2IXF | pdb_00002ixf

Crystal structure of the ATPase domain of TAP1 with ATP (D645Q, Q678H mutant)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.258 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2IXF

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Distinct Structural and Functional Properties of the ATPase Sites in an Asymmetric Abc Transporter.

Procko, E.Ferrin-O'Connell, I.Ng, S.-L.Gaudet, R.

(2001) Mol Cell 24: 51

  • DOI: https://doi.org/10.1016/j.molcel.2006.07.034
  • Primary Citation Related Structures: 
    2IXE, 2IXF, 2IXG

  • PubMed Abstract: 

    The ABC transporter associated with antigen processing (TAP) shuttles cytosolic peptides into the endoplasmic reticulum for loading onto class I MHC molecules. Transport is fueled by ATP binding and hydrolysis at two distinct cytosolic ATPase sites. One site comprises consensus motifs shared among most ABC transporters, while the second has substituted, degenerate motifs. Biochemical and crystallography experiments with a TAP cytosolic domain demonstrate that the consensus ATPase site has high catalytic activity and facilitates ATP-dependent dimerization of the cytosolic domains, which is an important conformational change during transport. In contrast, the degenerate site is defective in dimerization and ATP hydrolysis. Full-length TAP mutagenesis demonstrates the necessity for at least one consensus site, supporting our conclusion that the consensus site is the principal facilitator of substrate transport. Since asymmetry of the ATPase site motifs is a feature of many mammalian homologs, our proposed model has broad implications for ABC transporters.


  • Organizational Affiliation
    • Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.

Macromolecule Content 

  • Total Structure Weight: 120.61 kDa 
  • Atom Count: 8,862 
  • Modeled Residue Count: 1,012 
  • Deposited Residue Count: 1,084 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ANTIGEN PEPTIDE TRANSPORTER 1
A, B, C, D
271Rattus norvegicusMutation(s): 2 
EC: 7.4.2.14
UniProt
Find proteins for P36370 (Rattus norvegicus)
Explore P36370 
Go to UniProtKB:  P36370
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36370
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP

Query on ATP



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
L [auth C],
O [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A],
J [auth B],
K [auth B],
N [auth C],
Q [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B],
M [auth C],
P [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.258 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.269α = 90
b = 108.917β = 90
c = 123.561γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description