[English] 日本語
Yorodumi
- PDB-7r7y: Crystal structure of HLA-B*5701 complex with an HIV-1 Gag-derived... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7r7y
TitleCrystal structure of HLA-B*5701 complex with an HIV-1 Gag-derived epitope QW9 S3T variant
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • GLN-ALA-THR-GLN-GLU-VAL-LYS-ASN-TRP
  • MHC class I antigen
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / MHC / T Cell Immunity / Antigen Presentation / HIV / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway ...antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...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 / 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
Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
HIV-1 06TG.HT008 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsLi, X.L. / Ng, R. / Tan, K.M. / Walker, B.D. / Wang, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 HL103526; R01 AI149704; 5UM1Al144462; P30 AI060354 United States
CitationJournal: Nat Commun / Year: 2023
Title: Molecular basis of differential HLA class I-restricted T cell recognition of a highly networked HIV peptide.
Authors: Li, X. / Singh, N.K. / Collins, D.R. / Ng, R. / Zhang, A. / Lamothe-Molina, P.A. / Shahinian, P. / Xu, S. / Tan, K. / Piechocka-Trocha, A. / Urbach, J.M. / Weber, J.K. / Gaiha, G.D. / Takou ...Authors: Li, X. / Singh, N.K. / Collins, D.R. / Ng, R. / Zhang, A. / Lamothe-Molina, P.A. / Shahinian, P. / Xu, S. / Tan, K. / Piechocka-Trocha, A. / Urbach, J.M. / Weber, J.K. / Gaiha, G.D. / Takou Mbah, O.C. / Huynh, T. / Cheever, S. / Chen, J. / Birnbaum, M. / Zhou, R. / Walker, B.D. / Wang, J.H.
History
DepositionJun 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: 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
Revision 1.2Oct 25, 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: MHC class I antigen
B: Beta-2-microglobulin
C: GLN-ALA-THR-GLN-GLU-VAL-LYS-ASN-TRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8836
Polymers44,6073
Non-polymers2763
Water10,269570
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-23 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.335, 81.828, 109.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein MHC class I antigen / Human Leukocyte Antigen B*57:01 / HLA-B*5701 Heavy Chain


Mass: 31736.172 Da / Num. of mol.: 1 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: U6BR87
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11766.198 Da / Num. of mol.: 1 / Fragment: UNP residues 22-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide GLN-ALA-THR-GLN-GLU-VAL-LYS-ASN-TRP


Mass: 1104.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HIV-1 06TG.HT008 (virus)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 570 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 30% w/v PEG8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate trihydrate, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 60505 / % possible obs: 100 % / Redundancy: 18.5 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.028 / Rrim(I) all: 0.121 / Χ2: 4.894 / Net I/σ(I): 11.9 / Num. measured all: 1117738
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.6318.50.65729740.9560.1570.6761.724100
1.63-1.6618.60.57929810.9540.1380.5961.931100
1.66-1.6918.50.51729720.960.1230.5322.155100
1.69-1.7218.60.44729830.9690.1070.462.368100
1.72-1.7618.60.39529770.9720.0940.4072.509100
1.76-1.818.60.34230260.980.0810.3512.84100
1.8-1.8518.70.329870.9820.0710.3083.371100
1.85-1.918.60.26429630.9830.0630.2724.048100
1.9-1.9518.70.23130090.9870.0550.2384.944100
1.95-2.0218.70.19829990.9920.0470.2035.222100
2.02-2.0918.60.18430200.9920.0440.1896.009100
2.09-2.1718.70.16530070.9930.0390.1696.023100
2.17-2.2718.60.15229980.9940.0360.1566.245100
2.27-2.3918.60.1430490.9950.0330.1446.27100
2.39-2.5418.60.13330120.9950.0310.1366.542100
2.54-2.7418.50.12730400.9950.030.137.281100
2.74-3.0118.40.11430540.9960.0270.1178.097100
3.01-3.4518.10.0930840.9980.0220.0938.134100
3.45-4.3417.90.06531130.9990.0160.0666.985100
4.34-5017.50.0532570.9990.0120.0514.9599.5

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A1M

1a1m


Resolution: 1.601→33.804 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 3031 5.02 %
Rwork0.153 57396 -
obs0.1549 60427 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.25 Å2 / Biso mean: 20.8334 Å2 / Biso min: 5.52 Å2
Refinement stepCycle: final / Resolution: 1.601→33.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 0 18 570 3731
Biso mean--51.3 34.53 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093305
X-RAY DIFFRACTIONf_angle_d1.0754497
X-RAY DIFFRACTIONf_chiral_restr0.353457
X-RAY DIFFRACTIONf_plane_restr0.007592
X-RAY DIFFRACTIONf_dihedral_angle_d21.461256
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6012-1.62620.27321130.1947248596
1.6262-1.65280.2011310.17742572100
1.6528-1.68130.21181260.16422612100
1.6813-1.71190.20741260.15972585100
1.7119-1.74480.19611480.15522562100
1.7448-1.78040.17871680.15692565100
1.7804-1.81920.21221270.15572566100
1.8192-1.86150.17471370.15582613100
1.8615-1.9080.18061300.15912586100
1.908-1.95960.20371430.16012588100
1.9596-2.01730.22131300.15072592100
2.0173-2.08240.17381330.14232605100
2.0824-2.15680.20221290.15682600100
2.1568-2.24310.18761330.15032613100
2.2431-2.34520.18151350.15192613100
2.3452-2.46880.16611460.1552609100
2.4688-2.62340.18651470.15892609100
2.6234-2.82590.19851370.16192650100
2.8259-3.11010.18611420.16062629100
3.1101-3.55970.18611570.14672647100
3.5597-4.48320.16891520.12772678100
4.4832-33.80.19991410.15982817100

+
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://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