Alpha This is a work in progress and may change. Your feedback is very welcome.
  


1NAM

H2-Kb presenting "RGYVYQGL" to Alpha/Beta T cell receptor at 2.70Å 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 and alpha beta tcr

1. Beta 2 microglobulin
['L']
2. Class I alpha
H2-Kb
['H']
3. Peptide
RGYVYQGL
['P']
4. T cell receptor alpha
TRAV16
['A']
5. T cell receptor beta
TRBV1
['B']

Species


Locus / Allele group


Publication

CDR3 loop flexibility contributes to the degeneracy of TCR recognition.

Reiser JB, Darnault C, Grégoire C, Mosser T, Mazza G, Kearney A, van der Merwe PA, Fontecilla-Camps JC, Housset D, Malissen B
Nat. Immunol. (2003) 4, 241-7 [doi:10.1038/ni891]  [pubmed:12563259

T cell receptor (TCR) binding degeneracy lies at the heart of several physiological and pathological phenomena, yet its structural basis is poorly understood. We determined the crystal structure of a complex involving the BM3.3 TCR and an octapeptide (VSV8) bound to the H-2K(b) major histocompatibility complex molecule at a 2.7 A resolution, and compared it with the BM3.3 TCR bound to the H-2K(b) molecule loaded with a peptide that has no primary sequence identity with VSV8. Comparison of these structures showed that the BM3.3 TCR complementarity-determining region (CDR) 3alpha could undergo rearrangements to adapt to structurally different peptide residues. Therefore, CDR3 loop flexibility helps explain TCR binding cross-reactivity.

Structure deposition and release

Deposited: 2002-11-28
Released: 2003-03-11
Revised: 2020-07-29

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Octamer (8 amino acids)

Sequence: RGYVYQGL

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 ARG

LYS66
TYR59
GLU63
TRP167
GLU58
TYR171
THR163
LEU5
ARG62
TYR159
TYR7
P2 GLY

TYR159
TYR7
LYS66
GLU63
P3 TYR

ARG155
TYR159
GLN114
GLU152
LEU156
ASN70
LYS66
P4 VAL

ASN70
LYS66
ARG155
P5 TYR

SER99
SER73
GLU24
TYR22
VAL97
TYR116
TYR7
GLN114
ASN70
VAL9
PHE74
ARG155
P6 GLN

TYR116
TRP147
GLU152
ASP77
ARG155
SER73
P7 GLY

SER73
TRP147
THR143
ASP77
LYS146
P8 LEU

TRP147
THR143
LEU81
ILE95
ASP77
ILE124
TYR116
TYR84
TYR123
LYS146
THR80

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

TYR159
THR163
TRP167
TYR171
LEU5
TYR59
GLU63
LYS66
TYR7
B Pocket

GLU24
VAL34
TYR45
GLU63
LYS66
ALA67
TYR7
ASN70
VAL9
SER99
C Pocket

ASN70
SER73
PHE74
VAL9
VAL97
D Pocket

GLN114
ARG155
LEU156
TYR159
LEU160
SER99
E Pocket

GLN114
TRP147
GLU152
LEU156
VAL97
F Pocket

TYR116
TYR123
THR143
LYS146
TRP147
ASP77
THR80
LEU81
TYR84
ILE95

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-Kb
        10        20        30        40        50        60
GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYW
        70        80        90       100       110       120
ERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDG
       130       140       150       160       170       180
CDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLL
       190       200       210       220       230       240
RTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT
       250       260       270
FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWE

3. Peptide
RGYVYQGL

4. T cell receptor alpha
T cell receptor alpha
TRAV16
        10        20        30        40        50        60
QKVTQTQTSISVMEKTTVTMDCVYETQDSSYFLFWYKQTASGEIVFLIRQDSYKKENATV
        70        80        90       100       110
GHYSLNFQKPKSSIGLIITATQIEDSAVYFCAMRGDYGGSGNKLIFGTGTLLSVKP

5. T cell receptor beta
T cell receptor beta
TRBV1
        10        20        30        40        50        60
VTLLEQNPRWRLVPRGQAVNLRCILKNSQYPWMSWYQQDLQKQLQWLFTLRSPGDKEVKS
        70        80        90       100       110
LPGADYLATRVTDTELRLQVANMSQGRTLYCTCSADRVGNTLYFGEGSRLIVV


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.
Clicking on the clipboard icon will copy the url for the data to your clipboard.
This can then be used to load the structure/data directly from the url into an application like PyMol (for 3D structures) using the load command:
   e.g. load http://www.histo.fyi/structures/downloads/1hhk_1_peptide.cif
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. 1NAM assembly 1  

Components

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

Derived data

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

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