7ALO

Structure of B*27:09/photoRL9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1038/s41467-021-24401-4
  • Primary Citation of 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 ...

    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. christian.freund@fu-berlin.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lymphocyte antigen HLA-B27A, D292Homo sapiensMutation(s): 0 
Gene Names: HLA-B
UniProt
Find proteins for A0A2R7Z5J3 (Homo sapiens)
Explore A0A2R7Z5J3 
Go to UniProtKB:  A0A2R7Z5J3
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, E100Homo 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Vasoactive intestinal polypeptide receptor 1C, F9Homo sapiensMutation(s): 0 
Gene Names: VIPR1
UniProt & NIH Common Fund Data Resources
Find proteins for P32241 (Homo sapiens)
Explore P32241 
Go to UniProtKB:  P32241
PHAROS:  P32241
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / 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
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
N [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
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
 Ligand Interaction
PEG
Query on PEG

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

Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , I [auth A] , J [auth B] , K [auth B] , O [auth D] , P [auth D] , Q [auth D] , 
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: P 1
  • Diffraction Data DOI: 10.18430/m37alo Protein Diffraction
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

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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