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4HKJ

H2-Kb binding "SIINFEKL" with Cowpox CPXV203 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 and cowpox cpxv203

1. Beta 2 microglobulin
['B', 'F', 'J', 'N']
2. Class I alpha
H2-Kb
['A', 'E', 'I', 'M']
3. cowpox_cpxv203
['D', 'H', 'L', 'P']
5. Peptide
SIINFEKL
['C', 'G', 'K', 'O']

Species


Locus / Allele group


Publication

Structural Mechanism of ER Retrieval of MHC Class I by Cowpox.

McCoy WH, Wang X, Yokoyama WM, Hansen TH, Fremont DH
PLoS Biol. (2012) 10, e1001432 [doi:10.1371/journal.pbio.1001432]  [pubmed:23209377

One of the hallmarks of viral immune evasion is the capacity to disrupt major histocompatibility complex class I (MHCI) antigen presentation to evade T-cell detection. Cowpox virus encoded protein CPXV203 blocks MHCI surface expression by exploiting the KDEL-receptor recycling pathway, and here we show that CPXV203 directly binds a wide array of fully assembled MHCI proteins, both classical and non-classical. Further, the stability of CPXV203/MHCI complexes is highly pH dependent, with dramatically increased affinities at the lower pH of the Golgi relative to the endoplasmic reticulum (ER). Crystallographic studies reveal that CPXV203 adopts a beta-sandwich fold similar to poxvirus chemokine binding proteins, and binds the same highly conserved MHCI determinants located under the peptide-binding platform that tapasin, CD8, and natural killer (NK)-receptors engage. Mutagenesis of the CPXV203/MHCI interface identified the importance of two CPXV203 His residues that confer low pH stabilization of the complex and are critical to ER retrieval of MHCI. These studies clarify mechanistically how CPXV203 coordinates with other cowpox proteins to thwart antigen presentation.

Structure deposition and release

Deposited: 2012-10-15
Released: 2012-11-14
Revised: 2017-11-15

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

TYR7
TYR171
TYR159
THR163
TYR59
GLU63
TRP167
LYS66
LEU5
P2 ILE

TYR45
TYR159
GLU63
VAL9
TYR7
ASN70
GLU24
LYS66
P3 ILE

ARG155
ASN70
TYR159
LYS66
GLN114
LEU156
SER99
P4 ASN

ARG155
ASN70
LYS66
P5 PHE

SER73
ARG155
GLN114
TYR22
PHE74
VAL97
VAL9
ASN70
SER99
GLU24
TYR116
P6 GLU

ASP77
TYR116
GLU152
ARG155
TRP147
P7 LYS

VAL76
ASP77
SER73
TRP147
P8 LEU

ILE142
LYS146
TYR123
LEU81
ASP77
ILE124
TYR116
THR80
THR143
TRP147
TYR84
ILE95

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. Beta 2 microglobulin
Beta 2 microglobulin
        10        20        30        40        50        60
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
        70        80        90
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

2. 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
FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWEPPPST

3. cowpox_cpxv203
cowpox_cpxv203
        10        20        30        40        50        60
AMVIRRCEKMEEETWKLKIGMCIQAKDFYSKRTDCSVHRPDVGGGLITEGNGYRVVVHDQ
        70        80        90       100       110       120
CEEPNPFIIATTKQTHFGVTHSYIEFSNSNTGAPENIPDCSKHILISVYCDQEASGLDFH
       130       140       150       160       170       180
TLKYVESNYLHITVKYDTSCINHLGVNYSFMNECERKLTSIYETDTLTCGAKDIQTRDKY
       190       200
LKTCTNTKFDRSVYKTHMQKSKILHV

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]
  1. 4HKJ assembly 1  
  2. 4HKJ assembly 2  
  3. 4HKJ assembly 3  
  4. 4HKJ assembly 4  

Components

MHC Class I alpha chain [cif]
  1. 4HKJ assembly 1  
  2. 4HKJ assembly 2  
  3. 4HKJ assembly 3  
  4. 4HKJ assembly 4  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 4HKJ assembly 1  
  2. 4HKJ assembly 2  
  3. 4HKJ assembly 3  
  4. 4HKJ assembly 4  
Peptide only [cif]
  1. 4HKJ assembly 1  
  2. 4HKJ assembly 2  
  3. 4HKJ assembly 3  
  4. 4HKJ assembly 4  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/4hkj

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