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- PDB-6uj7: Crystal structure of HLA-B*07:02 with R140Q mutant IDH2 peptide -

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Basic information

Entry
Database: PDB / ID: 6uj7
TitleCrystal structure of HLA-B*07:02 with R140Q mutant IDH2 peptide
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, B-7 alpha chain
  • Isocitrate dehydrogenase [NADP], mitochondrial
KeywordsIMMUNE SYSTEM / HLA-B7 / MHC-I / immunotherapy / IDH2
Function / homology
Function and homology information


Citric acid cycle (TCA cycle) / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy ...Citric acid cycle (TCA cycle) / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / Mitochondrial protein degradation / detection of bacterium / tricarboxylic acid cycle / 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 / secretory granule membrane / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / Transcriptional activation of mitochondrial biogenesis / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / defense response / 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 / peroxisome / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / NAD binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / 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 / Interferon alpha/beta signaling / 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 / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / carbohydrate metabolic process / learning or memory / mitochondrial matrix / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 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 ...Isocitrate dehydrogenase NADP-dependent / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 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 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
: / HLA class I histocompatibility antigen, B alpha chain / Isocitrate dehydrogenase [NADP], mitochondrial / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsMiller, M.S. / Thirawatananond, P. / Gabelli, S.B.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)CDMRP BC151831 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA062924 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA006973 United States
CitationJournal: Nat Commun / Year: 2021
Title: Structural engineering of chimeric antigen receptors targeting HLA-restricted neoantigens.
Authors: Hwang, M.S. / Miller, M.S. / Thirawatananond, P. / Douglass, J. / Wright, K.M. / Hsiue, E.H. / Mog, B.J. / Aytenfisu, T.Y. / Murphy, M.B. / Aitana Azurmendi, P. / Skora, A.D. / Pearlman, A.H. ...Authors: Hwang, M.S. / Miller, M.S. / Thirawatananond, P. / Douglass, J. / Wright, K.M. / Hsiue, E.H. / Mog, B.J. / Aytenfisu, T.Y. / Murphy, M.B. / Aitana Azurmendi, P. / Skora, A.D. / Pearlman, A.H. / Paul, S. / DiNapoli, S.R. / Konig, M.F. / Bettegowda, C. / Pardoll, D.M. / Papadopoulos, N. / Kinzler, K.W. / Vogelstein, B. / Zhou, S. / Gabelli, S.B.
History
DepositionOct 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-7 alpha chain
B: Beta-2-microglobulin
C: Isocitrate dehydrogenase [NADP], mitochondrial
D: HLA class I histocompatibility antigen, B-7 alpha chain
E: Beta-2-microglobulin
F: Isocitrate dehydrogenase [NADP], mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,00011
Polymers98,7956
Non-polymers2045
Water8,935496
1
A: HLA class I histocompatibility antigen, B-7 alpha chain
B: Beta-2-microglobulin
C: Isocitrate dehydrogenase [NADP], mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4836
Polymers49,3983
Non-polymers853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-37 kcal/mol
Surface area19960 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, B-7 alpha chain
E: Beta-2-microglobulin
F: Isocitrate dehydrogenase [NADP], mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5175
Polymers49,3983
Non-polymers1192
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-25 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.038, 70.670, 87.482
Angle α, β, γ (deg.)90.000, 107.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein HLA class I histocompatibility antigen, B-7 alpha chain / MHC class I antigen B*7


Mass: 34609.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01889
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 13732.547 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide Isocitrate dehydrogenase [NADP], mitochondrial / IDH / ICD-M / IDP / NADP(+)-specific ICDH / Oxalosuccinate decarboxylase


Mass: 1056.171 Da / Num. of mol.: 2 / Mutation: R140Q / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P48735, isocitrate dehydrogenase (NADP+)

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Non-polymers , 4 types, 501 molecules

#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.01 Å3/Da / Density % sol: 38.71 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Hepes pH 7.5, 0.2 M NaCl, 25% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.999619 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999619 Å / Relative weight: 1
ReflectionResolution: 1.9→47.43 Å / Num. obs: 61233 / % possible obs: 99.2 % / Redundancy: 5.973 % / Biso Wilson estimate: 38.958 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.074 / Χ2: 1.038 / Net I/σ(I): 13.57 / Num. measured all: 365739 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.954.2770.6152.0217885453741820.7330.792.2
1.95-25.1130.4972.9222458440243920.8380.55499.8
2-2.065.9860.3864.125483427042570.9280.42499.7
2.06-2.126.390.3045.4127004423142260.9580.33299.9
2.12-2.196.4050.2586.2325890404740420.9690.28199.9
2.19-2.276.3880.2157.3625138394339350.9810.23499.8
2.27-2.366.3570.198.2423908376037610.9820.207100
2.36-2.456.3010.1599.823024366636540.9850.17499.7
2.45-2.566.1990.13311.4821723350635040.9890.14699.9
2.56-2.695.9830.11613.0119931334033310.990.12799.7
2.69-2.835.7140.09315.7218206319631860.9930.10399.7
2.83-36.1670.08219.0418501301030000.9950.08999.7
3-3.216.4610.06922.9218419285228510.9960.075100
3.21-3.476.3520.05926.8216706263926300.9970.06599.7
3.47-3.86.230.05229.6515126243124280.9980.05699.9
3.8-4.256.0960.04731.213514222422170.9980.05199.7
4.25-4.95.7380.04231.6211263196719630.9980.04699.8
4.9-6.015.3890.04530.088876165616470.9980.0599.5
6.01-8.496.3920.04433.178290130212970.9990.04799.6
8.49-47.436.0190.03835.1943947357300.9990.04199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.513
Highest resolutionLowest resolution
Rotation47.43 Å3.5 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VCL

3vcl


Resolution: 1.9→47.43 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2419 / WRfactor Rwork: 0.1846 / FOM work R set: 0.8114 / SU B: 4.327 / SU ML: 0.123 / SU R Cruickshank DPI: 0.1676 / SU Rfree: 0.1588 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 3062 5 %RANDOM
Rwork0.1819 ---
obs0.1846 58162 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.69 Å2 / Biso mean: 35.061 Å2 / Biso min: 17.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å2-1.04 Å2
2---0.47 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.9→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6397 0 9 496 6902
Biso mean--69.95 40.74 -
Num. residues----780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136584
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175707
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.668945
X-RAY DIFFRACTIONr_angle_other_deg1.341.58113262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2175776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.33521.462431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.267151068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1381564
X-RAY DIFFRACTIONr_chiral_restr0.0740.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027515
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021513
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 211 -
Rwork0.294 3999 -
all-4210 -
obs--93.31 %

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