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- PDB-4yhp: Crystal structure of 309M3-B Fab in complex with H3K9me3 peptide -

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Basic information

Entry
Database: PDB / ID: 4yhp
TitleCrystal structure of 309M3-B Fab in complex with H3K9me3 peptide
Components
  • Fab Heavy Chain
  • Fab Light Chain
  • H3K9me3 peptide
KeywordsIMMUNE SYSTEM / Antibody / Fab / Head-to-head dimerization / H3K9me3
Function / homology
Function and homology information


Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) ...Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
Similarity search - Function
Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / 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: 2.53 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
Revision 1.5Sep 27, 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
P: H3K9me3 peptide
A: Fab Heavy Chain
B: Fab Light Chain
Q: H3K9me3 peptide
C: Fab Heavy Chain
D: Fab Light Chain
E: Fab Heavy Chain
H: Fab Heavy Chain
L: Fab Light Chain
F: Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)195,17110
Polymers195,17110
Non-polymers00
Water8,755486
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.773, 159.885, 128.759
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide H3K9me3 peptide


Mass: 1704.992 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P68431*PLUS
#2: Antibody
Fab Heavy Chain


Mass: 24670.701 Da / Num. of mol.: 4
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
#3: Antibody
Fab Light Chain


Mass: 23269.580 Da / Num. of mol.: 4
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 4.29 Å3/Da / Density % sol: 71.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 22% PEG 3350, 8% Tacsimate (pH8.0), 3% Xylitol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 112308 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R8S, 2DD8, 1MHP

2r8s

2dd8

1mhp


Resolution: 2.53→31.38 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 5473 5.01 %
Rwork0.211 --
obs0.213 109249 99.7 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.55 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.6895 Å20 Å20.6792 Å2
2--3.0965 Å20 Å2
3----1.407 Å2
Refinement stepCycle: LAST / Resolution: 2.53→31.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13287 0 0 486 13773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413620
X-RAY DIFFRACTIONf_angle_d0.86218542
X-RAY DIFFRACTIONf_dihedral_angle_d13.6184824
X-RAY DIFFRACTIONf_chiral_restr0.0572091
X-RAY DIFFRACTIONf_plane_restr0.0042381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.55880.38281750.31893353X-RAY DIFFRACTION98
2.5588-2.58880.39411920.31913425X-RAY DIFFRACTION99
2.5888-2.62040.38721720.32283420X-RAY DIFFRACTION100
2.6204-2.65350.39531890.32613489X-RAY DIFFRACTION100
2.6535-2.68840.40422080.30613414X-RAY DIFFRACTION100
2.6884-2.72530.38621720.30113469X-RAY DIFFRACTION100
2.7253-2.76420.3441740.28423476X-RAY DIFFRACTION100
2.7642-2.80540.36681890.28183430X-RAY DIFFRACTION100
2.8054-2.84920.311900.26953501X-RAY DIFFRACTION100
2.8492-2.89590.32451640.27083414X-RAY DIFFRACTION100
2.8959-2.94580.3281800.27043485X-RAY DIFFRACTION100
2.9458-2.99930.31791770.25933477X-RAY DIFFRACTION100
2.9993-3.0570.29451720.24563455X-RAY DIFFRACTION100
3.057-3.11930.29141770.22773476X-RAY DIFFRACTION100
3.1193-3.18710.29371900.23883469X-RAY DIFFRACTION100
3.1871-3.26110.30311690.23233475X-RAY DIFFRACTION100
3.2611-3.34260.27911670.23213498X-RAY DIFFRACTION100
3.3426-3.43290.26391630.22113446X-RAY DIFFRACTION100
3.4329-3.53370.24791880.22293482X-RAY DIFFRACTION100
3.5337-3.64760.25522020.21823444X-RAY DIFFRACTION100
3.6476-3.77780.24491940.20413449X-RAY DIFFRACTION100
3.7778-3.92880.23541980.19483459X-RAY DIFFRACTION100
3.9288-4.10720.21922030.18493446X-RAY DIFFRACTION100
4.1072-4.32320.17531970.163457X-RAY DIFFRACTION100
4.3232-4.59330.17321830.13853479X-RAY DIFFRACTION100
4.5933-4.94670.15371740.14233497X-RAY DIFFRACTION100
4.9467-5.44220.17981870.16723466X-RAY DIFFRACTION100
5.4422-6.22440.23131830.18533467X-RAY DIFFRACTION100
6.2244-7.82190.2321700.19743513X-RAY DIFFRACTION100
7.8219-31.37970.17511740.17313445X-RAY DIFFRACTION96

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