[English] 日本語
Yorodumi
- PDB-7s8s: Crystal Structure of HLA A*1101 in complex with RVLVNGTFLK, an 10... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s8s
TitleCrystal Structure of HLA A*1101 in complex with RVLVNGTFLK, an 10-mer epitope from Influenza B
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • Non-structural protein 1 peptide RVLVNGTFLK
KeywordsIMMUNE SYSTEM / HLA A*1101 / influenza B / TCR / T cell
Function / homology
Function and homology information


symbiont-mediated suppression of host PKR/eIFalpha signaling / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib ...symbiont-mediated suppression of host PKR/eIFalpha signaling / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / symbiont-mediated suppression of host ISG15-protein conjugation / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / learning or memory / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / signaling receptor binding / host cell nucleus / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Influenza B non-structural protein (NS1) / Influenza non-structural protein (NS1) / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / S15/NS1, RNA-binding / Immunoglobulin/major histocompatibility complex, conserved site ...Influenza B non-structural protein (NS1) / Influenza non-structural protein (NS1) / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / S15/NS1, RNA-binding / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Non-structural protein 1 / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsNguyen, A.T. / Szeto, C. / Gras, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1159272 Australia
CitationJournal: Plos Pathog. / Year: 2022
Title: HLA-A*11:01-restricted CD8+ T cell immunity against influenza A and influenza B viruses in Indigenous and non-Indigenous people.
Authors: Habel, J.R. / Nguyen, A.T. / Rowntree, L.C. / Szeto, C. / Mifsud, N.A. / Clemens, E.B. / Loh, L. / Chen, W. / Rockman, S. / Nelson, J. / Davies, J. / Miller, A. / Tong, S.Y.C. / Rossjohn, J. ...Authors: Habel, J.R. / Nguyen, A.T. / Rowntree, L.C. / Szeto, C. / Mifsud, N.A. / Clemens, E.B. / Loh, L. / Chen, W. / Rockman, S. / Nelson, J. / Davies, J. / Miller, A. / Tong, S.Y.C. / Rossjohn, J. / Gras, S. / Purcell, A.W. / Hensen, L. / Kedzierska, K. / Illing, P.T.
History
DepositionSep 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: Non-structural protein 1 peptide RVLVNGTFLK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2664
Polymers45,1703
Non-polymers961
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-33 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.875, 82.262, 57.027
Angle α, β, γ (deg.)90.000, 113.040, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein HLA class I histocompatibility antigen, A alpha chain


Mass: 32142.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: U5YJK1
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide Non-structural protein 1 peptide RVLVNGTFLK / NS1 / NS1A


Mass: 1148.398 Da / Num. of mol.: 1 / Fragment: UNP residues 186-195 / Source method: obtained synthetically / Details: peptide from Influenza B / Source: (synth.) Influenza B virus / References: UniProt: P12601
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.41 % / Mosaicity: 0.18 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 26% PEG 3350, 0.1M BisTris pH 6.3, 0.2M Lithium Sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Oct 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.82→46.82 Å / Num. obs: 38748 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 26.21 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.052 / Rrim(I) all: 0.135 / Net I/σ(I): 9.9 / Num. measured all: 265223 / Scaling rejects: 113
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 7 % / Rmerge(I) obs: 1.183 / Num. unique obs: 2267 / CC1/2: 0.682 / Rpim(I) all: 0.481 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimless0.7.4data scaling
XDSdata processing
PDB_EXTRACT3.27data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MJ5

4mj5


Resolution: 1.87→25.39 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.143 / SU Rfree Blow DPI: 0.13 / SU Rfree Cruickshank DPI: 0.13
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1904 5.33 %RANDOM
Rwork0.194 ---
obs0.196 35694 99.8 %-
Displacement parametersBiso max: 98.71 Å2 / Biso mean: 29.98 Å2 / Biso min: 12.28 Å2
Baniso -1Baniso -2Baniso -3
1--2.0143 Å20 Å26.9701 Å2
2--8.1121 Å20 Å2
3----6.0978 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.87→25.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3153 0 5 230 3388
Biso mean--44.61 35.5 -
Num. residues----384
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1133SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes568HARMONIC5
X-RAY DIFFRACTIONt_it3261HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion403SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3843SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3261HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4429HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion17.16
LS refinement shellResolution: 1.87→1.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3021 40 5.6 %
Rwork0.1995 674 -
all0.2055 714 -
obs--99.71 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more