[English] 日本語
Yorodumi
- PDB-6vqz: HLA-B*27:05 presenting an HIV-1 6mer peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vqz
TitleHLA-B*27:05 presenting an HIV-1 6mer peptide
Components
  • 6-mer peptide
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Human Leukocyte Antigen / Human Immunodeficiency Virus
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / antigen processing and presentation of peptide antigen via MHC class I / Early Phase of HIV Life Cycle ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / antigen processing and presentation of peptide antigen via MHC class I / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / HIV-1 retropepsin / peptide antigen assembly with MHC class II protein complex / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / cellular response to iron(III) ion / exoribonuclease H / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / exoribonuclease H activity / ER to Golgi transport vesicle membrane / Assembly Of The HIV Virion / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / Budding and maturation of HIV virion / protein processing / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / host multivesicular body / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / specific granule lumen / viral penetration into host nucleus / RNA stem-loop binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / RNA-DNA hybrid ribonuclease activity / MHC class II protein complex binding / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / peptidase activity / host cell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / DNA recombination / protein homotetramerization / amyloid fibril formation / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / intracellular iron ion homeostasis / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / learning or memory / immune response
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / MHC classes I/II-like antigen recognition protein / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / : / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
ARGININE / MHC class I antigen / Gag-Pol polyprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPymm, P. / Tenzer, S. / Wee, E. / Weimershaus, M. / Burgevin, A. / Kollnberger, S. / Gerstoft, J. / Josephs, T.M. / Ladell, K. / Mclaren, J.E. ...Pymm, P. / Tenzer, S. / Wee, E. / Weimershaus, M. / Burgevin, A. / Kollnberger, S. / Gerstoft, J. / Josephs, T.M. / Ladell, K. / Mclaren, J.E. / Appay, V. / Price, D.A. / Fugger, L. / Bell, J.I. / Hansjorg, S. / Van Endert, P. / Harkiolaki, M. / Iversen, A.K.N.
CitationJournal: Cell Rep / Year: 2022
Title: Epitope length variants balance protective immune responses and viral escape in HIV-1 infection
Authors: Pymm, P. / Tenzer, S. / Wee, E. / Weimershaus, M. / Burgevin, A. / Kollnberger, S. / Gerstoft, J. / Josephs, T.M. / Ladell, K. / McLaren, J.E. / Appay, V. / Price, D.A. / Fugger, L. / Bell, ...Authors: Pymm, P. / Tenzer, S. / Wee, E. / Weimershaus, M. / Burgevin, A. / Kollnberger, S. / Gerstoft, J. / Josephs, T.M. / Ladell, K. / McLaren, J.E. / Appay, V. / Price, D.A. / Fugger, L. / Bell, J.I. / Schild, H. / van Endert, P. / Harkiolaki, M. / Iversen, A.K.
History
DepositionFeb 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: MHC class I antigen
D: Beta-2-microglobulin
G: 6-mer peptide
F: 6-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3638
Polymers89,0136
Non-polymers3502
Water2,072115
1
A: MHC class I antigen
B: Beta-2-microglobulin
F: 6-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6824
Polymers44,5063
Non-polymers1751
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-13 kcal/mol
Surface area19180 Å2
MethodPISA
2
C: MHC class I antigen
D: Beta-2-microglobulin
G: 6-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6824
Polymers44,5063
Non-polymers1751
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-10 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.495, 130.516, 90.170
Angle α, β, γ (deg.)90.000, 104.410, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D
13chain F
23chain G
14chain C
24chain A

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLUchain AAA1 - 2751 - 275
21GLYGLYGLUGLUchain CCC1 - 2751 - 275
12ILEILEMETMETchain BBB1 - 991 - 99
22ILEILEMETMETchain DDD1 - 991 - 99
13LYSLYSLEULEUchain FFF1 - 61 - 6
23LYSLYSLEULEUchain GGE1 - 61 - 6
14GLYGLYGLYGLYchain XCC11
24HISHISHISHISchain YAA33

NCS ensembles :
ID
1
2
3
4

-
Components

#1: Protein MHC class I antigen


Mass: 31928.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Production host: Escherichia coli (E. coli) / References: UniProt: O78189
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide 6-mer peptide


Mass: 830.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04585*PLUS
#4: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30 %w/v Polyethylene Glycol Monomethyl Ether 5000, 0.2 M Ammonium Sulphate, 0.1 M MES pH 6.5

-
Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.44
ReflectionResolution: 2.25→130.49 Å / Num. obs: 47317 / % possible obs: 98.1 % / Redundancy: 2.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2% possible all
2.25-2.372.60.4092.368300.84397.1
7.12-130.492.50.02913.715580.99898.6

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W0V

1w0v


Resolution: 2.25→87.333 Å / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 39.88 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2437 2305 4.88 %
Rwork0.2006 44999 -
obs0.2037 47275 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 192.77 Å2 / Biso mean: 38.2333 Å2 / Biso min: 11.02 Å2
Refinement stepCycle: final / Resolution: 2.25→87.333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6262 0 49 115 6426
Biso mean--35 31.25 -
Num. residues----760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046594
X-RAY DIFFRACTIONf_angle_d0.7868955
X-RAY DIFFRACTIONf_chiral_restr0.034914
X-RAY DIFFRACTIONf_plane_restr0.0041185
X-RAY DIFFRACTIONf_dihedral_angle_d13.1392477
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2493X-RAY DIFFRACTION7.446TORSIONAL
12C2493X-RAY DIFFRACTION7.446TORSIONAL
21B918X-RAY DIFFRACTION7.446TORSIONAL
22D918X-RAY DIFFRACTION7.446TORSIONAL
31F84X-RAY DIFFRACTION7.446TORSIONAL
32G84X-RAY DIFFRACTION7.446TORSIONAL
41C4X-RAY DIFFRACTION7.446TORSIONAL
42A4X-RAY DIFFRACTION7.446TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.29890.35271520.29682731288391
2.2989-2.35240.32141560.29852764292093
2.3524-2.41120.31511320.29672776290891
2.4112-2.47640.30191430.28052795293893
2.4764-2.54930.2831390.2772775291492
2.5493-2.63150.31691600.27482809296993
2.6315-2.72550.32571150.26462819293494
2.7255-2.83460.27991420.25092835297793
2.8346-2.96350.32331460.24912760290694
2.9635-3.11970.24581280.21692857298594
3.1197-3.3150.23361380.21122812295094
3.315-3.57070.28181440.20122829297393
3.5707-3.92960.22751500.17022824297494
3.9296-4.49720.21610.14342841300294
4.4972-5.6620.15141310.13722874300595
5.662-34.62670.18131230.15392898302194

+
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