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- PDB-6o9c: Crystal structure of HLA-A3*01 in complex with a mutant beta-cate... -

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Basic information

Entry
Database: PDB / ID: 6o9c
TitleCrystal structure of HLA-A3*01 in complex with a mutant beta-catenin peptide
Components
  • Beta-2-microglobulin
  • Catenin beta-1
  • HLA class I histocompatibility antigen, A-3 alpha chain
KeywordsIMMUNE SYSTEM / HLA-A3 / MHC Class I / beta catenin
Function / homology
Function and homology information


positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation / beta-catenin-ICAT complex / CDH11 homotypic and heterotypic interactions ...positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation / beta-catenin-ICAT complex / CDH11 homotypic and heterotypic interactions / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / neural plate development / metanephros morphogenesis / glial cell fate determination / Regulation of CDH19 Expression and Function / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / oviduct development / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / regulation of timing of anagen / negative regulation of mitotic cell cycle, embryonic / Binding of TCF/LEF:CTNNB1 to target gene promoters / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / central nervous system vasculogenesis / regulation of centriole-centriole cohesion / RUNX3 regulates WNT signaling / regulation of centromeric sister chromatid cohesion / Regulation of CDH11 function / embryonic axis specification / Specification of the neural plate border / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / lens morphogenesis in camera-type eye / beta-catenin-TCF complex / endodermal cell fate commitment / acinar cell differentiation / dorsal root ganglion development / synaptic vesicle clustering / positive regulation of fibroblast growth factor receptor signaling pathway / proximal/distal pattern formation / neuron fate determination / layer formation in cerebral cortex / Formation of the nephric duct / positive regulation of myoblast proliferation / establishment of blood-retinal barrier / dorsal/ventral axis specification / sympathetic ganglion development / fungiform papilla formation / positive regulation of endothelial cell differentiation / presynaptic active zone cytoplasmic component / mesenchymal to epithelial transition / embryonic foregut morphogenesis / hindbrain development / lung epithelial cell differentiation / positive regulation of determination of dorsal identity / positive regulation of skeletal muscle tissue development / ectoderm development / regulation of protein localization to cell surface / hair cell differentiation / cellular response to indole-3-methanol / detection of muscle stretch / mesenchymal stem cell differentiation / smooth muscle cell differentiation / positive regulation of odontoblast differentiation / endothelial tube morphogenesis / mesenchymal cell proliferation involved in lung development / midbrain dopaminergic neuron differentiation / positive regulation of homotypic cell-cell adhesion / histone methyltransferase binding / alpha-catenin binding / cranial skeletal system development / regulation of calcium ion import / Germ layer formation at gastrulation / establishment of blood-brain barrier / negative regulation of oligodendrocyte differentiation / fascia adherens / epithelial cell differentiation involved in prostate gland development / flotillin complex / apicolateral plasma membrane / regulation of epithelial to mesenchymal transition / positive regulation of epithelial cell proliferation involved in prostate gland development / male genitalia development / cell-cell adhesion mediated by cadherin / Formation of definitive endoderm / regulation of smooth muscle cell proliferation / epithelial cell proliferation involved in prostate gland development / embryonic brain development / catenin complex / beta-catenin destruction complex / lung-associated mesenchyme development / Formation of axial mesoderm / negative regulation of protein sumoylation / Apoptotic cleavage of cell adhesion proteins / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated
Similarity search - Function
Beta-catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / 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 ...Beta-catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / 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 / MHC classes I/II-like antigen recognition protein / : / Armadillo-like helical / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Armadillo-type fold / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / HLA class I histocompatibility antigen, A alpha chain / Catenin beta-1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsMiller, M.S. / Gabelli, S.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P50CA062924 United States
Department of Defense (DOD, United States)W81XWH-16-1-0486 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: An engineered antibody fragment targeting mutant beta-catenin via major histocompatibility complex I neoantigen presentation.
Authors: Miller, M.S. / Douglass, J. / Hwang, M.S. / Skora, A.D. / Murphy, M. / Papadopoulos, N. / Kinzler, K.W. / Vogelstein, B. / Zhou, S. / Gabelli, S.B.
History
DepositionMar 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.4Oct 11, 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 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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, A-3 alpha chain
B: Beta-2-microglobulin
C: Catenin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,80717
Polymers49,2443
Non-polymers1,56314
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-99 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.123, 155.123, 85.316
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, A-3 alpha chain / MHC class I antigen A*3


Mass: 34589.211 Da / Num. of mol.: 1 / Fragment: UNP residues 25-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04439
#2: Protein Beta-2-microglobulin


Mass: 13732.547 Da / Num. of mol.: 1
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, 1 molecules C

#3: Protein/peptide Catenin beta-1 / Beta-catenin


Mass: 922.056 Da / Num. of mol.: 1 / Fragment: UNP residues 41-49 / Mutation: S45F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNB1, CTNNB, OK/SW-cl.35, PRO2286 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35222

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Non-polymers , 4 types, 57 molecules

#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.01 Å3/Da / Density % sol: 59.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, pH 6.5, 0.2 M ammonium sulfate, 30% PEG5000 MME

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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: 0.918394 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 15, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918394 Å / Relative weight: 1
ReflectionResolution: 2.45→44.78 Å / Num. obs: 22620 / % possible obs: 99.9 % / Redundancy: 18.089 % / Biso Wilson estimate: 48.941 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.172 / Rrim(I) all: 0.177 / Χ2: 1.016 / Net I/σ(I): 13.89 / Num. measured all: 409173 / Scaling rejects: 21
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
2.45-2.5218.8391.3962.1430746163716320.7671.43499.7
2.52-2.5919.0581.2082.5230722161216120.8291.241100
2.59-2.6619.0360.9323.3129277153815380.8910.957100
2.66-2.7418.9330.8083.8228702151615160.920.83100
2.74-2.8318.8330.6764.5927515146214610.9420.69599.9
2.83-2.9318.7620.5126.0626736142514250.9590.527100
2.93-3.0418.6190.4017.6725750138313830.980.412100
3.04-3.1718.5560.3159.8224550132313230.9830.324100
3.17-3.3118.3790.23912.723323126912690.990.246100
3.31-3.4718.1140.20514.5122244122812280.9920.211100
3.47-3.6617.7790.15718.5520641116111610.9950.161100
3.66-3.8817.0830.12721.5819116111911190.9970.131100
3.88-4.1516.1510.11323.5916781103910390.9960.117100
4.15-4.4814.9950.09127.43147709879850.9980.09499.8
4.48-4.9116.0630.08130.35144419028990.9980.08499.7
4.91-5.4918.4060.08331.14153148328320.9980.086100
5.49-6.3418.5080.09328.54136227377360.9980.09699.9
6.34-7.7618.0140.07830.56116376496460.9980.08199.5
7.76-10.9817.4960.05540.388535095060.9990.05699.4
10.98-44.7814.30.0536.7644333243100.9990.05295.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.417
Highest resolutionLowest resolution
Rotation44.78 Å3.5 Å

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Processing

Software
NameVersionClassification
REFMACrefinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6O9B

6o9b


Resolution: 2.45→44.78 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 9.535 / SU ML: 0.21 / SU R Cruickshank DPI: 0.3377 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.338 / ESU R Free: 0.254
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1132 5 %RANDOM
Rwork0.2137 ---
obs0.216 21494 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 137.7 Å2 / Biso mean: 47.758 Å2 / Biso min: 22.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----1.74 Å2
Refinement stepCycle: final / Resolution: 2.45→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3161 0 88 43 3292
Biso mean--89.84 42.07 -
Num. residues----388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133343
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172897
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.6544537
X-RAY DIFFRACTIONr_angle_other_deg1.4811.5816731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4725389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.26621.401207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26115534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3281530
X-RAY DIFFRACTIONr_chiral_restr0.0760.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023717
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02761
LS refinement shellResolution: 2.454→2.517 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 80 -
Rwork0.321 1522 -
all-1602 -
obs--99.2 %

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