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1BII

H2-Dd binding "RGPGRAFVTI" at 2.40Å 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
H2-Dd
['A']
3. Peptide
RGPGRAFVTI
['P']

Species

Locus / Allele group

H2-D / H2-Dd

Publication

The crystal structure of H-2Dd MHC class I complexed with the HIV-1-derived peptide P18-I10 at 2.4 A resolution: implications for T cell and NK cell recognition.

Achour A, Persson K, Harris RA, Sundb��ck J, Sentman CL, Lindqvist Y, Schneider G, K��rre K
Immunity (1998) 9, 199-208 [doi:10.1016/s1074-7613(00)80602-0]  [pubmed:9729040] 

The structure of H-2Dd complexed with the HIV-derived peptide P18-I10 (RGPGRAFVTI) has been determined by X-ray crystallography at 2.4 A resolution. This MHC class I molecule has an unusual binding motif with four anchor residues in the peptide (G2, P3, R/K/H5, and I/L/F9 or 10). The cleft architecture of H-2Dd includes a deep narrow passage accomodating the N-terminal part of the peptide, explaining the obligatory G2P3 anchor motif. Toward the C-terminal half of the peptide, p5R to p8V form a type I' reverse turn; residues p6A to p9T, and in particular p7F, are readily exposed. The structure is discussed in relation to functional data available for T cell and natural killer cell recognition of the H-2Dd molecule.

Structure deposition and release

Deposited: 1998-06-11
Released: 1998-10-14
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: Decamer (10 amino acids)

Sequence: RGPGRAFVTI

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

P401 ARG

LEU5
TYR159
GLU163
TRP167
TYR59
ARG66
TYR171
GLU63
TYR7
ARG62
 P402 GLY

GLU163
TYR7
GLU63
TYR159
ARG66
 P403 PRO

ASN70
ARG66
GLU24
ALA99
TYR7
TRP114
ARG155
TRP97
TYR159
 P404 GLY

TRP97
TRP114
ARG155
ASN70
ASP156
ARG66
 P405 ARG

ASN70
SER73
ASP77
TRP147
PHE116
PHE74
TRP97
 P406 ALA

ARG155
ASN70
 P407 PHE

GLN72
GLY69
SER73
 P408 VAL

SER73
ASP77
ALA152
TRP147
 P409 THR

SER73
ASP77
VAL76
THR143
TRP147
LYS146
 P410 ILE

THR80
THR143
TRP147
LEU95
ILE142
ALA81
TYR123
LYS146
TYR84
ASP77

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
ALA163
THR167
TRP171
ALA5
ARG59
ASP63
ASN66
ARG7
B Pocket

ALA24
THR34
ARG45
ASP63
ASN66
PRO67
ARG7
GLU70
LEU9
ARG99
C Pocket

GLU70
ALA73
ARG74
LEU9
SER97
D Pocket

GLY114
LYS155
THR156
ALA159
ALA160
ARG99
E Pocket

GLY114
TYR147
GLU152
THR156
SER97
F Pocket

SER116
ALA123
ASP143
ASP146
TYR147
GLU77
GLY80
PRO81
TRP84
GLU95

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
MARSVTLVFLVLVSLTGLYAIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQML
        70        80        90       100       110
KNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM
2. Class I alpha
H2-Dd
        10        20        30        40        50        60
MGAMAPRTLLLLLAAALGPTQTRAGSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRF
        70        80        90       100       110       120
DSDAENPRYEPRARWIEQEGPEYWERETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQ
       130       140       150       160       170       180
WMAGCDVESDGRLLRGYWQFAYDGCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERD
       190       200       210       220       230       240
RAYLEGECVEWLRRYLKNGNATLLRTDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLT
       250       260       270       280       290       300
WQLNGEELTQEMELVETRPAGDGTFQKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRWGK
       310       320       330       340       350       360
EEPPSSTKTNTVIIAVPVVLGAVVILGAVMAFVMKRRRNTGGKGGDYALAPGSQSSDMSL

PDCKV
3. Peptide
RGPGRAFVTI

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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Complete structures

Aligned structures [cif]
  1. 1BII assembly 1  

Components

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

Derived data

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

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.