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3GIV

HLA-A*02:01 binding "SLFNTVATLY" at 2.00Å 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

1. Beta 2 microglobulin
['B', 'E']
2. Class I alpha
HLA-A*02:01
['A', 'D']
3. Peptide
SLFNTVATLY
['C', 'F']

Species


Locus / Allele group


Publication

Antigen processing influences HIV-specific cytotoxic T lymphocyte immunodominance.

Tenzer S, Wee E, Burgevin A, Stewart-Jones G, Friis L, Lamberth K, Chang CH, Harndahl M, Weimershaus M, Gerstoft J, Akkad N, Klenerman P, Fugger L, Jones EY, McMichael AJ, Buus S, Schild H, van Endert P, Iversen AK
Nat. Immunol. (2009) 10, 636-46 [doi:10.1038/ni.1728]  [pubmed:19412183

Metal oxide heterostructures have gained huge attention in the energy storage applications due to their outstanding properties compared to pristine metal oxides. Herein, magnetic Fe2O3@SnO2 heterostructures were synthesized by the sol-gel electrospinning method at calcination temperatures of 450 and 600 °C. XRD line profile analysis indicated that fraction of tetragonal tin oxide phase compared to rhombohedral hematite was enhanced by increasing calcination temperature. FESEM images revealed that hexagonal nanoplatelets of Fe2O3 were hierarchically anchored on SnO2 hollow nanofibers. Optical band gap of heterogeneous structures was increased from 2.06 to 2.40 eV by calcination process. Vibrating sample magnetometer analysis demonstrated that increasing calcination temperature of the samples reduces saturation magnetization from 2.32 to 0.92 emu g-1. The Fe2O3@SnO2-450 and Fe2O3@SnO2-600 nanofibers as active materials coated onto Ni foams (NF) and their electrochemical performance were evaluated in three and two-electrode configurations in 3 M KOH electrolyte solution. Fe2O3@SnO2-600/NF electrode exhibits a high specific capacitance of 562.3 F g-1 at a current density of 1 A g-1 and good cycling stability with 92.8% capacitance retention at a high current density of 10 A g-1 after 3000 cycles in three-electrode system. The assembled Fe2O3@SnO2-600//activated carbon asymmetric supercapacitor device delivers a maximum energy density of 50.2 Wh kg-1 at a power density of 650 W kg-1. The results display that the Fe2O3@SnO2-600 can be a promising electrode material in supercapacitor applications.

Structure deposition and release

Deposited: 2009-03-06
Released: 2009-06-30
Revised: 2011-07-13

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: SLFNTVATLY

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
GLU63
LYS66
TYR159
TYR59
TRP167
PHE33
MET5
TYR7
P10 TYR

THR80
LYS146
ASP77
TYR84
P2 LEU

TYR159
PHE9
MET45
TYR7
TYR99
HIS70
GLU63
LYS66
VAL67
P3 PHE

TYR99
LYS66
TYR159
GLN155
LEU156
HIS70
P4 ASN

ARG65
LYS66
P5 THR

GLN155
P6 VAL

ALA69
THR73
HIS70
ARG97
P7 ALA

THR73
TRP147
ARG97
VAL152
ASP77
P8 THR

TRP147
VAL76
ASP77
THR73
P9 LEU

THR143
TRP147
ILE124
TYR116
TYR123
LYS146
ASP77
THR80
TYR84
LEU81

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
MET5
TYR59
GLU63
LYS66
TYR7
B Pocket

ALA24
VAL34
MET45
GLU63
LYS66
VAL67
TYR7
HIS70
PHE9
TYR99
C Pocket

HIS70
THR73
HIS74
PHE9
ARG97
D Pocket

HIS114
GLN155
LEU156
TYR159
LEU160
TYR99
E Pocket

HIS114
TRP147
VAL152
LEU156
ARG97
F Pocket

TYR116
TYR123
THR143
LYS146
TRP147
ASP77
THR80
LEU81
TYR84
VAL95

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*02:01
IPD-IMGT/HLA
[ipd-imgt:HLA35266]
        10        20        30        40        50        60
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
        70        80        90       100       110       120
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
       130       140       150       160       170       180
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
       190       200       210       220       230       240
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
       250       260       270
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

3. Peptide
SLFNTVATLY


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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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. 3GIV assembly 1  
  2. 3GIV assembly 2  

Components

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

Derived data

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

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