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3RWF

Mamu-B*017:01 binding "QTSQWDDPW" at 2.60Å 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
Mamu-B*017:01
['A']
3. Peptide
QTSQWDDPW
['C']

Species


Locus / Allele group


Publication

Structural basis of diverse peptide accommodation by the rhesus macaque MHC class I molecule Mamu-B*17: insights into immune protection from simian immunodeficiency virus.

Wu Y, Gao F, Liu J, Qi J, Gostick E, Price DA, Gao GF
J. Immunol. (2011) 187, 6382-92 [doi:10.4049/jimmunol.1101726]  [pubmed:22084443

The MHC class I molecule Mamu-B*17 has been associated with elite control of SIV infection in rhesus macaques, akin to the protective effects described for HLA-B*57 in HIV-infected individuals. In this study, we determined the crystal structures of Mamu-B*17 in complex with eight different peptides corresponding to immunodominant SIV(mac)239-derived CD8(+) T cell epitopes: HW8 (HLEVQGYW), GW10 (GSHLEVQGYW), MW9 (MHPAQTSQW), QW9 (QTSQWDDPW), FW9 (FQWMGYELW), MF8 (MRHVLEPF), IW9 (IRYPKTFGW), and IW11 (IRYPKTFGWLW). The structures reveal that not only P2, but also P1 and P3, can be used as N-terminal anchor residues by Mamu-B*17-restricted peptides. Moreover, the N-terminal anchor residues exhibit a broad chemical specificity, encompassing basic (H and R), bulky polar aliphatic (Q), and small (T) residues. In contrast, Mamu-B*17 exhibits a very narrow preference for aromatic residues (W and F) at the C terminus, similar to that displayed by HLA-B*57. Flexibility within the whole peptide-binding groove contributes to the accommodation of these diverse peptides, which adopt distinct conformations. Furthermore, the unusually large pocket D enables compensation from other peptide residues if P3 is occupied by an amino acid with a small side chain. In addition, residues located at likely TCR contact regions present highly flexible conformations, which may impact TCR repertoire profiles. These findings provide novel insights into the structural basis of diverse peptide accommodation by Mamu-B*17 and highlight unique atomic features that might contribute to the protective effect of this MHC I molecule in SIV-infected rhesus macaques.

Structure deposition and release

Deposited: 2011-05-09
Released: 2012-03-21
Revised: 2012-03-21

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: QTSQWDDPW

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

GLU62
TRP167
MET5
TYR159
TYR171
TYR59
TYR7
ARG66
GLU163
ALA63
P2 THR

TYR7
TYR9
TYR99
SER24
ALA63
GLU45
ALA67
ARG66
TYR159
P3 SER

PHE156
TYR159
TYR9
ARG66
TYR99
P4 GLN

ARG66
TYR159
P5 TRP

PHE156
TYR152
LYS97
TYR159
ARG155
P6 ASP

LYS97
THR73
ASN77
TYR9
TYR152
ALA70
HIS74
P7 ASP

ASN150
ARG155
THR73
ASN77
TYR152
TRP147
P8 PRO

GLU76
THR73
ASN77
LYS146
THR143
TRP147
P9 TRP

SER116
ALA81
TYR123
TRP147
ASN142
ALA117
TYR84
ILE95
THR80
LYS146
THR143
ASN77
TYR118

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
GLU163
TRP167
TYR171
MET5
TYR59
ALA63
ARG66
TYR7
B Pocket

SER24
VAL34
GLU45
ALA63
ARG66
ALA67
TYR7
ALA70
TYR9
TYR99
C Pocket

ALA70
THR73
HIS74
TYR9
LYS97
D Pocket

HIS114
ARG155
PHE156
TYR159
LEU160
TYR99
E Pocket

HIS114
TRP147
TYR152
PHE156
LYS97
F Pocket

SER116
TYR123
THR143
LYS146
TRP147
ASN77
THR80
ALA81
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
MIQRTPKIQVYSRHPPENGKPNFLNCYVSGFHPSDIEVDLLKNGEKMGKVEHSDLSFSKD
        70        80        90
WSFYLLYYTEFTPNEKDEYACRVNHVTLSGPRTVKWDRDM

2. Class I alpha
Mamu-B*017:01
        10        20        30        40        50        60
GSHSMKYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAESPREEPRAPWVEQEGPEYW
        70        80        90       100       110       120
EEATRRAKEAAQTHRENLRTALRYYNQSEAGSHTIQKMYGCDLGPDGRLLRGYHQSAYDG
       130       140       150       160       170       180
KDYIALNGDLRSWTAADMAAQNTQRKWEGNRYAERFRAYLEGECLEWLRRYLENGKETLQ
       190       200       210       220       230       240
RADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEEQTQDTEFVETRPGGDGT
       250       260       270
FQKWGAVVVPSGEEQRYTCHVQHEGLPEPLTLRWEP

3. Peptide
QTSQWDDPW


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. 3RWF assembly 1  

Components

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

Derived data

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

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