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- PDB-6w51: Structure of the antibody fragment H2 in complex with HLA-A*02:01... -

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Basic information

Entry
Database: PDB / ID: 6w51
TitleStructure of the antibody fragment H2 in complex with HLA-A*02:01/p53R175H
Components
  • (Immunoglobulin ...) x 2
  • Beta-2-microglobulin
  • Cellular tumor antigen p53 peptide
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Immunotherapy / MHC-I / HLA-A2 / p53
Function / homology
Function and homology information


negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity ...negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / Activation of NOXA and translocation to mitochondria / regulation of cell cycle G2/M phase transition / regulation of fibroblast apoptotic process / intrinsic apoptotic signaling pathway in response to hypoxia / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / mRNA transcription / positive regulation of programmed necrotic cell death / bone marrow development / circadian behavior / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / glucose catabolic process to lactate via pyruvate / TP53 Regulates Transcription of Death Receptors and Ligands / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / Activation of PUMA and translocation to mitochondria / regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase regulator activity / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / mitochondrial DNA repair / T cell lineage commitment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / thymocyte apoptotic process / B cell lineage commitment / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of mitophagy / cardiac septum morphogenesis / negative regulation of DNA replication / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TFIID-class transcription factor complex binding / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of reactive oxygen species metabolic process / rRNA transcription / Transcriptional Regulation by VENTX / replicative senescence / general transcription initiation factor binding / cellular response to UV-C / cellular response to actinomycin D / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of execution phase of apoptosis / positive regulation of RNA polymerase II transcription preinitiation complex assembly / neuroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / hematopoietic stem cell differentiation / Pyroptosis / viral process / embryonic organ development / chromosome organization / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / hematopoietic progenitor cell differentiation / glial cell proliferation / negative regulation of fibroblast proliferation / core promoter sequence-specific DNA binding / positive regulation of cardiac muscle cell apoptotic process / negative regulation of stem cell proliferation / cellular response to glucose starvation / mitophagy / cis-regulatory region sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / Regulation of TP53 Activity through Acetylation / gastrulation / response to salt stress / mitotic G1 DNA damage checkpoint signaling / 14-3-3 protein binding / negative regulation of proteolysis / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription repressor complex / cellular response to ionizing radiation
Similarity search - Function
Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family ...Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Cellular tumor antigen p53 / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.53 Å
AuthorsWright, K.M. / Gabelli, S.B.
CitationJournal: Science / Year: 2021
Title: Targeting a neoantigen derived from a common TP53 mutation.
Authors: Hsiue, E.H. / Wright, K.M. / Douglass, J. / Hwang, M.S. / Mog, B.J. / Pearlman, A.H. / Paul, S. / DiNapoli, S.R. / Konig, M.F. / Wang, Q. / Schaefer, A. / Miller, M.S. / Skora, A.D. / ...Authors: Hsiue, E.H. / Wright, K.M. / Douglass, J. / Hwang, M.S. / Mog, B.J. / Pearlman, A.H. / Paul, S. / DiNapoli, S.R. / Konig, M.F. / Wang, Q. / Schaefer, A. / Miller, M.S. / Skora, A.D. / Azurmendi, P.A. / Murphy, M.B. / Liu, Q. / Watson, E. / Li, Y. / Pardoll, D.M. / Bettegowda, C. / Papadopoulos, N. / Kinzler, K.W. / Vogelstein, B. / Gabelli, S.B. / Zhou, S.
History
DepositionMar 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 1.2Nov 20, 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

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Cellular tumor antigen p53 peptide
D: MHC class I antigen
E: Beta-2-microglobulin
F: Cellular tumor antigen p53 peptide
G: MHC class I antigen
H: Beta-2-microglobulin
I: Cellular tumor antigen p53 peptide
J: MHC class I antigen
K: Beta-2-microglobulin
L: Cellular tumor antigen p53 peptide
M: Immunoglobulin heavy chain H2
N: Immunoglobulin light chain H2
O: Immunoglobulin heavy chain H2
P: Immunoglobulin light chain H2
Q: Immunoglobulin heavy chain H2
R: Immunoglobulin light chain H2
S: Immunoglobulin heavy chain H2
T: Immunoglobulin light chain H2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)386,13321
Polymers386,03820
Non-polymers951
Water181
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: Cellular tumor antigen p53 peptide
M: Immunoglobulin heavy chain H2
N: Immunoglobulin light chain H2


Theoretical massNumber of molelcules
Total (without water)96,5095
Polymers96,5095
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: Cellular tumor antigen p53 peptide
O: Immunoglobulin heavy chain H2
P: Immunoglobulin light chain H2


Theoretical massNumber of molelcules
Total (without water)96,5095
Polymers96,5095
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: MHC class I antigen
H: Beta-2-microglobulin
I: Cellular tumor antigen p53 peptide

Q: Immunoglobulin heavy chain H2
R: Immunoglobulin light chain H2


Theoretical massNumber of molelcules
Total (without water)96,5095
Polymers96,5095
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
4
J: MHC class I antigen
K: Beta-2-microglobulin
L: Cellular tumor antigen p53 peptide
S: Immunoglobulin heavy chain H2
T: Immunoglobulin light chain H2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6046
Polymers96,5095
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.210, 123.690, 136.909
Angle α, β, γ (deg.)90.000, 100.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ADGJBEHK

#1: Protein
MHC class I antigen


Mass: 34183.738 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: U5YKE0
#2: Protein
Beta-2-microglobulin


Mass: 13732.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769

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Protein/peptide , 1 types, 4 molecules CFIL

#3: Protein/peptide
Cellular tumor antigen p53 peptide / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 1114.320 Da / Num. of mol.: 4 / Mutation: R175H / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04637

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Antibody , 2 types, 8 molecules MOQSNPRT

#4: Antibody
Immunoglobulin heavy chain H2


Mass: 23780.512 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#5: Antibody
Immunoglobulin light chain H2


Mass: 23698.314 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)

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Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.46 Å3/Da / Density % sol: 49.95 % / Mosaicity: 0.18 °
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.2 M Ammonium chloride, 20% w/v PEG 3350

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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: 0.97931 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 3.53→30.37 Å / Num. obs: 43734 / % possible obs: 95.3 % / Redundancy: 2.4 % / CC1/2: 0.938 / Rmerge(I) obs: 0.247 / Rpim(I) all: 0.186 / Rrim(I) all: 0.311 / Net I/σ(I): 3.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.53-3.662.30.76977442730.5410.5770.961.489.2
13.2-30.372.40.08218347590.9870.0610.1038.682.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O4Y, 6UJ9

6o4y

6uj9


Resolution: 3.53→30.37 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.823 / SU B: 43.916 / SU ML: 0.656 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.816 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2832 2193 5 %RANDOM
Rwork0.2003 ---
obs0.2044 41530 95.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 245.65 Å2 / Biso mean: 61.859 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.22 Å20 Å2-0.88 Å2
2--2.89 Å20 Å2
3---1.55 Å2
Refinement stepCycle: final / Resolution: 3.53→30.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25786 0 5 1 25792
Biso mean--160.5 0.5 -
Num. residues----3264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01326611
X-RAY DIFFRACTIONr_bond_other_d0.0020.01723362
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.64936187
X-RAY DIFFRACTIONr_angle_other_deg1.3821.57554362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.41753271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67721.9441404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.051154250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.05215166
X-RAY DIFFRACTIONr_chiral_restr0.0750.23390
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0230036
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025874
LS refinement shellResolution: 3.53→3.618 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.348 143 -
Rwork0.299 2749 -
obs--85.79 %

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