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4MVB

Truncated H2-Ld presenting "QPAEGGFQL" to Alpha/Beta T cell receptor at 3.09Å 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

Truncated class i with peptide and alpha beta tcr

1. Class I alpha
H2-Ld
['A']
2. Peptide
QPAEGGFQL
['B']
3. T cell receptor alpha
TRAV9
['C']
4. T cell receptor beta
TRBV13
['D']

Species


Locus / Allele group


Publication

Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity.

Adams JJ, Narayanan S, Birnbaum ME, Sidhu SS, Blevins SJ, Gee MH, Sibener LV, Baker BM, Kranz DM, Garcia KC
Nat. Immunol. (2016) 17, 87-94 [doi:10.1038/ni.3310]  [pubmed:26523866

Estimates of mutation rates for various regions of the human mitochondrial genome (mtGenome) vary widely, depending on whether they are inferred using a phylogenetic approach or obtained directly from pedigrees. Traditionally, only the control region, or small portions of the coding region have been targeted for analysis due to the cost and effort required to produce whole mtGenome Sanger profiles. Here, we report one of the first pedigree derived mutation rates for the entire human mtGenome. The entire mtGenome from 225 individuals originating from Norfolk Island was analysed to estimate the pedigree derived mutation rate and compared against published mutation rates. These individuals were from 45 maternal lineages spanning 345 generational events. Mutation rates for various portions of the mtGenome were calculated. Nine mutations (including two transitions and seven cases of heteroplasmy) were observed, resulting in a rate of 0.058 mutations/site/million years (95% CI 0.031-0.108). These mutation rates are approximately 16 times higher than estimates derived from phylogenetic analysis with heteroplasmy detected in 13 samples (nā€‰=ā€‰225, 5.8% individuals). Providing one of the first pedigree derived estimates for the entire mtGenome, this study provides a better understanding of human mtGenome evolution and has relevance to many research fields, including medicine, anthropology and forensics.

Structure deposition and release

Deposited: 2013-09-23
Released: 2015-08-19
Revised: 2018-09-26

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: QPAEGGFQL

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 GLN

MET5
TYR99
TYR171
TYR159
GLU163
ARG62
TYR59
TYR7
ILE63
TRP167
ILE66
P2 PRO

ILE66
TYR45
TYR99
GLU9
TYR159
ILE63
TYR7
P3 ALA

GLU9
TYR159
TRP97
ILE66
GLN70
TYR99
P4 GLU

TYR155
TYR156
GLN70
ARG62
GLY69
ILE66
TRP97
P5 GLY

TRP73
TRP97
GLN70
TYR155
TYR156
P6 GLY

TRP73
GLN70
TYR155
P7 PHE

TYR155
ALA150
TRP147
GLY151
TRP73
TYR156
ALA152
ASN77
P8 GLN

VAL76
TRP73
ASN77
TRP147
P9 LEU

TYR84
TRP147
TRP73
PHE116
TYR123
THR80
ASN77
THR143
LEU81

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

THR24
PHE34
ARG45
ARG63
GLN66
ILE67
ARG7
GLY70
TYR9
MET99
C Pocket

GLY70
GLN73
TRP74
TYR9
GLN97
D Pocket

TYR114
GLU155
TYR156
ALA159
TYR160
MET99
E Pocket

TYR114
LYS147
GLY152
TYR156
GLN97
F Pocket

GLN116
ASP123
ILE143
ARG146
LYS147
VAL77
ARG80
THR81
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. Class I alpha
H2-Ld
        10        20        30        40        50        60
MGPHSMRYYETATSRRGLGEPRYTSVGYVDDKEFVRFDSDAENPRYEPQVPWMEQEGPEY
        70        80        90       100       110       120
WERITQIAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQWMYGCDVGSDGRLLRGYEQFAYD
       130       140       150       160       170
GCDYIALNEDLRTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNGNATL

2. Peptide
QPAEGGFQL

3. T cell receptor alpha
T cell receptor alpha
TRAV9
        10        20        30        40        50        60
GSHMAQSVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGLQMLLKYYSGDPV
        70        80        90       100       110       120
VQGVNGFEAEFSKSDSSFHLRKASVHWSDSAVYFCAVSAKGTGSKLSFGKGAKLTVSPNI
       130       140       150       160       170       180
QNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSA
       190       200       210
VAWSNKSDFACANAFNNSIIPEDTFFPSPESS

4. T cell receptor beta
T cell receptor beta
TRBV13
        10        20        30        40        50        60
MGEAAVTQSPRNKVTVTGGNVTLSCRQTNSHNYMYWYRQDTGHGLRLIHYSYGAGNLQIG
        70        80        90       100       110       120
DVPDGYKATRTTQEDFFLLLELASPSQTSLYFCASSDAPGQLYFGEGSKLTVLEDLKNVF
       130       140       150       160       170       180
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
       190       200       210       220       230       240
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG

RAD


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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   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. 4MVB assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 4MVB assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 4MVB assembly 1  
Peptide only [cif]
  1. 4MVB assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/4mvb

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