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- PDB-4yhz: Crystal structure of 304M3-B Fab in complex with H3K4me3 peptide -

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Basic information

Entry
Database: PDB / ID: 4yhz
TitleCrystal structure of 304M3-B Fab in complex with H3K4me3 peptide
Components
  • Fab Heavy ChainFragment antigen-binding
  • Fab Light ChainFragment antigen-binding
  • H3K4me3 peptide
KeywordsIMMUNE SYSTEM / Antibody / Fab / Head-to-head dimerization / H3K4me3
Function / homology
Function and homology information


Chromatin modifying enzymes / regulation of gene expression, epigenetic / Interleukin-7 signaling / telomere organization / RNA Polymerase I Promoter Opening / DNA replication-dependent chromatin assembly / Assembly of the ORC complex at the origin of replication / DNA methylation / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression ...Chromatin modifying enzymes / regulation of gene expression, epigenetic / Interleukin-7 signaling / telomere organization / RNA Polymerase I Promoter Opening / DNA replication-dependent chromatin assembly / Assembly of the ORC complex at the origin of replication / DNA methylation / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Condensation of Prophase Chromosomes / chromatin organization => GO:0006325 / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / HDACs deacetylate histones / nuclear chromosome / NoRC negatively regulates rRNA expression / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RMTs methylate histone arginines / HDMs demethylate histones / nucleosome assembly / Meiotic recombination / Pre-NOTCH Transcription and Translation / PKMTs methylate histone lysines / HCMV Early Events / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / DNA binding / extracellular exosome / extracellular region / membrane / nucleoplasm / nucleus
Similarity search - Function
Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Core histone H2A/H2B/H3/H4 / Histone H2A/H2B/H3 / Histone-fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.304 Å
AuthorsHattori, T. / Dementieva, I.S. / Montano, S.P. / Koide, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R21 DA025725 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)RC1 DA028779 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation.
Authors: Hattori, T. / Lai, D. / Dementieva, I.S. / Montano, S.P. / Kurosawa, K. / Zheng, Y. / Akin, L.R. / Swist-Rosowska, K.M. / Grzybowski, A.T. / Koide, A. / Krajewski, K. / Strahl, B.D. / ...Authors: Hattori, T. / Lai, D. / Dementieva, I.S. / Montano, S.P. / Kurosawa, K. / Zheng, Y. / Akin, L.R. / Swist-Rosowska, K.M. / Grzybowski, A.T. / Koide, A. / Krajewski, K. / Strahl, B.D. / Kelleher, N.L. / Ruthenburg, A.J. / Koide, S.
History
DepositionFeb 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab Heavy Chain
L: Fab Light Chain
P: H3K4me3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,15011
Polymers49,4093
Non-polymers7418
Water3,135174
1
H: Fab Heavy Chain
L: Fab Light Chain
P: H3K4me3 peptide
hetero molecules

H: Fab Heavy Chain
L: Fab Light Chain
P: H3K4me3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,29922
Polymers98,8186
Non-polymers1,48116
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area15260 Å2
ΔGint-80 kcal/mol
Surface area37890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.375, 130.375, 96.365
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide H3K4me3 peptide


Mass: 1350.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P68431*PLUS

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Antibody , 2 types, 2 molecules HL

#1: Antibody Fab Heavy Chain / Fragment antigen-binding


Mass: 24788.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): ATCC 55244
#2: Antibody Fab Light Chain / Fragment antigen-binding


Mass: 23269.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): ATCC 55244

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Non-polymers , 3 types, 182 molecules

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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 4.78 Å3/Da / Density % sol: 74.29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% glycerol, 1.8 M ammonium sulfate, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 42048 / % possible obs: 100 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 20.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YHY
Resolution: 2.304→48.711 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2129 1954 4.65 %
Rwork0.183 --
obs0.1844 41978 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.304→48.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3351 0 47 174 3572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073484
X-RAY DIFFRACTIONf_angle_d1.0934732
X-RAY DIFFRACTIONf_dihedral_angle_d14.1911242
X-RAY DIFFRACTIONf_chiral_restr0.043527
X-RAY DIFFRACTIONf_plane_restr0.005604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3036-2.36120.30461110.25772763X-RAY DIFFRACTION96
2.3612-2.4250.29631610.2482804X-RAY DIFFRACTION100
2.425-2.49640.2661120.22852858X-RAY DIFFRACTION100
2.4964-2.5770.3271430.22822837X-RAY DIFFRACTION100
2.577-2.66910.24781350.22372834X-RAY DIFFRACTION100
2.6691-2.77590.25351300.21612854X-RAY DIFFRACTION100
2.7759-2.90220.25041530.21762836X-RAY DIFFRACTION100
2.9022-3.05520.26441380.21722861X-RAY DIFFRACTION100
3.0552-3.24660.2391240.21132850X-RAY DIFFRACTION100
3.2466-3.49720.21081420.19692851X-RAY DIFFRACTION100
3.4972-3.8490.19461400.17282891X-RAY DIFFRACTION100
3.849-4.40570.16741280.14582901X-RAY DIFFRACTION100
4.4057-5.54940.14871490.13862905X-RAY DIFFRACTION100
5.5494-48.72150.22071880.17242979X-RAY DIFFRACTION100

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