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1ZT7

H2-Kk binding "SEFLLEKRI" at 3.00Å 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', 'D']
2. Class I alpha
H2-Kk
['A', 'C']
3. Peptide
SEFLLEKRI
['P', 'Q']

Species


Locus / Allele group


Publication

The H-2Kk MHC peptide-binding groove anchors the backbone of an octameric antigenic peptide in an unprecedented mode.

Kellenberger C, Roussel A, Malissen B
J. Immunol. (2005) 175, 3819-25 [doi:10.4049/jimmunol.175.6.3819]  [pubmed:16148128

A wealth of data has accumulated on the structure of mouse MHC class I (MHCI) molecules encoded by the H-2(b) and H-2(d) haplotypes. In contrast, there is a dearth of structural data regarding H-2(k)-encoded molecules. Therefore, the structures of H-2K(k) complexed to an octameric peptide from influenza A virus (HA(259-266)) and to a nonameric peptide from SV40 (SV40(560-568)) have been determined by x-ray crystallography at 2.5 and 3.0 A resolutions, respectively. The structure of the H-2K(k)-HA(259-266) complex reveals that residues located on the floor of the peptide-binding groove contact directly the backbone of the octameric peptide and force it to lie deep within the H-2K(k) groove. This unprecedented mode of peptide binding occurs despite the presence of bulky residues in the middle of the floor of the H-2K(k) peptide-binding groove. As a result, the Calpha atoms of peptide residues P5 and P6 are more buried than the corresponding residues of H-2K(b)-bound octapeptides, making them even less accessible to TCR contact. When bound to H-2K(k), the backbone of the SV40(560-568) nonapeptide bulges out of the peptide-binding groove and adopts a conformation reminiscent of that observed for peptides bound to H-2L(d). This structural convergence occurs despite the totally different architectures of the H-2L(d) and H-2K(k) peptide-binding grooves. Therefore, these two H-2K(k)-peptide complexes provide insights into the mechanisms through which MHC polymorphism outside primary peptide pockets influences the conformation of the bound peptides and have implications for TCR recognition and vaccine design.

Structure deposition and release

Deposited: 2005-05-26
Released: 2005-10-18
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: Nonamer (9 amino acids)

Sequence: SEFLLEKRI

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 SER

TYR59
TYR171
TYR7
TRP167
TYR159
THR163
ASN63
P2 GLU

TYR159
ASN63
ASN70
TYR7
TYR45
HIS9
ILE66
TYR99
SER24
P3 PHE

ARG155
TYR159
ASN70
ILE66
GLU114
TYR99
ASP156
ARG97
P4 LEU

GLY69
ASN70
ILE73
ILE66
P5 LEU

PHE74
TYR116
ASN70
ILE73
ASN77
GLU114
ARG97
P6 GLU

ARG155
ASP152
P7 LYS

ILE73
ASN77
TRP133
GLU114
ASP152
ASP156
TRP147
ARG97
TYR116
P8 ARG

THR143
LYS146
TRP147
ILE73
ASN77
P9 ILE

TYR123
THR143
TYR116
ASN77
LYS146
TRP147
PHE95
ILE142
ALA81
THR80
TYR84

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
GLY163
GLU167
ARG171
SER5
GLU59
ARG63
GLN66
ARG7
B Pocket

ILE24
PHE34
ARG45
ARG63
GLN66
ILE67
ARG7
GLY70
PHE9
MET99
C Pocket

GLY70
GLN73
ILE74
PHE9
GLN97
D Pocket

TYR114
GLU155
ARG156
ALA159
TYR160
MET99
E Pocket

TYR114
LYS147
GLY152
ARG156
GLN97
F Pocket

GLN116
ASP123
ILE143
HIS146
LYS147
VAL77
ARG80
THR81
ARG84
THR95

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
MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD
        70        80        90
WSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

2. Class I alpha
H2-Kk
        10        20        30        40        50        60
MGPHSLRYFHTAVSRPGLGKPRFISVGYVDDTQFVRFDSDAENPRYEPRVRWMEQVEPEY
        70        80        90       100       110       120
WERNTQIAKGNEQIFRVNLRTALRYYNQSAGGSHTFQRMYGCEVGSDWRLLRGYEQYAYD
       130       140       150       160       170       180
GCDYIALNEDLKTWTAADMAALITKHKWEQAGDAERDRAYLEGTCVEWLRRYLQLGNATL
       190       200       210       220       230       240
PRTDSPKAHVTRHSRPEDKVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDG
       250       260       270
TFQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWE

3. Peptide
SEFLLEKRI


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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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. 1ZT7 assembly 1  
  2. 1ZT7 assembly 2  

Components

MHC Class I alpha chain [cif]
  1. 1ZT7 assembly 1  
  2. 1ZT7 assembly 2  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 1ZT7 assembly 1  
  2. 1ZT7 assembly 2  
Peptide only [cif]
  1. 1ZT7 assembly 1  
  2. 1ZT7 assembly 2  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/1zt7

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