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1JPF

H2-Db binding "SGVENPGGYCL" at 2.18Å resolution

Data provenance

Structure downloaded from PDB Europe using the Coordinate Server. Aligned to residues 1-180 of 1HHK2 using the CEALIGN3 function of PyMol4. Chain assigment using a Levenshtein distance5 method using data from the PDBe REST API6. Organism data from PDBe REST API. Data for both of these operations from the Molecules endpoint. Structure visualised with 3DMol7.

Information sections


Complex type

Class i with peptide

1. Beta 2 microglobulin
['B']
2. Class I alpha
H2-Db
['A']
3. Peptide
SGVENPGGYCL
['C']

Species


Locus / Allele group


Publication

Zooming in on the hydrophobic ridge of H-2D(b): implications for the conformational variability of bound peptides.

Ciatto C, Tissot AC, Tschopp M, Capitani G, Pecorari F, Plückthun A, Grütter MG
J. Mol. Biol. (2001) 312, 1059-71 [doi:10.1006/jmbi.2001.5016]  [pubmed:11580250

Class I major histocompatibility complex (MHC) molecules, which display intracellularly processed peptides on the cell surface for scanning by T-cell receptors (TCRs), are extraordinarily polymorphic. MHC polymorphism is believed to result from natural selection, since individuals heterozygous at the corresponding loci can cope with a larger number of pathogens. Here, we present the crystal structures of the murine MHC molecule H-2D(b) in complex with the peptides gp276 and np396 from the lymphocytic choriomeningitis virus (LCMV), solved at 2.18 A and 2.20 A resolution, respectively. The most prominent feature of H-2D(b) is a hydrophobic ridge that cuts across its antigen-binding site, which is conserved in the L(d)-like family of class I MHC molecules. The comparison with previously solved crystal structures of peptide/H-2D(b) complexes shows that the hydrophobic ridge focuses the conformational variability of the bound peptides in a "hot-spot", which could allow optimal TCR interaction and discrimination. This finding suggests a functional reason for the conservation of this structural element.

Structure deposition and release

Deposited: 2001-08-02
Released: 2001-10-24
Revised: 2011-07-13

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Undecamer (11 amino acids)

Sequence: SGVENPGGYCL

Interactive view
Cutaway side view (static)
Surface top view (static - coloured by atom property)
Cutaway top view (static)

Data provenance

MHC:peptide complexes are visualised using PyMol. The peptide is superimposed on a consistent cutaway slice of the MHC binding cleft (displayed as a grey mesh) which best indicates the binding pockets for the P1/P5/PC positions (side view - pockets A, E, F) and for the P2/P3/PC-2 positions (top view - pockets B, C, D). In some cases peptides will use a different pocket for a specific peptide position (atypical anchoring). On some structures the peptide may appear to sterically clash with a pocket. This is an artefact of picking a standardised slice of the cleft and overlaying the peptide.


Peptide neighbours

P1 SER

PHE33
LYS66
MET5
GLU163
TRP167
GLU63
ARG62
TYR171
TYR159
TYR59
TYR7
P10 CYS

THR143
LYS146
TRP147
SER77
ASN80
TRP73
VAL76
P11 LEU

SER77
TYR123
ASN80
TYR84
LEU95
TRP73
THR143
ILE124
LYS146
PHE116
LEU81
TRP147
P2 GLY

LYS66
GLU163
GLU63
TYR159
TYR7
P3 VAL

SER99
LYS66
GLN70
LEU114
TYR159
GLU9
TYR156
GLN97
P4 GLU

TYR156
GLN65
GLY69
GLN70
HIS155
LYS66
P5 ASN

GLN70
HIS155
TRP73
TYR156
GLN97
PHE74
PHE116
P6 PRO

TRP73
TYR156
ALA152
HIS155
P7 GLY

TRP73
P9 TYR

TRP73
TYR156
TRP147
GLY151
SER150
ALA152

Colour key

Aromatic Hydrophobic Acidic Basic Neutral/polar

Data provenance

Neighbours are calculated by finding residues with atoms within 5Å of each other using BioPython Neighboursearch module. The list of neighbours is then sorted and filtered to inlcude only neighbours where between the peptide and the MHC Class I alpha chain.

Colours selected to match the YRB scheme. [https://www.frontiersin.org/articles/10.3389/fmolb.2015.00056/full]


Binding cleft pockets


Peptide sidechain binding pockets (static)
Peptide terminii and backbone binding residues (static)
A Pocket

ALA159
GLY163
GLU167
ARG171
SER5
GLU59
ARG63
GLN66
ARG7
B Pocket

ILE24
PHE34
ARG45
ARG63
GLN66
LYS67
ARG7
GLY70
PHE9
MET99
C Pocket

GLY70
GLN73
TRP74
PHE9
GLN97
D Pocket

TYR114
GLU155
HIS156
ALA159
TYR160
MET99
E Pocket

TYR114
LYS147
GLY152
HIS156
GLN97
F Pocket

GLN116
ASP123
ILE143
ARG146
LYS147
VAL77
ARG80
ASN81
GLY84
THR95

Colour key

Binds N-terminus Binds P1 backbone Binds P2 backbone Binds PC-1 backbone Binds C-terminus

Data provenance

N-/C-terminus and peptide backbone binding residues are assigned according to previously published information and pockets are assigned according to an adaptation of a previously published set of residues. All numbering is currently that of the 'canonical' structures of human and mouse MHC Class I molecules.

Chain sequences

1. Beta 2 microglobulin
Beta 2 microglobulin
        10        20        30        40        50        60
MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD
        70        80        90
WSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

2. Class I alpha
H2-Db
        10        20        30        40        50        60
MGPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEY
        70        80        90       100       110       120
WERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYE
       130       140       150       160       170       180
GRDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATL
       190       200       210       220       230       240
LRTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDG
       250       260       270       280
TFQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEPPPST

3. Peptide
SGVENPGGYCL


Data provenance

Sequences are retrieved via the Uniprot method of the RSCB REST API. Sequences are then compared to those derived from the PDB file and matched against sequences retrieved from the IPD-IMGT/HLA database for human sequences, or the IPD-MHC database for other species. Mouse sequences are matched against FASTA files from Uniprot. Sequences for the mature extracellular protein (signal petide and cytoplasmic tail removed) are compared to identical length sequences from the datasources mentioned before using either exact matching or Levenshtein distance based matching.


Downloadable data

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Please take note of the data license. Using data from this site assumes that you have read and will comply with the license.

Complete structures

Aligned structures [cif]
  1. 1JPF assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 1JPF assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 1JPF assembly 1  
Peptide only [cif]
  1. 1JPF assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/1jpf

Data license

The data above is made available under a Creative Commons CC-BY 4.0 license. This means you can copy, remix, transform, build upon and redistribute the material, but you must give appropriate credit, provide a link to the license, and indicate if changes were made.
If you use any data downloaded from this site in a publication, please cite 'https://www.histo.fyi/'. A preprint is in preparation.

Footnotes