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3NFN

HLA-A*24:02 binding "RYPLTFGWCF" at 2.39Å 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
HLA-A*24:02
['A']
3. Peptide
RYPLTFGWCF
['C']

Species

Locus / Allele group

HLA-A / HLA-A*24

Publication

Plasticity of human CD8���� binding to peptide-HLA-A*2402.

Shi Y, Qi J, Iwamoto A, Gao GF
Mol. Immunol. (2011) 48, 2198-202 [doi:10.1016/j.molimm.2011.05.009]  [pubmed:21645925] 

The human CD8 functions as a co-receptor for specific T cell recognition, and only one complex structure of human CD8αα binding to HLA-A*0201 has been solved, revealing the molecular basis of CD8 interacting with its ligand pHLA. Here, we present the complex structures of human CD8αα bound to HLA-A*2402, which demonstrate two opposite α3 domain CD loop shifts (either pull or push) in the HLA heavy chain upon CD8 engagement. Taking the previously reported mouse CD8-pMHC complex structures into account, from the structural view, all of the data indicate the plasticity of CD8 binding to pMHC/HLA, which facilitates its co-receptor function for T cells. The plasticity of CD8 binding appears not to affect the specificity of TCR recognition, as no peptide conformation change extends to the pMHC interface for TCR contacting.

Structure deposition and release

Deposited: 2010-06-10
Released: 2011-07-13
Revised: 2013-09-11

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication

Peptide details

Length: Decamer (10 amino acids)

Sequence: RYPLTFGWCF

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

THR163
GLU63
GLU55
ARG170
TYR171
TYR159
LYS66
ASP166
TYR59
TYR7
GLY167
MET5
 P10 PHE

THR143
TYR123
ALA81
LEU95
TRP147
LYS146
TYR116
ASN77
TYR84
ILE80
 P2 TYR

MET97
LYS66
HIS70
TYR7
MET45
VAL67
ALA24
GLU63
PHE22
TYR159
SER9
 P3 PRO

MET97
TYR159
TYR7
LYS66
PHE99
GLN156
 P4 LEU

TYR159
LYS66
GLN156
 P5 THR

LYS66
HIS70
ALA69
THR73
 P7 GLY

TRP147
VAL152
 P8 TRP

GLN156
PHE99
TYR116
THR73
TRP147
MET97
VAL152
HIS70
ASN77
HIS114
 P9 CYS

ILE80
THR143
GLU76
TRP147
LYS146
THR73
ASN77

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
GLY167
TYR171
MET5
TYR59
GLU63
LYS66
TYR7
B Pocket

ALA24
VAL34
MET45
GLU63
LYS66
VAL67
TYR7
HIS70
SER9
PHE99
C Pocket

HIS70
THR73
ASP74
SER9
MET97
D Pocket

HIS114
GLN155
GLN156
TYR159
LEU160
PHE99
E Pocket

HIS114
TRP147
VAL152
GLN156
MET97
F Pocket

TYR116
TYR123
THR143
LYS146
TRP147
ASN77
ILE80
ALA81
TYR84
LEU95

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
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
        70        80        90
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
2. Class I alpha
HLA-A*24:02
IPD-IMGT/HLA
[ipd-imgt:HLA34790]
        10        20        30        40        50        60
GSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
        70        80        90       100       110       120
DEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYDG
       130       140       150       160       170       180
KDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETLQ
       190       200       210       220       230       240
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
       250       260       270
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW
3. Peptide
RYPLTFGWCF

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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   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. 3NFN assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 3NFN assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 3NFN assembly 1  
Peptide only [cif]
  1. 3NFN assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/3nfn

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.