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- PDB-3jts: GY9-Mamu-A*02-hb2m -

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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 / : / : / 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 ...antigen processing and presentation of peptide antigen via MHC class I / : / : / 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 / 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 / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / 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 / DNA integration / 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 / 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 / host cell cytoplasm / DNA-directed DNA polymerase activity / learning or memory / immune response / symbiont-mediated suppression of host gene expression / Amyloid fiber formation / endoplasmic reticulum lumen / symbiont entry into host cell / viral translational frameshifting / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus
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 / Beta-2-Microglobulin ...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 / 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 / Immunoglobulins / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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