboj.2009.274
• Primary Citation Related Structures: 
  3GF5, 3GNF, 3GNG


• PubMed Abstract: 
  

  Vaults are ubiquitous ribonucleoprotein complexes involved in a diversity of cellular processes, including multidrug resistance, transport mechanisms and signal transmission. The vault particle shows a barrel-shaped structure organized in two identical moieties, each consisting of 39 copies of the major vault protein MVP. Earlier data indicated that vault halves can dissociate at acidic pH. The crystal structure of the vault particle solved at 8 A resolution, together with the 2.1-A structure of the seven N-terminal domains (R1-R7) of MVP, reveal the interactions governing vault association and provide an explanation for a reversible dissociation induced by low pH. The structural comparison with the recently published 3.5 A model shows major discrepancies, both in the main chain tracing and in the side chain assignment of the two terminal domains R1 and R2.

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Organizational Affiliation: 
• Department of Structural Biology, Institut de Biología Molecular de Barcelona (CSIC), Baldiri i Reixac, Barcelona, Spain.

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: 88.12 kDa 
• Atom Count: 6,095 
• Modeled Residue Count: 758 
• Deposited Residue Count: 774 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major vault protein	A, B	387	Mus musculus	Mutation(s): 0  Gene Names: MVP
UniProt
Find proteins for Q9EQK5 (Mus musculus) Explore Q9EQK5  Go to UniProtKB:  Q9EQK5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.267 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.523	α = 90
b = 98.892	β = 97.18
c = 140.581	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-10 
Deposition Author(s): Querol-Audi, J., Casanas, A., Luque, D., Caston, J.R., Fita, I., Verdaguer, N.

Revision History  

• Version 1.0: 2009-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations