Alpha This is a work in progress and may change. Your feedback is very welcome.
  


1LDP

H2-Ld binding "APAAAAAAM" at 3.10Å 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
['L']
2. Class I alpha
H2-Ld
['H']
4. Peptide
APAAAAAAM
['P', 'Q']

Species

Locus / Allele group

H2-L / H2-Ld

Publication

Structural basis of 2C TCR allorecognition of H-2Ld peptide complexes.

Speir JA, Garcia KC, Brunmark A, Degano M, Peterson PA, Teyton L, Wilson IA
Immunity (1998) 8, 553-62 [doi:10.1016/s1074-7613(00)80560-9]  [pubmed:9620676] 

MHC class I H-2Ld complexed with peptide QL9 (or p2Ca) is a high-affinity alloantigen for the 2C TCR. We used the crystal structure of H-2Ld with a mixture of bound peptides at 3.1 A to construct a model of the allogeneic 2C-Ld/QL9 complex for comparison with the syngeneic 2C-Kb/dEV8 structure. A prominent ridge on the floor of the Ld peptide-binding groove, not present in Kb, creates a C-terminal bulge in Ld peptides that greatly increases interactions with the 2C beta-chain. Furthermore, weak electrostatic complementarity between Asp77 on the alpha1 helix of Kb and 2C is enhanced in the allogeneic complex by closer proximity of QL9 peptide residue AspP8 to the 2C HV4 loop.

Structure deposition and release

Deposited: 1998-03-15
Released: 1998-06-17
Revised: 2020-07-29

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: APAAAAAAM

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

ILE66
ILE63
TRP167
MET5
TYR171
ARG62
PHE33
TYR59
TYR7
TYR159
GLU163
 P2 LEU

TYR99
GLN70
ILE66
TYR45
GLU9
ILE63
SER24
ALA67
TYR22
TYR7
 P3 SER

TYR155
TRP97
TYR159
ILE66
TYR99
GLN70
 P4 PRO

TYR156
GLN70
ILE66
TYR155
TRP97
 P5 PHE

TYR156
TYR155
TRP97
TRP147
TRP73
PHE116
GLN70
GLU114
 P6 PRO

TRP73
TYR155
 P7 PHE

TRP147
ALA150
TRP73
ASN77
GLY151
ALA152
TYR155
TYR156
 P8 ASP

TRP147
LYS146
THR143
VAL76
TRP73
ASN77
 P9 LEU

PHE116
THR80
TRP73
ASN77
TYR84
TYR123
LEU95
ILE124
THR143
LEU81
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
ILE63
ILE66
TYR7
B Pocket

SER24
VAL34
TYR45
ILE63
ILE66
ALA67
TYR7
GLN70
GLU9
TYR99
C Pocket

GLN70
TRP73
PHE74
GLU9
TRP97
D Pocket

GLU114
TYR155
TYR156
TYR159
LEU160
TYR99
E Pocket

GLU114
TRP147
ALA152
TYR156
TRP97
F Pocket

PHE116
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
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
        70        80        90
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM
2. Class I alpha
H2-Ld
        10        20        30        40        50        60
GPHSMRYFETAVSRPGLGEPRYISVGYVDNKEFVRFDSDAENPRYEPQAPWMEQEGPEYW
        70        80        90       100       110       120
ERITQIAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQWMYGCDVGSDGRLLRGYEQFAYDG
       130       140       150       160       170       180
CDYIALNEDLKTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNGNATLL
       190       200       210       220       230       240
RTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT
       250       260       270
FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTL
4. Peptide
APAAAAAAM

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.
Clicking on the clipboard icon will copy the url for the data to your clipboard.
This can then be used to load the structure/data directly from the url into an application like PyMol (for 3D structures) using the load command:
   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. 1LDP assembly 1  

Components

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

Derived data

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

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


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