[English] 日本語
Yorodumi
- PDB-6o9c: Crystal structure of HLA-A3*01 in complex with a mutant beta-cate... -

+
Open data


ID or keywords:

Loading...

-
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 / cranial ganglion development / CDH11 homotypic and heterotypic interactions / embryonic skeletal limb joint morphogenesis / Regulation of CDH19 Expression and Function / astrocyte-dopaminergic neuron signaling / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / regulation of timing of anagen / negative regulation of mitotic cell cycle, embryonic ...positive regulation of heparan sulfate proteoglycan biosynthetic process / cranial ganglion development / CDH11 homotypic and heterotypic interactions / embryonic skeletal limb joint morphogenesis / Regulation of CDH19 Expression and Function / astrocyte-dopaminergic neuron signaling / 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 / regulation of centriole-centriole cohesion / RUNX3 regulates WNT signaling / regulation of centromeric sister chromatid cohesion / Regulation of CDH11 function / Scrib-APC-beta-catenin complex / regulation of fibroblast proliferation / beta-catenin-TCF complex / Specification of the neural plate border / positive regulation of skeletal muscle tissue development / synaptic vesicle clustering / Formation of the nephric duct / dorsal root ganglion development / endothelial tube morphogenesis / hindbrain development / mesenchymal to epithelial transition / sympathetic ganglion development / cranial skeletal system development / presynaptic active zone cytoplasmic component / regulation of protein localization to cell surface / fascia adherens / mesenchymal stem cell differentiation / detection of muscle stretch / positive regulation of odontoblast differentiation / alpha-catenin binding / cellular response to indole-3-methanol / regulation of epithelial to mesenchymal transition / regulation of calcium ion import / histone methyltransferase binding / hair cell differentiation / apicolateral plasma membrane / Germ layer formation at gastrulation / positive regulation of homotypic cell-cell adhesion / cell-cell adhesion mediated by cadherin / flotillin complex / Formation of definitive endoderm / regulation of smooth muscle cell proliferation / beta-catenin destruction complex / Formation of axial mesoderm / negative regulation of protein sumoylation / Apoptotic cleavage of cell adhesion proteins / midbrain dopaminergic neuron differentiation / catenin complex / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / embryonic brain development / positive regulation of blood vessel branching / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / Regulation of CDH1 Function / I-SMAD binding / protein localization to cell surface / Wnt signalosome / Adherens junctions interactions / adherens junction assembly / Cardiogenesis / positive regulation of neuroblast proliferation / neuron projection extension / Disassembly of the destruction complex and recruitment of AXIN to the membrane / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / stem cell population maintenance / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / Myogenesis / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / hypothalamus development / TAP complex binding / Formation of paraxial mesoderm / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / regulation of synapse assembly / Somitogenesis / microvillus membrane / outflow tract morphogenesis / SMAD binding / CD8 receptor binding / canonical Wnt signaling pathway / Regulation of MITF-M-dependent genes involved in pigmentation / protection from natural killer cell mediated cytotoxicity / Transcriptional Regulation by VENTX / endoplasmic reticulum exit site / epithelial to mesenchymal transition / TAP binding
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more