[English] 日本語
Yorodumi
- PDB-1q94: Structures of HLA-A*1101 in complex with immunodominant nonamer a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1q94
TitleStructures of HLA-A*1101 in complex with immunodominant nonamer and decamer HIV-1 epitopes clearly reveal the presence of a middle anchor residue
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-11 alpha chain
  • nonamer reverse transcriptase (AIFQSSMTK)
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / TAP complex binding / Golgi medial cisterna / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / antigen processing and presentation of exogenous peptide antigen via MHC class I / CD8 receptor binding ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / TAP complex binding / Golgi medial cisterna / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / antigen processing and presentation of exogenous peptide antigen via MHC class I / CD8 receptor binding / beta-2-microglobulin binding / protection from natural killer cell mediated cytotoxicity / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / detection of bacterium / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / retroviral ribonuclease H / exoribonuclease H / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / exoribonuclease H activity / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / transferrin transport / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / DNA integration / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / viral genome integration into host DNA / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / establishment of integrated proviral latency / RNA-directed DNA polymerase / multicellular organismal-level iron ion homeostasis / RNA stem-loop binding / specific granule lumen / peptide antigen binding / viral penetration into host nucleus / antigen processing and presentation of exogenous peptide antigen via MHC class II / host multivesicular body / positive regulation of type II interferon production / phagocytic vesicle membrane / positive regulation of immune response / RNA-directed DNA polymerase activity / recycling endosome membrane / RNA-DNA hybrid ribonuclease activity / Interferon gamma signaling / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / T cell receptor signaling pathway / host cell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / DNA recombination / amyloid fibril formation / DNA-directed DNA polymerase / protein homotetramerization / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / intracellular iron ion homeostasis
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Beta-2-Microglobulin / Integrase Zinc binding domain / : / Zinc finger integrase-type profile. / MHC class I-like antigen recognition-like / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / MHC class I-like antigen recognition-like superfamily / Integrase, N-terminal zinc-binding domain / Integrase-like, N-terminal / 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 / Matrix protein, lentiviral and alpha-retroviral, N-terminal / RNase H type-1 domain profile. / Ribonuclease H domain / MHC classes I/II-like antigen recognition protein / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / : / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / 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 / Immunoglobulins / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / Gag-Pol polyprotein / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus type 1 group M subtype D
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLi, L. / McNicholl, J.M. / Bouvier, M.
CitationJournal: J.Immunol. / Year: 2004
Title: Structures of HLA-A*1101 complexed with immunodominant nonamer and decamer HIV-1 epitopes clearly reveal the presence of a middle, secondary anchor residue.
Authors: Li, L. / Bouvier, M.
History
DepositionAug 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / pdbx_entity_src_syn ...entity / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct / struct_biol / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_fragment / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _struct.pdbx_descriptor / _struct_ref_seq_dif.details
Revision 1.5Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-11 alpha chain
B: Beta-2-microglobulin
C: nonamer reverse transcriptase (AIFQSSMTK)
D: HLA class I histocompatibility antigen, A-11 alpha chain
E: Beta-2-microglobulin
F: nonamer reverse transcriptase (AIFQSSMTK)


Theoretical massNumber of molelcules
Total (without water)89,4956
Polymers89,4956
Non-polymers00
Water2,738152
1
A: HLA class I histocompatibility antigen, A-11 alpha chain
B: Beta-2-microglobulin
C: nonamer reverse transcriptase (AIFQSSMTK)


Theoretical massNumber of molelcules
Total (without water)44,7483
Polymers44,7483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-13 kcal/mol
Surface area19040 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-11 alpha chain
E: Beta-2-microglobulin
F: nonamer reverse transcriptase (AIFQSSMTK)


Theoretical massNumber of molelcules
Total (without water)44,7483
Polymers44,7483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-20 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.400, 46.400, 124.300
Angle α, β, γ (deg.)91.50, 97.90, 114.80
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein HLA class I histocompatibility antigen, A-11 alpha chain


Mass: 31855.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: from 1 major histocompatibility complex / Gene: HLA-A OR HLAA / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYsS / References: UniProt: P13746, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / HDCMA22P


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: PHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P61769
#3: Protein/peptide nonamer reverse transcriptase (AIFQSSMTK)


Mass: 1013.188 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: PEPTIDE WAS OBTAINED THROUGH STANDARD SOLID-PHASE PEPTIDE SYNTHESIS
Source: (synth.) Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34) (HIV-1)
References: UniProt: P12499
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000,sodium acetate,sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 100K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F110.9474
SYNCHROTRONCHESS F120.9474
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 1, 2002
ADSC QUANTUM 42CCDJul 11, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9474 Å / Relative weight: 1
ReflectionResolution: 2.3→24 Å / Num. all: 40363 / Num. obs: 36125 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.124 / Net I/σ(I): 17.9
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 7.3 / % possible all: 40.7

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→23.7 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1639 -RANDOM
Rwork0.232 ---
all0.234 35525 --
obs0.234 33184 93.5 %-
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→23.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6304 0 0 152 6456
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.023
RfactorNum. reflection% reflection
Rfree0.383 273 -
Rwork0.331 --
obs-5082 85.9 %

+
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