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- PDB-6uj8: Crystal structure of HLA-B*07:02 with wild-type IDH2 peptide -

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Basic information

Entry
Database: PDB / ID: 6uj8
TitleCrystal structure of HLA-B*07:02 with wild-type IDH2 peptide
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-7 alpha chain
  • Isocitrate dehydrogenase [NADP], mitochondrial
KeywordsIMMUNE SYSTEM / HLA-B7 / immunotherapy / IDH2 / MHC-I
Function / homology
Function and homology information


Citric acid cycle (TCA cycle) / Maturation of TCA enzymes and regulation of 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 ...Citric acid cycle (TCA cycle) / Maturation of TCA enzymes and regulation of 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 / detection of bacterium / tricarboxylic acid cycle / Mitochondrial protein degradation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / secretory granule membrane / 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 / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / Transcriptional activation of mitochondrial biogenesis / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / defense response / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen 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 / positive regulation of immune response / Interferon gamma signaling / NAD binding / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / peroxisome / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / 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 / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / innate immune response / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses
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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 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: 2.25 Å
AuthorsMiller, M.S. / Thirawatananond, P. / Gabelli, S.B.
Funding support United States, 3items
OrganizationGrant numberCountry
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
Department of Defense (DOD, United States)CDMRP BC151831 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)100,36118
Polymers98,8546
Non-polymers1,50812
Water3,063170
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)50,43211
Polymers49,4273
Non-polymers1,0058
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-16 kcal/mol
Surface area18740 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)49,9297
Polymers49,4273
Non-polymers5034
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-24 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.690, 70.480, 88.146
Angle α, β, γ (deg.)90.000, 107.650, 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) / References: UniProt: P01889
#2: Protein 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) / 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: 1085.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P48735, isocitrate dehydrogenase (NADP+)

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Non-polymers , 6 types, 182 molecules

#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 0.2 M KI, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979321 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979321 Å / Relative weight: 1
ReflectionResolution: 2.25→47.58 Å / Num. obs: 37664 / % possible obs: 99.7 % / Redundancy: 5.078 % / Biso Wilson estimate: 46.168 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.107 / Χ2: 1.007 / Net I/σ(I): 10.44 / Num. measured all: 191270
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
2.25-2.314.660.6552.1312921278027730.7660.73599.7
2.31-2.375.240.5952.6314105269726920.7930.66299.8
2.37-2.445.2490.5023.1813788263726270.8410.55999.6
2.44-2.525.2210.4143.8513381256325630.9040.46100
2.52-2.65.2110.3534.4712939248524830.9230.39399.9
2.6-2.695.0950.2795.4112178239023900.9470.311100
2.69-2.794.9070.2286.6311272230522970.9590.25599.7
2.79-2.95.060.2027.6611207222322150.9690.22599.6
2.9-3.035.0240.1589.510766214421430.980.176100
3.03-3.185.3630.13511.4210973205120460.9860.1599.8
3.18-3.355.2980.11413.2210331195319500.990.12799.8
3.35-3.565.1770.09215.919531184818410.9920.10299.6
3.56-3.85.0320.07917.718691173217270.9930.08899.7
3.8-4.114.7330.06819.357620162116100.9930.07799.3
4.11-4.54.8860.05821.977353151515050.9950.06699.3
4.5-5.035.1890.05623.426876132413250.9960.063100
5.03-5.815.2140.05423.166298121712080.9950.0699.3
5.81-7.124.9940.05621.695054101310120.9950.06299.9
7.12-10.064.650.04224.0737438078050.9980.04799.8
10.06-47.584.9620.03825.7922434584520.9960.04398.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.517
Highest resolutionLowest resolution
Rotation47.59 Å3.5 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UJ7

6uj7


Resolution: 2.25→47.58 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.212 / SU ML: 0.2 / SU R Cruickshank DPI: 0.4141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.417 / ESU R Free: 0.256
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 1884 5 %RANDOM
Rwork0.2156 ---
obs0.2179 35786 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 121.94 Å2 / Biso mean: 42.004 Å2 / Biso min: 18.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0.49 Å2
2---0.56 Å20 Å2
3---0.56 Å2
Refinement stepCycle: final / Resolution: 2.25→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6354 0 96 170 6620
Biso mean--66.86 42.63 -
Num. residues----772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136616
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175789
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.6638953
X-RAY DIFFRACTIONr_angle_other_deg1.3241.58613445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9945766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.86121.296432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.965151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4841566
X-RAY DIFFRACTIONr_chiral_restr0.0710.2806
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027452
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021514
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 139 -
Rwork0.312 2624 -
all-2763 -
obs--99.78 %

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