7ALO | pdb_00007alo

Structure of B*27:09/photoRL9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.266 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7ALO

This is version 2.2 of the entry. See complete history

Literature

Exchange catalysis by tapasin exploits conserved and allele-specific features of MHC-I molecules.

Lan, H.Abualrous, E.T.Sticht, J.Fernandez, L.M.A.Werk, T.Weise, C.Ballaschk, M.Schmieder, P.Loll, B.Freund, C.

(2021) Nat Commun 12: 4236-4236

  • DOI: https://doi.org/10.1038/s41467-021-24401-4
  • Primary Citation Related Structures: 
    7ALO

  • PubMed Abstract: 

    The repertoire of peptides presented by major histocompatibility complex class I (MHC-I) molecules on the cell surface is tailored by the ER-resident peptide loading complex (PLC), which contains the exchange catalyst tapasin. Tapasin stabilizes MHC-I molecules and promotes the formation of stable peptide-MHC-I (pMHC-I) complexes that serve as T cell antigens. Exchange of suboptimal by high-affinity ligands is catalyzed by tapasin, but the underlying mechanism is still elusive. Here we analyze the tapasin-induced changes in MHC-I dynamics, and find the catalyst to exploit two essential features of MHC-I. First, tapasin recognizes a conserved allosteric site underneath the α 2-1 -helix of MHC-I, 'loosening' the MHC-I F-pocket region that accomodates the C-terminus of the peptide. Second, the scoop loop 11-20 of tapasin relies on residue L18 to target the MHC-I F-pocket, enabling peptide exchange. Meanwhile, tapasin residue K16 plays an accessory role in catalysis of MHC-I allotypes bearing an acidic F-pocket. Thus, our results provide an explanation for the observed allele-specificity of catalyzed peptide exchange.


  • Organizational Affiliation
    • Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany.

Macromolecule Content 

  • Total Structure Weight: 96.25 kDa 
  • Atom Count: 7,344 
  • Modeled Residue Count: 768 
  • Deposited Residue Count: 802 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lymphocyte antigen HLA-B27
A, D
292Homo sapiensMutation(s): 0 
Gene Names: HLA-B
UniProt
Find proteins for A0A2R7Z5J3 (Homo sapiens)
Explore A0A2R7Z5J3 
Go to UniProtKB:  A0A2R7Z5J3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2R7Z5J3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, E
100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Vasoactive intestinal polypeptide receptor 1
C, F
9Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P32241 (Homo sapiens)
Explore P32241 
Go to UniProtKB:  P32241
PHAROS:  P32241
GTEx:  ENSG00000114812 
Entity Groups
UniProt GroupP32241
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
M [auth B]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
N [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
L [auth B],
S [auth D]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG

Query on PEG



Download:Ideal Coordinates CCD File
T [auth D]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth B]
K [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth B],
K [auth B],
O [auth D],
P [auth D],
Q [auth D],
R [auth D],
U [auth E],
V [auth E],
W [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.266 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.2α = 80.24
b = 69.61β = 88.362
c = 82.54γ = 89.877
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany1325/17-1
German Research Foundation (DFG)GermanyTRR186 A21N

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-16
    Type: Initial release
  • Version 1.1: 2021-07-21
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2024-01-31
    Changes: Refinement description
  • Version 2.2: 2024-10-16
    Changes: Structure summary