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- PDB-5wer: Crystal Structure of TAPBPR and H2-Dd complex -

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Basic information

Entry
Database: PDB / ID: 5wer
TitleCrystal Structure of TAPBPR and H2-Dd complex
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-D alpha chain
  • TAP binding protein related
KeywordsIMMUNE SYSTEM / Antigen presentation / peptide editing / MAJOR HISTOMPATIBILITY COMPLEX CLASS I / MHC-I / TAPASIN / Peptide Loading Complex / PLC / IMMUNE RESPONSE
Function / homology
Function and homology information


negative regulation of antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein complex binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / 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 antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein complex binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / signaling receptor binding / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane / 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 / identical protein binding / membrane / plasma membrane / cytosol
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 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set 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 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / H-2 class I histocompatibility antigen, D-D alpha chain / Beta-2-microglobulin / Tapasin-related protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.412 Å
AuthorsJiang, J.S. / Natarajan, K. / Boyd, L.F. / Margulies, D.H.
CitationJournal: Science / Year: 2017
Title: Crystal structure of a TAPBPR-MHC I complex reveals the mechanism of peptide editing in antigen presentation.
Authors: Jiang, J. / Natarajan, K. / Boyd, L.F. / Morozov, G.I. / Mage, M.G. / Margulies, D.H.
History
DepositionJul 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 6, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.content_type
Revision 1.3Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.4Aug 28, 2019Group: Data collection / Database references / Category: pdbx_related_exp_data_set

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-D alpha chain
B: Beta-2-microglobulin
C: TAP binding protein related
D: H-2 class I histocompatibility antigen, D-D alpha chain
E: Beta-2-microglobulin
F: TAP binding protein related
G: H-2 class I histocompatibility antigen, D-D alpha chain
H: Beta-2-microglobulin
I: TAP binding protein related
J: H-2 class I histocompatibility antigen, D-D alpha chain
K: Beta-2-microglobulin
L: TAP binding protein related
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,59119
Polymers345,76012
Non-polymers8317
Water00
1
A: H-2 class I histocompatibility antigen, D-D alpha chain
B: Beta-2-microglobulin
C: TAP binding protein related
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5945
Polymers86,4403
Non-polymers1542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: H-2 class I histocompatibility antigen, D-D alpha chain
E: Beta-2-microglobulin
F: TAP binding protein related
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5945
Polymers86,4403
Non-polymers1542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: H-2 class I histocompatibility antigen, D-D alpha chain
H: Beta-2-microglobulin
I: TAP binding protein related


Theoretical massNumber of molelcules
Total (without water)86,4403
Polymers86,4403
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: H-2 class I histocompatibility antigen, D-D alpha chain
K: Beta-2-microglobulin
L: TAP binding protein related
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9636
Polymers86,4403
Non-polymers5223
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.050, 169.050, 139.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 3 types, 12 molecules ADGJBEHKCFIL

#1: Protein
H-2 class I histocompatibility antigen, D-D alpha chain / H-2D(D)


Mass: 32281.965 Da / Num. of mol.: 4 / Fragment: residues 26-301 / Mutation: S73C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: PET21-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01900
#2: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 4 / Fragment: residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein
TAP binding protein related


Mass: 42278.754 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMT_V5_HIS / Production host: Drosophila acanthoptera (fry) / Strain (production host): S2 / References: UniProt: Q9BX59*PLUS

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Non-polymers , 4 types, 7 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7

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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: 3.33 Å3/Da / Density % sol: 66.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 1.0 M ammonium sulfate, 0.1 M TRIS pH 8.8, 0.2 M NaCl, 0.15-0.20 M sodium citrate, 2%-5% PEG 400

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12771
22771
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID11.0333
SYNCHROTRONAPS 23-ID-B21.0333
Detector
TypeIDDetectorDate
RAYONIX MX300-HS1CCDMar 30, 2017
DECTRIS EIGER X 16M2PIXELMar 30, 2017
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI 100SINGLE WAVELENGTHMx-ray1
2SISINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.03331
21.03331
ReflectionResolution: 3.41→84.55 Å / Num. obs: 60245 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 83 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.425 / Rpim(I) all: 0.138 / Net I/av σ(I): 1.7 / Net I/σ(I): 8
Reflection shellResolution: 3.41→3.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.092 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5748 / CC1/2: 0.496 / Rpim(I) all: 0.61 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.412→48.801 Å / Cross valid method: THROUGHOUT / σ(F): 2.1 / Phase error: 27.4 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2694 2996 5.08 %RANDOM
Rwork0.2389 ---
obs0.2434 58963 97.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.412→48.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20100 0 55 0 20155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00420590
X-RAY DIFFRACTIONf_angle_d0.75228085
X-RAY DIFFRACTIONf_dihedral_angle_d16.09812208
X-RAY DIFFRACTIONf_chiral_restr0.0453176
X-RAY DIFFRACTIONf_plane_restr0.0063654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4123-3.47110.35581120.28992169X-RAY DIFFRACTION70
3.4711-3.53420.31171360.27982457X-RAY DIFFRACTION81
3.5342-3.60220.321430.26642789X-RAY DIFFRACTION93
3.6022-3.67570.29931410.27192760X-RAY DIFFRACTION91
3.6757-3.75560.32581500.27532823X-RAY DIFFRACTION93
3.7556-3.84290.31671520.2672873X-RAY DIFFRACTION94
3.8429-3.93890.31651470.26442791X-RAY DIFFRACTION94
3.9389-4.04540.26651500.25222861X-RAY DIFFRACTION95
4.0454-4.16430.26311520.24762891X-RAY DIFFRACTION95
4.1643-4.29870.27931520.23682878X-RAY DIFFRACTION94
4.2987-4.45220.24221510.22632865X-RAY DIFFRACTION95
4.4522-4.63030.24611510.21142862X-RAY DIFFRACTION95
4.6303-4.84080.21851500.20082856X-RAY DIFFRACTION95
4.8408-5.09570.22171520.21492876X-RAY DIFFRACTION95
5.0957-5.41450.24641500.22692859X-RAY DIFFRACTION95
5.4145-5.83190.28761530.24562907X-RAY DIFFRACTION95
5.8319-6.41740.28461510.26382871X-RAY DIFFRACTION95
6.4174-7.34290.28431530.2642889X-RAY DIFFRACTION95
7.3429-9.23930.24951500.21812863X-RAY DIFFRACTION95
9.2393-46.47430.26651520.24332872X-RAY DIFFRACTION95

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