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- PDB-6o51: Structure of HLA-A2:01 with peptide MM90 -

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Basic information

Entry
Database: PDB / ID: 6o51
TitleStructure of HLA-A2:01 with peptide MM90
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • MHC class I antigen
  • MM90
KeywordsIMMUNE SYSTEM / MHC class 1 molecule / antigen presentation / peptide interaction / PEPTIDE COMPLEX
Function / homology
Function and homology information


forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants ...forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / antigen processing and presentation / SHC1 events in ERBB4 signaling / Signalling to RAS / glial cell proliferation / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / homeostasis of number of cells within a tissue / positive regulation of glial cell proliferation / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / striated muscle cell differentiation / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / small monomeric GTPase / G protein activity / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / early endosome lumen / positive regulation of receptor binding / 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 / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / Constitutive Signaling by EGFRvIII / visual learning / MAP2K and MAPK activation / negative regulation of forebrain neuron differentiation / Signaling by ERBB2 ECD mutants / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / Signaling by ERBB2 KD Mutants / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / 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
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase ...Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Rab subfamily of small GTPases / 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 / Small GTP-binding protein domain / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / GTPase KRas / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Actinomyces radingae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsYing, G. / Bitra, A. / Zajonc, D.M.
CitationJournal: Front Immunol / Year: 2019
Title: Anin silico-in vitroPipeline Identifying an HLA-A*02:01+KRAS G12V+Spliced Epitope Candidate for a Broad Tumor-Immune Response in Cancer Patients.
Authors: Mishto, M. / Mansurkhodzhaev, A. / Ying, G. / Bitra, A. / Cordfunke, R.A. / Henze, S. / Paul, D. / Sidney, J. / Urlaub, H. / Neefjes, J. / Sette, A. / Zajonc, D.M. / Liepe, J.
History
DepositionMar 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: MM90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,11614
Polymers44,4483
Non-polymers66811
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-73 kcal/mol
Surface area18280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.260, 79.467, 57.251
Angle α, β, γ (deg.)90.000, 115.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 31725.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Details (production host): PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: U5YJM1, UniProt: A0A140T913*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Details (production host): PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide MM90


Mass: 975.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Actinomyces radingae (bacteria) / References: UniProt: P01116*PLUS

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Non-polymers , 3 types, 448 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4000, 0.1M TRIS-HCL PH 8.5, 0.2M LITHIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→40 Å / Num. obs: 63926 / % possible obs: 97 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.03 / Rrim(I) all: 0.056 / Χ2: 0.71 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.592.60.36838970.8370.2650.4570.48588.9
1.59-1.633.10.34242420.870.230.4140.47397.4
1.63-1.673.30.28242990.9170.1820.3370.4898.2
1.67-1.723.40.2443000.9370.1550.2870.49597.7
1.72-1.773.30.19242450.960.1240.2290.597.6
1.77-1.843.30.1542570.9730.0980.180.51896.9
1.84-1.913.10.11341540.9820.0760.1370.57594.8
1.91-23.50.0943290.990.0590.1080.64198.7
2-2.13.50.06942960.9930.0440.0830.66398.1
2.1-2.243.40.05742860.9950.0360.0680.71297.8
2.24-2.413.20.05142410.9950.0340.0620.79496.1
2.41-2.653.50.04343540.9970.0270.0510.7899.1
2.65-3.033.50.03743460.9970.0230.0440.88698.4
3.03-3.823.30.03242630.9980.020.0381.1196.4
3.82-403.40.03144170.9970.020.0371.35498.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ENW

5enw


Resolution: 1.55→31.47 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.71 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.088
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 3191 5 %RANDOM
Rwork0.1923 ---
obs0.1939 60501 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 59.97 Å2 / Biso mean: 18.159 Å2 / Biso min: 8.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.55→31.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3090 0 41 437 3568
Biso mean--43.68 33.07 -
Num. residues----383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133273
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172857
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.654453
X-RAY DIFFRACTIONr_angle_other_deg1.3371.586599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8135394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.36520.928194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46415502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4191528
X-RAY DIFFRACTIONr_chiral_restr0.0610.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02774
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 238 -
Rwork0.269 4115 -
all-4353 -
obs--89.57 %

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