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5XOV

HLA-A*24:02 presenting "RYPLTFGWCF" to Alpha/Beta T cell receptor at 2.68Å 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 alpha beta tcr

1. Beta 2 microglobulin
['B', 'E']
2. Class I alpha
HLA-A*24:02
['A', 'D']
3. Peptide
RYPLTFGWCF
['C', 'F']
4. T cell receptor alpha
None
['I']
5. T cell receptor beta
TRBV30
['J']

Species


Locus / Allele group


Publication

Conserved V��1 binding geometry in a setting of locus-disparate pHLA recognition by ��/����TCRs: insight into recognition of HIV peptides by TCR.

Shi Y, Kawana-Tachikawa A, Gao F, Qi J, Liu C, Gao J, Cheng H, Ueno T, Iwamoto A, Gao GF
J. Virol. (2017) [doi:10.1128/JVI.00725-17]  [pubmed:28615212

An essential step in the development of effective antiviral humoral responses is cytokine-triggered class switch recombination resulting in the production of antibodies of a specific isotype. Most viral and parasitic infections in mice induce predominantly IgG2a-specific antibody responses that are stimulated by interferon gamma (IFN-γ). However, in some mice deficient in IFN-γ, class switching to IgG2a antibodies is relatively unaffected, indicating that another signal(s) can be generated upon viral or parasitic infections that trigger this response. Here, we found that a single recessive locus, provisionally called IFN-γ-independent IgG2a (Igii), confers the ability to produce IFN-γ-independent production of IgG2a antibodies upon retroviral infection. The Igii locus was mapped to chromosome 9 and was found to function in the radiation-resistant compartment. Thus, our data implicate nonhematopoietic cells in activation of antiviral antibody responses in the absence of IFN-γ.IMPORTANCE Understanding the signals that stimulate antibody production and class switch recombination to specific antibody isotypes is crucial for the development of novel vaccines and adjuvants. While an interferon gamma-mediated switch to the IgG2a isotype upon viral infection in mice has been well established, this investigation reveals a noncanonical, interferon gamma-independent pathway for antiretroviral antibody production and IgG2a class switch recombination that is controlled by a single recessive locus. Furthermore, this study indicates that the radiation-resistant compartment can direct antiviral antibody responses, suggesting that detection of infection by nonhematopoietic cells is involved is stimulating adaptive immunity.

Structure deposition and release

Deposited: 2017-05-31
Released: 2017-06-14
Revised: 2019-04-17

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Decamer (10 amino acids)

Sequence: RYPLTFGWCF

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
GLU63
LYS66
GLY167
MET5
TYR171
TYR7
ARG170
THR163
P10 PHE

LYS146
TRP147
ILE142
THR143
TYR84
TYR123
LEU95
ASN77
ILE80
TYR116
ALA81
P2 TYR

MET97
VAL67
SER9
HIS70
TYR7
ALA24
TYR159
PHE22
GLU63
LYS66
MET45
P3 PRO

MET97
GLN156
TYR7
PHE99
TYR159
LYS66
P4 LEU

TYR159
LYS66
GLN156
P5 THR

ALA69
THR73
LYS66
HIS70
GLN156
P6 PHE

VAL152
GLN156
GLN155
P7 GLY

VAL152
TRP147
ALA150
P8 TRP

TYR116
THR73
ASN77
PHE99
HIS114
VAL152
HIS70
TRP147
GLN156
MET97
P9 CYS

ASN77
THR73
GLU76
LYS146
TRP147
THR143

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
GLY167
TYR171
MET5
TYR59
GLU63
LYS66
TYR7
B Pocket

ALA24
VAL34
MET45
GLU63
LYS66
VAL67
TYR7
HIS70
SER9
PHE99
C Pocket

HIS70
THR73
ASP74
SER9
MET97
D Pocket

HIS114
GLN155
GLN156
TYR159
LEU160
PHE99
E Pocket

HIS114
TRP147
VAL152
GLN156
MET97
F Pocket

TYR116
TYR123
THR143
LYS146
TRP147
ASN77
ILE80
ALA81
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-A*24:02
IPD-IMGT/HLA
[ipd-imgt:HLA34790]
        10        20        30        40        50        60
GSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
        70        80        90       100       110       120
DEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYDG
       130       140       150       160       170       180
KDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETLQ
       190       200       210       220       230       240
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
       250       260       270
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW

3. Peptide
RYPLTFGWCF

4. T cell receptor alpha
T cell receptor alpha
None
        10        20        30        40        50        60
QKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNAKSG
        70        80        90       100       110       120
RYSVNFKKAAKSVALTISALQLEDSAKYFCALGELARSGGYQKVTFGTGTKLQVIPNIQN
       130       140       150       160       170       180
PDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVA
       190       200
WSNKSDFACANAFNNSIIPEDTFFPSP

5. T cell receptor beta
T cell receptor beta
TRBV30
        10        20        30        40        50        60
SQTIHQWPATLVQPVGSPLSLECTVEGTSNPNLYWYRQAAGRGLQLLFYSVGIGQISSEV
        70        80        90       100       110       120
PQNLSASRPQDRQFILSSKKLLLSDSGFYLCAWSVSVGAGVPTIYFGEGSWLTVVEDLNK
       130       140       150       160       170       180
VFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKE
       190       200       210       220       230       240
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA

WGRAD


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. 5XOV assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 5XOV assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 5XOV assembly 1  
Peptide only [cif]
  1. 5XOV assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/5xov

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