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1NEZ

H2-TLA with CD8a at 2.10Å 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 cd8a

1. Beta 2 microglobulin
['B']
2. cd8a
['G', 'H']
3. Class I alpha
H2-TLA
['A']

Species

Locus / Allele group

H2-TL / H2-TLA

Publication

The crystal structure of a TL/CD8alphaalpha complex at 2.1 A resolution: implications for modulation of T cell activation and memory.

Liu Y, Xiong Y, Naidenko OV, Liu JH, Zhang R, Joachimiak A, Kronenberg M, Cheroutre H, Reinherz EL, Wang JH
Immunity (2003) 18, 205-15 [doi:10.1016/s1074-7613(03)00027-x]  [pubmed:12594948] 

TL is a nonclassical MHC class I molecule that modulates T cell activation through relatively high-affinity interaction with CD8alphaalpha. To investigate how the TL/CD8alphaalpha interaction influences TCR signaling, we characterized the structure of the TL/CD8alphaalpha complex using X-ray crystallography. Unlike antigen-presenting molecules, the TL antigen-binding groove is occluded by specific conformational changes. This feature eliminates antigen presentation, severely hampers direct TCR recognition, and prevents TL from participating in the TCR activation complex. At the same time, the TL/CD8alphaalpha interaction is strengthened through subtle structure changes in the TL alpha3 domain. Thus, TL functions to sequester and redirect CD8alphaalpha away from the TCR, modifying lck-dependent signaling.

Structure deposition and release

Deposited: 2002-12-12
Released: 2003-04-08
Revised: 2020-07-29

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication

Binding cleft pockets


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

TYR159
PRO163
SER167
TYR171
LEU5
TYR59
GLU63
ILE66
TYR7
B Pocket

ALA24
ALA34
TYR45
GLU63
ILE66
VAL67
TYR7
ASN70
TYR9
TYR99
C Pocket

ASN70
PHE73
PHE74
TYR9
VAL97
D Pocket

GLU114
LEU155
ARG156
TYR159
LEU160
TYR99
E Pocket

GLU114
TRP147
TYR152
ARG156
VAL97
F Pocket

HIS116
TYR123
THR143
LYS146
TRP147
ASN77
THR80
MET81
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
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
        70        80        90
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM
2. cd8a
cd8a
        10        20        30        40        50        60
KPQAPELRIFPKKMDAELGQKVDLVCEVLGSVSQGCSWLFQNSSSKLPQPTFVVYMASSH
        70        80        90       100       110       120
NKITWDEKLNSSKLFSAMRDTNNKYVLTLNKFSKENEGYYFCSVISNSVMYFSSVVPVLQ

KVSSALVP
3. Class I alpha
H2-TLA
        10        20        30        40        50        60
GSHSLRYFYTALSRPAISEPWYIAVGYLDDTQFARFDSAGETGTYKLSAPWVEQEGPEYW
        70        80        90       100       110       120
ARETEIVTSNAQFFRENLQTMLDYYNLSQNGSHTIQVMYGCEVEFFGSLFRAYEQHGYDG
       130       140       150       160       170       180
QDYIALNEDLKTWTAADMAAEITRSKWEQAGYTELRRTYLEGPCKDSLLRYLENRKKTQE
       190       200       210       220       230       240
CTDPPKTHVTHHARPEGDVTLRCWALGFYPAHITLTWQLNGEELIQDTELVETRPAGDGT
       250       260       270
FQKWAAVVVPSGEEQKYTCHVYHEGLPEPLTLRW

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. 1NEZ assembly 1  

Components

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

Derived data

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

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


Creative Commons Licence
This work is licensed under a Creative Commons Attribution 4.0 International License.