3F8U | pdb_00003f8u

Tapasin/ERp57 heterodimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.285 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.245 (Depositor), 0.247 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Insights into MHC class I peptide loading from the structure of the tapasin-ERp57 thiol oxidoreductase heterodimer.

Dong, G.Wearsch, P.A.Peaper, D.R.Cresswell, P.Reinisch, K.M.

(2009) Immunity 30: 21-32

  • DOI: https://doi.org/10.1016/j.immuni.2008.10.018
  • Primary Citation Related Structures: 
    3F8U

  • PubMed Abstract: 

    Tapasin is a glycoprotein critical for loading major histocompatibility complex (MHC) class I molecules with high-affinity peptides. It functions within the multimeric peptide-loading complex (PLC) as a disulfide-linked, stable heterodimer with the thiol oxidoreductase ERp57, and this covalent interaction is required to support optimal PLC activity. Here, we present the 2.6 A resolution structure of the tapasin-ERp57 core of the PLC. The structure revealed that tapasin interacts with both ERp57 catalytic domains, accounting for the stability of the heterodimer, and provided an example of a protein disulfide isomerase family member interacting with substrate. Mutational analysis identified a conserved surface on tapasin that interacted with MHC class I molecules and was critical for peptide loading and editing functions of the tapasin-ERp57 heterodimer. By combining the tapasin-ERp57 structure with those of other defined PLC components, we present a molecular model that illuminates the processes involved in MHC class I peptide loading.


  • Organizational Affiliation
    • Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA.

Macromolecule Content 

  • Total Structure Weight: 194.63 kDa 
  • Atom Count: 13,051 
  • Modeled Residue Count: 1,653 
  • Deposited Residue Count: 1,764 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein disulfide-isomerase A3ERp57
A, C
481Homo sapiensMutation(s): 1 
Gene Names: PDIA3ERP57ERP60GRP58
EC: 5.3.4.1
UniProt & NIH Common Fund Data Resources
Find proteins for P30101 (Homo sapiens)
Explore P30101 
Go to UniProtKB:  P30101
PHAROS:  P30101
GTEx:  ENSG00000167004 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30101
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tapasin
B, D
401Homo sapiensMutation(s): 0 
Gene Names: TAPBPNGS17TAPA
UniProt & NIH Common Fund Data Resources
Find proteins for O15533 (Homo sapiens)
Explore O15533 
Go to UniProtKB:  O15533
PHAROS:  O15533
GTEx:  ENSG00000231925 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15533
Glycosylation
Glycosylation Sites: 1Go to GlyGen: O15533-1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.285 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.245 (Depositor), 0.247 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.101α = 90
b = 72.295β = 94.613
c = 200.193γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHARPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2021-10-20
    Changes: Database references, Structure summary
  • Version 1.4: 2023-12-27
    Changes: Data collection
  • Version 1.5: 2024-10-30
    Changes: Structure summary