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1FFP

H2-Db binding "SAVYNFATM" at 2.60Å 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', 'E']
2. Class I alpha
H2-Db
['A', 'D']
3. Peptide
SAVYNFATM
['C', 'F']

Species


Locus / Allele group


Publication

Peptidic termini play a significant role in TCR recognition.

Wang B, Sharma A, Maile R, Saad M, Collins EJ, Frelinger JA
J. Immunol. (2002) 169, 3137-45 [doi:10.4049/jimmunol.169.6.3137]  [pubmed:12218131

TCR recognition of class I MHC is dependent on the composition of the antigenic peptide and the MHC. Single amino acid substitutions in either the MHC or the peptide may dramatically alter recognition. While the major interactions between TCR and the peptide/MHC complex appear to be focused on the complementarity-determining region (CDR)3, it is also clear from the cocrystal structure of class I MHC and TCR that the amino and carboxyl ends of the peptide may play a role through interactions with the CDR1. In this work we show that gp33 variants substituted at the peptidic termini at the putative CDR1 contact regions show improved recognition in B6 mice. The rank order of recognition is different using the P14 transgenic T cells, suggesting that one reason for improved recognition is a change in the TCR repertoire that recognizes the peptide. However, the affinity of the TCR by some of the peptide/MHC complex with increased recognition is improved, as shown by increased tetramer binding to P14 T cells. These substitutions at the termini of the peptide-binding cleft cause localized conformational changes as seen by changes in mAb binding and crystallographic structures. The different peptide structures also show different conformations in the center of the peptide, but these are shown to be energetically similar and thus most likely have no significance with respect to TCR recognition. Therefore, small conformational changes, localized to the CDR1 contact regions, may play a significant role in TCR recognition.

Structure deposition and release

Deposited: 2000-07-25
Released: 2002-12-11
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: Nonamer (9 amino acids)

Sequence: SAVYNFATM

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

TYR59
GLU63
TRP167
MET5
TYR171
TYR159
GLU163
LYS66
TYR7
P2 ALA

GLU163
LYS66
TYR7
TYR45
GLU63
TYR159
P3 VAL

TYR156
GLU9
TYR7
GLN70
SER99
TYR159
GLU163
LYS66
LEU114
GLN97
P4 TYR

GLN70
GLN65
LYS66
HIS155
GLY69
TYR156
P5 ASN

PHE74
TRP73
TYR156
GLU9
PHE116
GLN70
HIS155
GLN97
P6 PHE

SER150
ALA152
HIS155
GLY151
TRP73
TYR156
P7 ALA

SER150
TRP147
LYS146
TRP73
TYR156
P8 THR

TRP147
LYS146
VAL76
TRP73
ASN80
SER77
THR143
P9 MET

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

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

LEU159
CYS163
LEU167
LEU171
ARG5
TRP59
THR63
ALA66
PHE7
B Pocket

VAL24
ARG34
GLU45
THR63
ALA66
LYS67
PHE7
GLU70
THR9
GLY99
C Pocket

GLU70
PHE73
ARG74
THR9
MET97
D Pocket

GLN114
TYR155
LYS156
LEU159
GLU160
GLY99
E Pocket

GLN114
GLU147
ALA152
LYS156
MET97
F Pocket

ALA116
ILE123
ARG143
TRP146
GLU147
LEU77
LEU80
LEU81
TYR84
GLN95

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
PHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYWE
        70        80        90       100       110       120
RETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEGR
       130       140       150       160       170       180
DYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLLR
       190       200       210       220       230       240
TDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGTF
       250       260       270
QKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRW

3. Peptide
SAVYNFATM


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

Data can be downloaded to your local machine from the links below.
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or in the case of JSON formatted files to retrieve it and use it as part of notebooks such as Jupyter or GoogleColab.
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. 1FFP assembly 1  
  2. 1FFP assembly 2  

Components

MHC Class I alpha chain [cif]
  1. 1FFP assembly 1  
  2. 1FFP assembly 2  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 1FFP assembly 1  
  2. 1FFP assembly 2  
Peptide only [cif]
  1. 1FFP assembly 1  
  2. 1FFP assembly 2  

Derived data

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

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