7DC6
Aime-128 binding "NGYNFFSTF" 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
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
1. Beta 2 microglobulin
['B', 'D']
2. Class I alpha
Aime-128
Aime-128
['A', 'C']
3. Peptide
NGYNFFSTF
NGYNFFSTF
['E', 'F']
Species
Locus / Allele group
Crystal structure of the giant panda MHC class I complex: First insights into the viral peptide presentation profile in the bear family.
Yuan H, Ma L, Zhang L, Li X, Xia C
Protein Sci (2020) 29,
2468-2481 [doi:10.1002/pro.3980]
[pubmed:33078460]
Background
Initiating ivabradine in acute heart failure (HF) is still controversial.Hypothesis
Ivabradine might be effective to be added in acute but hemodynamically stable HF.Methods
A retrospective cohort of hemodynamically stable acute HF patients was enrolled from January 2018 to January 2020 and followed until July 2020. The primary endpoints were all-cause mortality and rehospitalization for HF. Secondary endpoints included heart rate (HR), cardiac function measured by New York Heart Association (NYHA) class, and left ventricular ejection fraction (LVEF) and adverse events, which were compared between patients with or without ivabradine.Results
A total of 126 patients were enrolled (50 males, median age 54 years, 81% with decompensated HF, median follow-up of 9 months). In patients treated with ivabradine, although baseline HRs were higher than the reference group (96 vs. 80 bpm), they were comparable after 3 months; more patients tolerated high doses of β-blockers (27% vs. 7.9%), improved to NYHA class I function (55.6% vs. 23.8%) and exhibited normal LVEFs (37.8% vs. 14.3%) than the reference group (all p < .05). Ivabradine was associated with a significant reduction of rehospitalization for HF than the reference group (25.4% vs.61.9%), with longer event-free survival times (hazard ratio: 0.45, 95% confidence interval [CI]: 0.25-0.79), and was related with primary endpoints negatively (hazard ratio 0.51, 95% CI: 0.28-0.91) (all p < .05).Conclusion
In patients with acute but hemodynamically stable HF, ivabradine may significantly reduce HR, improve cardiac function, and reduce HF rehospitalization.Structure deposition and release
Deposited: 2020-10-23
Released: 2021-06-16
Revised: 2021-06-16
Data provenance
Publication data retrieved from PDBe REST API8 and PMCe REST API9
Other structures from this publication
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
ASN
ARG63
ASN64
MET6
TYR8
GLU164
TYR60
TYR172
TYR160
ILE67
TRP168
|
P2
GLY
TYR160
ILE67
TYR10
ASN64
TYR8
|
P3
TYR
ILE67
ARG156
TYR157
TYR10
TRP98
HIS100
GLU153
TYR160
ASN71
|
P4
ASN
ASP70
GLU153
ARG66
ASN71
ILE67
ARG156
|
P5
PHE
TRP134
ARG156
TRP148
TRP98
GLU153
ASP70
SER115
ALA74
ASN71
|
P6
PHE
ALA74
ARG156
GLU153
ASP70
|
P7
SER
GLU153
ASP78
ALA74
ALA151
TRP148
|
P8
THR
VAL77
THR144
LYS147
TRP148
ASP78
ALA74
|
P9
PHE
TYR124
ILE96
TYR85
THR144
ILE143
THR81
ALA82
LEU117
ASP78
LYS147
TRP148
|
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]
Peptide sidechain binding pockets (static)
Peptide terminii and backbone binding residues (static)
|
A Pocket
TYR159
GLU163
TRP167
TYR171
MET5
TYR59
ASN63
ILE66
TYR7
|
B Pocket
ALA24
VAL34
MET45
ASN63
ILE66
ALA67
TYR7
ASN70
TYR9
HIS99
|
C Pocket
ASN70
ALA73
PHE74
TYR9
TRP97
|
D Pocket
SER114
ARG155
TYR156
TYR159
VAL160
HIS99
|
E Pocket
SER114
TRP147
GLU152
TYR156
TRP97
|
F Pocket
LEU116
TYR123
THR143
LYS146
TRP147
ASP77
THR80
ALA81
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.
|
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
MVQHAPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGEKMKAEQSDLSFSKDW 70 80 90 TFYLLVHTEFTPNGQDEFSCRVKHVTLSEPQIIKWERDN |
|
2. Class I alpha
Aime-128
|
10 20 30 40 50 60
GSHSMRYFYTAVSRPGRGEPRFIAVGYVDDTQFVRFDSDSASRRMEPRAPWIEQEGPEYW 70 80 90 100 110 120 DRNTRIAEDNAQAFRVDLQTALRYYNQSEAGSHTIQWMHGCDVGPDGRLLRGYSQLAYDG 130 140 150 160 170 180 ADYIALNEDLRSWTAADTAAQITRRKWEAAGEAERYRNYVEGECVEWLRRYLENGKETLQ 190 200 210 220 230 240 RAETPDTRVTRHPISDQKVTLRCWALGFYPAEITLTWQQDGEDLTQDTELVETRPAGDGT 250 260 270 FQKWAAVVVPSGQEQRYTCHVQHEGLPEPLTRSWE |
|
3. Peptide
|
NGYNFFSTF
|
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.
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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.
Components
MHC Class I alpha chain [cif]
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
Peptide only [cif]
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
- Protein Data Bank Europe - Coordinate Server
- 1HHK - HLA-A*02:01 binding LLFGYPVYV at 2.5Å resolution - PDB entry for 1HHK
- Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. - PyMol CEALIGN Method - Publication
- PyMol - PyMol.org/pymol
- Levenshtein distance - Wikipedia entry
- Protein Data Bank Europe REST API - Molecules endpoint
- 3Dmol.js: molecular visualization with WebGL - 3DMol.js - Publication
- Protein Data Bank Europe REST API - Publication endpoint
- PubMed Central Europe REST API - Articles endpoint
This work is licensed under a Creative Commons Attribution 4.0 International License.