4L29

Structure of wtMHC class I with NY-ESO1 double mutant

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Class I Major Histocompatibility Complex, the Trojan Horse for Secretion of Amyloidogenic beta 2-Microglobulin.

Halabelian, L., Ricagno, S., Giorgetti, S., Santambrogio, C., Barbiroli, A., Pellegrino, S., Achour, A., Grandori, R., Marchese, L., Raimondi, S., Mangione, P.P., Esposito, G., Al-Shawi, R., Simons, J.P., Speck, I., Stoppini, M., Bolognesi, M., Bellotti, V.

(2014) J Biol Chem 289: 3318-3327

  • DOI: https://doi.org/10.1074/jbc.M113.524157
  • Primary Citation of Related Structures:  
    4L29, 4L3C

  • PubMed Abstract: 

    • To form extracellular aggregates, amyloidogenic proteins bypass the intracellular quality control, which normally targets unfolded/aggregated polypeptides. Human D76N β2-microglobulin (β2m) variant is the prototype of unstable and amyloidogenic protein that forms abundant extracellular fibrillar deposits ...

    To form extracellular aggregates, amyloidogenic proteins bypass the intracellular quality control, which normally targets unfolded/aggregated polypeptides. Human D76N β2-microglobulin (β2m) variant is the prototype of unstable and amyloidogenic protein that forms abundant extracellular fibrillar deposits. Here we focus on the role of the class I major histocompatibility complex (MHCI) in the intracellular stabilization of D76N β2m. Using biophysical and structural approaches, we show that the MHCI containing D76N β2m (MHCI76) displays stability, dissociation patterns, and crystal structure comparable with those of the MHCI with wild type β2m. Conversely, limited proteolysis experiments show a reduced protease susceptibility for D76N β2m within the MHCI76 as compared with the free variant, suggesting that the MHCI has a chaperone-like activity in preventing D76N β2m degradation within the cell. Accordingly, D76N β2m is normally assembled in the MHCI and circulates as free plasma species in a transgenic mouse model.

    Organizational Affiliation: 

    From the Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133 Milano, Italy.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chain276Homo sapiensMutation(s): 0 
Gene Names: HLA-A, HLAA, HLA_A0201
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
PHAROS:  P04439
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04439
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P, NM_004048
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NY-ESO1 DOUBLE MUTANT (1Y, 9V)9N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
BC [auth o]
DB [auth f]
EC [auth c]
GC [auth g]
IB [auth l]
BC [auth o],
DB [auth f],
EC [auth c],
GC [auth g],
IB [auth l],
IC [auth Y],
KB [auth K],
KC [auth q],
MB [auth h],
MC [auth a],
PB [auth e],
RA [auth A],
RB [auth O],
SB [auth O],
UA [auth C],
VA [auth C],
WB [auth Q],
XA [auth i],
ZA [auth E],
ZB [auth S]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
AB [auth F]
AC [auth T]
BB [auth G]
CB [auth H]
CC [auth U]
AB [auth F],
AC [auth T],
BB [auth G],
CB [auth H],
CC [auth U],
DC [auth V],
EB [auth I],
FB [auth I],
FC [auth W],
GB [auth I],
HB [auth J],
HC [auth Y],
JB [auth K],
JC [auth Z],
LB [auth L],
LC [auth a],
NB [auth N],
NC [auth b],
OB [auth N],
QA [auth A],
QB [auth O],
SA [auth B],
TA [auth C],
TB [auth P],
UB [auth Q],
VB [auth Q],
WA [auth D],
XB [auth R],
YA [auth E],
YB [auth S]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.57α = 90
b = 313.36β = 90
c = 314.46γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-01-08
    Changes: Database references
  • Version 1.2: 2014-02-26
    Changes: Database references