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3RWH

Mamu-B*017:01 binding "MRHVLEPF" 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', 'E']
2. Class I alpha
Mamu-B*017:01
['A', 'D']
3. Peptide
MRHVLEPF
['C', 'F']

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: Octamer (8 amino acids)

Sequence: MRHVLEPF

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 MET

TYR59
ARG66
TYR7
GLU163
TRP167
MET5
TYR171
TYR159
GLU62
P2 ARG

GLU163
ALA63
PHE36
GLU45
VAL34
TYR159
ARG66
TYR7
VAL25
TYR9
ARG35
ALA67
TYR99
SER24
P3 HIS

TYR152
TYR99
PHE156
ARG155
ARG66
HIS114
TYR159
TYR9
P4 VAL

ARG66
TYR152
GLU69
P5 LEU

LYS97
ALA70
THR73
HIS74
HIS114
TYR9
TYR152
TYR99
P6 GLU

ASN150
THR73
ASN77
TYR152
TRP147
LYS97
ARG155
P7 PRO

LYS146
TRP147
THR73
GLU76
ASN77
THR143
P8 PHE

LYS97
TYR123
ILE95
SER116
ASN77
ILE124
TYR84
ASN142
THR80
THR143
LYS146
TRP147

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
IQRTPKIQVYSRHPPENGKPNFLNCYVSGFHPSDIEVDLLKNGEKMGKVEHSDLSFSKDW
        70        80        90
SFYLLYYTEFTPNEKDEYACRVNHVTLSGPRTVKWDRDM

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
MRHVLEPF


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. 3RWH assembly 1  
  2. 3RWH assembly 2  

Components

MHC Class I alpha chain [cif]
  1. 3RWH assembly 1  
  2. 3RWH assembly 2  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 3RWH assembly 1  
  2. 3RWH assembly 2  
Peptide only [cif]
  1. 3RWH assembly 1  
  2. 3RWH assembly 2  

Derived data

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

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