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3DTX

HLA-B*27:05 binding "RRKWRRWHL" at 2.10Å 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
['B']
2. Class I alpha
HLA-B*27:05
['A']
3. Peptide
RRKWRRWHL
['C']

Species


Locus / Allele group


Publication

Citrullination-and mhc polymorphism-dependent conformational changes of a self peptide

Beltrami, A., Gabdulkhakov, A., Rossmann, M., Ziegler, A., Uchanska-Ziegler, B., Saenger, W.

Structure deposition and release

Deposited: 2008-07-16
Released: 2009-05-05
Revised: 2011-10-12

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: RRKWRRWHL

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 ARG

TYR159
TYR59
GLU163
ARG62
TRP167
TYR7
TYR171
GLU63
MET5
P2 ARG

GLU163
GLU63
GLU45
TYR159
HIS9
ARG62
VAL25
ILE66
GLY26
TYR7
CYS67
VAL34
TYR99
THR24
P3 LYS

TYR99
ILE66
GLN155
LEU156
TYR159
P4 TRP

ALA69
GLN65
ARG62
ILE66
P7 TRP

GLN155
THR73
HIS114
LEU156
TRP147
VAL152
ASP77
P8 HIS

GLU76
THR143
THR73
TRP147
ASP77
LYS146
P9 LEU

ASP116
ASP77
LYS146
TYR84
LEU81
LEU95
ILE142
THR143
THR80
TYR123
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
GLU63
ILE66
TYR7
B Pocket

THR24
VAL34
GLU45
GLU63
ILE66
CYS67
TYR7
LYS70
HIS9
TYR99
C Pocket

LYS70
THR73
ASP74
HIS9
ASN97
D Pocket

HIS114
GLN155
LEU156
TYR159
LEU160
TYR99
E Pocket

HIS114
TRP147
VAL152
LEU156
ASN97
F Pocket

ASP116
TYR123
THR143
LYS146
TRP147
ASP77
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
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
        70        80        90
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

2. Class I alpha
HLA-B*27:05
IPD-IMGT/HLA
[ipd-imgt:HLA34811]
        10        20        30        40        50        60
GSHSMRYFHTSVSRPGRGEPRFITVGYVDDTLFVRFDSDAASPREEPRAPWIEQEGPEYW
        70        80        90       100       110       120
DRETQICKAKAQTDREDLRTLLRYYNQSEAGSHTLQNMYGCDVGPDGRLLRGYHQDAYDG
       130       140       150       160       170       180
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGECVEWLRRYLENGKETLQ
       190       200       210       220       230       240
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
       250       260       270
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

3. Peptide
RRKWRRWHL


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. 3DTX assembly 1  

Components

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

Derived data

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

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