3CVH

H2-Kb binding "SIINFEKL" with antibody at 2.90Å 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.

Complex type

Class i with peptide and antibody

1. ab_heavy

['Q']

2. ab_light

['R']

3. Beta 2 microglobulin

['B', 'N']

4. Class I alpha
H2-Kb

['A', 'M']

5. Peptide
SIINFEKL

['C', 'O']

Species

Mus musculus (Mouse)

Locus / Allele group

H2-K / H2-Kb

Publication

How a T cell receptor-like antibody recognizes major histocompatibility complex-bound peptide.

Mareeva T, Martinez-Hackert E, Sykulev Y

J. Biol. Chem. (2008) 283, 29053-9 [doi:10.1074/jbc.m804996200] [pubmed:18703505]

We determined the crystal structures of the T cell receptor (TCR)-like antibody 25-D1.16 Fab fragment bound to a complex of SIINFEKL peptide from ovalbumin and the H-2K(b) molecule. Remarkably, this antibody directly "reads" the structure of the major histocompatibility complex (MHC)-bound peptide, employing the canonical diagonal binding mode utilized by most TCRs. This is in marked contrast with another TCR-like antibody, Hyb3, bound to melanoma peptide MAGE-A1 in association with HLA-A1 MHC class I. Hyb3 assumes a non-canonical orientation over its cognate peptide-MHC and appears to recognize a conformational epitope in which the MHC contribution is dominant. We conclude that TCR-like antibodies can recognize MHC-bound peptide via two different mechanisms: one is similar to that exploited by the preponderance of TCRs and the other requires a non-canonical antibody orientation over the peptide-MHC complex.

Structure deposition and release

Deposited: 2008-04-18

Released: 2008-09-23

Revised: 2017-10-25

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: SIINFEKL

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

TYR171

TYR159

TYR59

LYS66

TYR7

THR163

TRP167

GLU63

LEU5

P2 ILE

TYR7

LYS66

ASN70

GLU63

TYR45

GLU24

VAL9

TYR159

P3 ILE

TYR159

SER99

LYS66

ASN70

GLN114

LEU156

ARG155

P4 ASN

ASN70

ARG155

LYS66

P5 PHE

ASN70

GLN114

ARG155

SER99

GLU24

VAL9

PHE74

TYR22

TYR116

SER73

VAL97

P6 GLU

ARG155

TYR116

ASP77

ALA150

TRP147

GLU152

P7 LYS

TRP147

SER73

ASP77

P8 LEU

TRP147

THR143

TYR123

LYS146

TYR116

THR80

TYR84

LEU81

ILE95

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

TYR159

THR163

TRP167

TYR171

LEU5

TYR59

GLU63

LYS66

TYR7

B Pocket

GLU24

VAL34

TYR45

GLU63

LYS66

ALA67

TYR7

ASN70

VAL9

SER99

C Pocket

ASN70

SER73

PHE74

VAL9

VAL97

D Pocket

GLN114

ARG155

LEU156

TYR159

LEU160

SER99

E Pocket

GLN114

TRP147

GLU152

LEU156

VAL97

F Pocket

TYR116

TYR123

THR143

LYS146

TRP147

ASP77

THR80

LEU81

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. ab_heavy ab_heavy	10 20 30 40 50 60 VLLQQSGPELVKPGASVKIPCKASGYTFTDYNMDWVKQSHGKSLEWIGDINPNNGGTIYN 70 80 90 100 110 120 QKFKGKATLTVDKSSSAAYMEVRSLTSEDTAVYYCARKPYYGNFAWFAYWGQGTLVTVSA 130 140 150 160 170 180 AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSD 190 200 210 LYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP

2. ab_light ab_light	10 20 30 40 50 60 IQVTQSSSSFSVSLGDRVTITCKASEDIYNRLAWYQQKPGNAPRLLISGATSLETGVPDR 70 80 90 100 110 120 FSGSGSRKDYTLIITSLQTEDVATYYCQQYWSTPLTFGAGTKLELKRADAAPTVSIFPPS 130 140 150 160 170 180 SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL 190 200 TKDEYERHNSYTCEATHKTSTSPIVKSFN

3. Beta 2 microglobulin Beta 2 microglobulin	10 20 30 40 50 60 IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW 70 80 90 SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

4. Class I alpha H2-Kb	10 20 30 40 50 60 GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYW 70 80 90 100 110 120 ERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDG 130 140 150 160 170 180 CDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLL 190 200 210 220 230 240 RTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT 250 260 270 FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRW

5. Peptide	SIINFEKL

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]

3CVH assembly 1

Components

MHC Class I alpha chain [cif]

3CVH assembly 1

MHC Class I antigen binding domain (alpha1/alpha2) [cif]

3CVH assembly 1

Peptide only [cif]

3CVH assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/3cvh

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

Protein Data Bank Europe - Coordinate Server
1HHK - HLA-A*02:01 binding LLFGYPVYV at 2.5Å resolution - PDB entry for 1HHK
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. - PyMol CEALIGN Method - Publication
PyMol - PyMol.org/pymol
Levenshtein distance - Wikipedia entry
Protein Data Bank Europe REST API - Molecules endpoint
3Dmol.js: molecular visualization with WebGL - 3DMol.js - Publication
Protein Data Bank Europe REST API - Publication endpoint
PubMed Central Europe REST API - Articles endpoint

This work is licensed under a Creative Commons Attribution 4.0 International License.