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1ZVS

Mamu-A1*001:01 binding "TTPESANL" at 2.80Å 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-A1*001:01
['A', 'D']
3. Peptide
TTPESANL
['C', 'F']

Species


Locus / Allele group


Publication

First glimpse of the peptide presentation by rhesus macaque MHC class I: crystal structures of Mamu-A*01 complexed with two immunogenic SIV epitopes and insights into CTL escape.

Chu F, Lou Z, Chen YW, Liu Y, Gao B, Zong L, Khan AH, Bell JI, Rao Z, Gao GF
J. Immunol. (2007) 178, 944-52 [doi:10.4049/jimmunol.178.2.944]  [pubmed:17202356

The infection of rhesus macaques (Macaca mulatta) by the SIV is the best animal model for studying HIV infection and for AIDS vaccine development. A prevalent MHC class I allele, Mamu-A*01, is known to correlate with containment of SIV, which has been extensively explored in studies of CTL-based vaccination concepts. We determined the crystal structures of Mamu-A*01 complexed with two immunodominant SIV epitopes: the nonamer CM9 of group-specific Ag (Gag, 181-189; CTPYDINQM) and the octamer TL8 of transcription activator (Tat, 28-35; TTPESANL). The overall structures of the two Mamu-A*01 complexes are similar to other MHC class I molecules. Both structures confirm the presence of an absolutely conserved proline anchor residue in the P3 position of the Ag, bound to a D pocket of the Mamu-A*01 H chain with optimal surface complementarity. Like other MHC/peptide complex structures, the P2 and C-terminal residues of the epitopes are also important for anchoring to the MHC molecule, whereas the middle residues form an arch and their side chains are directed into solvent. These two structures reveal details of how Mamu-A*01 interacts with two well-studied epitopes at the atomic level. We discuss the structural basis of CTL escape, based on molecular models made possible by these two structures. The results we present in this study are most relevant for the rational design of Mamu-A*01-restricted CTL epitopes with improved binding, as a step toward development of AIDS vaccines.

Structure deposition and release

Deposited: 2005-06-02
Released: 2006-06-13
Revised: 2019-11-06

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: TTPESANL

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 THR

ARG62
TRP167
MET5
TYR171
TYR159
GLN163
TYR59
GLU63
TYR7
P2 THR

TYR159
GLN163
GLU63
TYR9
TYR7
ASN66
MET67
MET45
P3 PRO

GLN163
MET156
ARG97
GLU70
TYR9
VAL99
TYR159
TYR7
ASN66
P4 GLU

ARG97
GLU70
SER155
ASN66
MET156
P5 SER

ARG97
THR69
ASN73
GLU70
P6 ALA

ASN77
VAL152
TRP147
TYR116
P7 ASN

LYS146
ASN77
ASN73
TRP147
P8 LEU

TYR116
LEU81
TYR84
LEU95
TRP147
THR143
TYR123
THR80
LYS146
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
GLN163
TRP167
TYR171
MET5
TYR59
GLU63
ASN66
TYR7
B Pocket

ALA24
VAL34
MET45
GLU63
ASN66
MET67
TYR7
GLU70
TYR9
VAL99
C Pocket

GLU70
ASN73
ALA74
TYR9
ARG97
D Pocket

GLU114
SER155
MET156
TYR159
LEU160
VAL99
E Pocket

GLU114
TRP147
VAL152
MET156
ARG97
F Pocket

TYR116
TYR123
THR143
LYS146
TRP147
ASN77
THR80
LEU81
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
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
        70        80        90
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

2. Class I alpha
Mamu-A1*001:01
        10        20        30        40        50        60
GSHSMKYFYTSMSRPGRGQPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWVEQEGPEYW
        70        80        90       100       110       120
DRETRNMKTETQNAPVNLRTLLRYYNQSEAGSHTLQRMVGCDLGPDGRLLRGYEQYAYDG
       130       140       150       160       170       180
KDYIALNEDLRSWTAADVAAQNTQRKWEAADVAESMRAYLEGQCVEWLPRYLEKGKETLQ
       190       200       210       220       230       240
RTDPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
       250       260       270
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPHTLKWEPHH

3. Peptide
TTPESANL


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

Data can be downloaded to your local machine from the links below.
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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. 1ZVS assembly 1  
  2. 1ZVS assembly 2  

Components

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

Derived data

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

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