[English] 日本語
Yorodumi
- PDB-3jts: GY9-Mamu-A*02-hb2m -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jts
TitleGY9-Mamu-A*02-hb2m
Components
  • Beta-2-microglobulin
  • MHC class I Mamu-A*02
  • peptide of Gag-Pol polyprotein
KeywordsIMMUNE SYSTEM / ALPHA HELIX / BETA SHEET / BETA BARREL / Immune response / MHC I / Membrane / Transmembrane / Disease mutation / Disulfide bond / Glycation / Glycoprotein / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / HIV-1 retropepsin / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / retroviral ribonuclease H / exoribonuclease H / negative regulation of iron ion transport ...antigen processing and presentation of peptide antigen via MHC class I / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / HIV-1 retropepsin / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / retroviral ribonuclease H / exoribonuclease H / negative regulation of iron ion transport / lumenal side of endoplasmic reticulum membrane / T cell mediated cytotoxicity / cellular response to iron(III) ion / 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 / transferrin transport / regulation of iron ion transport / regulation of erythrocyte differentiation / negative regulation of receptor-mediated endocytosis / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / cellular response to iron ion / 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 / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA stem-loop binding / specific granule lumen / viral penetration into host nucleus / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / phagocytic vesicle membrane / RNA-directed DNA polymerase activity / positive regulation of immune response / recycling endosome membrane / RNA-DNA hybrid ribonuclease activity / Interferon gamma signaling / positive regulation of T cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 / negative regulation of neuron projection development / host cell / 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 / DNA-directed DNA polymerase activity / host cell cytoplasm / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / symbiont-mediated suppression of host gene expression / external side of plasma membrane / viral translational frameshifting / lysosomal membrane / focal adhesion / Neutrophil degranulation / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / proteolysis / extracellular space
Similarity search - Function
gag protein p24 N-terminal 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 ...gag protein p24 N-terminal 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 / MHC class I-like antigen recognition-like superfamily / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / 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 / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / MHC classes I/II-like antigen recognition protein / : / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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
Gag-Pol polyprotein / Beta-2-microglobulin / MHC class I Mamu-A*02
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsDai, L. / Feng, Y. / Qi, J. / Gao, G.F.
CitationJournal: To be Published
Title: Structure of Mamu A*2
Authors: Dai, L.
History
DepositionSep 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC class I Mamu-A*02
B: Beta-2-microglobulin
C: peptide of Gag-Pol polyprotein
D: MHC class I Mamu-A*02
E: Beta-2-microglobulin
F: peptide of Gag-Pol polyprotein
G: MHC class I Mamu-A*02
H: Beta-2-microglobulin
I: peptide of Gag-Pol polyprotein


Theoretical massNumber of molelcules
Total (without water)140,5509
Polymers140,5509
Non-polymers00
Water3,117173
1
A: MHC class I Mamu-A*02
B: Beta-2-microglobulin
C: peptide of Gag-Pol polyprotein


Theoretical massNumber of molelcules
Total (without water)46,8503
Polymers46,8503
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-15 kcal/mol
Surface area19790 Å2
MethodPISA
2
D: MHC class I Mamu-A*02
E: Beta-2-microglobulin
F: peptide of Gag-Pol polyprotein


Theoretical massNumber of molelcules
Total (without water)46,8503
Polymers46,8503
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-14 kcal/mol
Surface area19410 Å2
MethodPISA
3
G: MHC class I Mamu-A*02
H: Beta-2-microglobulin
I: peptide of Gag-Pol polyprotein


Theoretical massNumber of molelcules
Total (without water)46,8503
Polymers46,8503
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-12 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.960, 110.331, 100.095
Angle α, β, γ (deg.)90.00, 114.32, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein MHC class I Mamu-A*02 / GY9-Mamu-A*02-hb2m


Mass: 32106.320 Da / Num. of mol.: 3 / Fragment: Rhesus MHC class I, UNP residues 17-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: Mamu / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q30597
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 13732.547 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein/peptide peptide of Gag-Pol polyprotein


Mass: 1011.108 Da / Num. of mol.: 3 / Fragment: peptite, UNP residues 71-79 / Source method: obtained synthetically
Details: This sequence occurs from Simian immunodeficiency virus
References: UniProt: P19505
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: (i) 0.1M Tris-HCl pH 5.5, 0.12M ammonium sulfate, 38% polyethene glycol monomethyl ether 20000; (ii) 0.1M MES pH 6.5, 0.32M ammonium sulfate, 38% polyethene glycol monomethyl ether 20 000, ...Details: (i) 0.1M Tris-HCl pH 5.5, 0.12M ammonium sulfate, 38% polyethene glycol monomethyl ether 20000; (ii) 0.1M MES pH 6.5, 0.32M ammonium sulfate, 38% polyethene glycol monomethyl ether 20 000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5478 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 10, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5478 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 30177 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.157 / Rsym value: 0.157 / Net I/σ(I): 17.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 4.2 / Num. unique all: 3055 / Rsym value: 0.589 / % possible all: 100

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1zvs

1zvs


Resolution: 2.801→38.695 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.82 / SU ML: 0.41 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 2 / Phase error: 25.38 / Stereochemistry target values: ML / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 1526 5.06 %RANDOM
Rwork0.1967 ---
all0.1994 30177 --
obs0.1994 30177 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.699 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 124.32 Å2 / Biso mean: 38.694 Å2 / Biso min: 12.34 Å2
Baniso -1Baniso -2Baniso -3
1--4.473 Å2-0 Å26.937 Å2
2--4.634 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.801→38.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9486 0 0 173 9659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059753
X-RAY DIFFRACTIONf_angle_d0.84813218
X-RAY DIFFRACTIONf_dihedral_angle_d19.4443567
X-RAY DIFFRACTIONf_chiral_restr0.0581323
X-RAY DIFFRACTIONf_plane_restr0.0041758
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8014-2.89180.32521160.2539256498
2.8918-2.99510.33421390.25472591100
2.9951-3.1150.34571420.24532592100
3.115-3.25670.29151430.23792593100
3.2567-3.42830.2591470.21292599100
3.4283-3.64290.29061330.20392617100
3.6429-3.92390.27851330.19132610100
3.9239-4.31840.21411230.15952626100
4.3184-4.94210.17971520.13522619100
4.9421-6.22240.16921470.15352605100
6.2224-38.6990.21931510.182263599

+
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