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- PDB-6o9b: Crystal structure of HLA-A3*01 in complex with a wild-type beta-c... -

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Basic information

Entry
Database: PDB / ID: 6o9b
TitleCrystal structure of HLA-A3*01 in complex with a wild-type beta-catenin peptide
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Catenin beta-1
  • HLA class I histocompatibility antigen, A-3 alpha chain
KeywordsIMMUNE SYSTEM / HLA-A3 / MHC Class I
Function / homology
Function and homology information


CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / 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 ...CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / 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 / mesenchymal stem cell differentiation / beta-catenin-ICAT complex / metanephros morphogenesis / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / neural plate development / glial cell fate determination / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / negative regulation of mitotic cell cycle, embryonic / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / oviduct development / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / regulation of timing of anagen / Binding of TCF/LEF:CTNNB1 to target gene promoters / central nervous system vasculogenesis / RUNX3 regulates WNT signaling / regulation of centriole-centriole cohesion / Regulation of CDH11 function / regulation of centromeric sister chromatid cohesion / embryonic axis specification / endodermal cell fate commitment / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / positive regulation of fibroblast growth factor receptor signaling pathway / beta-catenin-TCF complex / lens morphogenesis in camera-type eye / dorsal root ganglion development / synaptic vesicle clustering / acinar cell differentiation / dorsal/ventral axis specification / proximal/distal pattern formation / neuron fate determination / layer formation in cerebral cortex / positive regulation of myoblast proliferation / positive regulation of endothelial cell differentiation / sympathetic ganglion development / establishment of blood-retinal barrier / fungiform papilla formation / lung epithelial cell differentiation / embryonic foregut morphogenesis / hindbrain development / regulation of calcium ion import / positive regulation of determination of dorsal identity / positive regulation of skeletal muscle tissue development / ectoderm development / positive regulation of odontoblast differentiation / cranial skeletal system development / endothelial tube morphogenesis / regulation of protein localization to cell surface / hair cell differentiation / mesenchymal cell proliferation involved in lung development / detection of muscle stretch / smooth muscle cell differentiation / histone methyltransferase binding / midbrain dopaminergic neuron differentiation / presynaptic active zone cytoplasmic component / alpha-catenin binding / cellular response to indole-3-methanol / flotillin complex / Germ layer formation at gastrulation / establishment of blood-brain barrier / male genitalia development / negative regulation of oligodendrocyte differentiation / apicolateral plasma membrane / fascia adherens / epithelial cell proliferation involved in prostate gland development / embryonic brain development / Formation of definitive endoderm / epithelial cell differentiation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / regulation of smooth muscle cell proliferation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / oocyte development / beta-catenin destruction complex / lung-associated mesenchyme development / Formation of axial mesoderm / negative regulation of protein sumoylation / adherens junction assembly / embryonic heart tube development / 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 / Adherens junctions interactions / catenin complex
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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / 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: 2.2 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

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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)51,15521
Polymers49,1843
Non-polymers1,97118
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9850 Å2
ΔGint59 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.770, 152.770, 84.835
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 / 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: 861.960 Da / Num. of mol.: 1 / Fragment: UNP residues 41-49 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P35222

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Non-polymers , 6 types, 184 molecules

#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.91 Å3/Da / Density % sol: 57.66 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES/imidazole, pH 6.5, 0.03 M diethylene glycol, 0.03 M triethylene glycol, 0.03 M tetraethylene glycol, 0.03 M pentaethylene glycol, 20% PEG500 MME, 10% PEG20000

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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: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→28.87 Å / Num. obs: 29999 / % possible obs: 99.2 % / Redundancy: 10.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.052 / Rrim(I) all: 0.172 / Net I/σ(I): 9.7 / Num. measured all: 313372
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.269.81.08123450.7040.3481.13891.2
9.06-28.879.30.0525010.9980.0170.05596.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.349
Highest resolutionLowest resolution
Rotation28.87 Å3.5 Å

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
XDSdata reduction
Aimless0.5.21data scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2XPG

2xpg


Resolution: 2.2→28.87 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.781 / SU ML: 0.123 / SU R Cruickshank DPI: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.177
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 1452 4.8 %RANDOM
Rwork0.1824 ---
obs0.1846 28546 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 120.15 Å2 / Biso mean: 37.94 Å2 / Biso min: 19.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.13 Å20 Å2
2--0.27 Å20 Å2
3----0.87 Å2
Refinement stepCycle: final / Resolution: 2.2→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3159 0 138 166 3463
Biso mean--54.69 43.03 -
Num. residues----388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0133384
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173012
X-RAY DIFFRACTIONr_angle_refined_deg1.9321.664554
X-RAY DIFFRACTIONr_angle_other_deg1.5361.587000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1085389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.35221.346208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42315537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5031531
X-RAY DIFFRACTIONr_chiral_restr0.0940.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023743
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02766
LS refinement shellResolution: 2.197→2.254 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 106 -
Rwork0.231 1873 -
all-1979 -
obs--90.7 %

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