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3LV3

HLA-B*27:05 binding "SRRWRRWNR" at 1.94Å 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
SRRWRRWNR
['C']

Species

Locus / Allele group

HLA-B / HLA-B*27

Publication

Loss of recognition by cross-reactive T cells and its relation to a C-terminus-induced conformational reorientation of an HLA-B*2705-bound peptide.

Loll B, Rückert C, Hee CS, Saenger W, Uchanska-Ziegler B, Ziegler A
Protein Sci. (2011) 20, 278-90 [doi:10.1002/pro.559]  [pubmed:21280120] 

Background

NT Pro-BNP is a blood marker secreted by cardiomyocytes. Myocardial stretch is the main factor to stimulate NT Pro-BNP secretion in cardiomyocytes. NT Pro-BNP is an important risk factor for cardiac dysfunction, stroke, and pulmonary embolism. So does atrial myocyte stretching occur when patients have atrial fibrillation (AF)? Whether atrial muscle stretch induced by AF leads to increased NT Pro-BNP remains unclear. The purpose of this study is to investigate the relationship between NT Pro-BNP and AF.

Hypothesis

AF can cause changes in myocardial tension. Changes in myocardial tension may lead to increased secretion of NT Pro-BNP. We hypothesize that NT Pro-BNP may increase in AF with or without LAD enlargement.

Methods

This clinical study is an observational study and has been approved by the Ethics Committee of the First Affiliated Hospital of Xi'an Jiaotong University. Ethical approval documents is attached. The study retrospectively reviewed 1345 patients with and without AF. After excluding 102 patients who were not eligible, the final total sample size was 1243 cases: AF group 679 patients (378, 55.7% males) and non-AF group 564 patients (287, 50.8% males). NT Pro-BNP was observed in AF group and non-AF group with or without LAD. After adjusting for age, gender, BMI, left atrial diameter, hypertension, diabetes, coronary heart disease, and cerebral infarction, NT Pro-BNP remains statistically significant with AF.

Conclusion

NT Pro-BNP can be used as a risk predictor of AF with or without left atrial enlargement.

Structure deposition and release

Deposited: 2010-02-19
Released: 2010-11-24
Revised: 2012-10-31

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: SRRWRRWNR

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

TRP167
GLU63
MET5
TYR171
TYR159
ARG62
TYR59
TYR7
GLU163
 P2 ARG

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

TYR159
ARG62
ILE66
TYR99
GLU163
HIS114
LEU156
 P4 TRP

ARG62
ILE66
GLN65
 P5 ARG

GLN155
 P6 ARG

ALA69
THR73
 P7 TRP

GLN155
ALA150
ASP77
LEU156
VAL152
TRP147
 P8 ASN

ASP77
THR143
LYS146
TRP147
THR73
GLU76
 P9 ARG

ASP116
LYS70
TYR84
LEU95
ILE142
ASP77
GLN96
THR80
THR143
LYS146
TRP147
ASN97
TYR123
ASP74
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
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
SRRWRRWNR

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. 3LV3 assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 3LV3 assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 3LV3 assembly 1  
Peptide only [cif]
  1. 3LV3 assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/3lv3

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


Creative Commons Licence
This work is licensed under a Creative Commons Attribution 4.0 International License.