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- PDB-5svy: MORC3 CW in complex with histone H3K4me1 -

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Basic information

Entry
Database: PDB / ID: 5svy
TitleMORC3 CW in complex with histone H3K4me1
Components
  • H3K4me1
  • MORC family CW-type zinc finger protein 3
KeywordsTRANSCRIPTION / reader / histone / chromatin / methylation / methyllysine
Function / homology
Function and homology information


negative regulation of interferon-beta production / maintenance of protein location in nucleus / antiviral innate immune response / Chromatin modifying enzymes / epigenetic regulation of gene expression / negative regulation of fibroblast proliferation / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling ...negative regulation of interferon-beta production / maintenance of protein location in nucleus / antiviral innate immune response / Chromatin modifying enzymes / epigenetic regulation of gene expression / negative regulation of fibroblast proliferation / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / post-embryonic development / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PML body / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nuclear matrix / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / positive regulation of cellular senescence / nucleosome / protein-macromolecule adaptor activity / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / protein stabilization / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / protein phosphorylation / chromatin / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / RNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus
Similarity search - Function
MICRORCHIDIA ATPase family / Morc, S5 domain 2-like / Morc6 ribosomal protein S5 domain 2-like / Herpes Virus-1 - #100 / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / Herpes Virus-1 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histone H3 signature 1. ...MICRORCHIDIA ATPase family / Morc, S5 domain 2-like / Morc6 ribosomal protein S5 domain 2-like / Herpes Virus-1 - #100 / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / Herpes Virus-1 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histone H3 signature 1. / Histidine kinase/HSP90-like ATPase superfamily / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Histone H3.1 / MORC family CW-type zinc finger protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.05 Å
AuthorsTong, Q. / Andrews, F.H. / Kutateladze, T.G.
CitationJournal: Cell Rep / Year: 2016
Title: Multivalent Chromatin Engagement and Inter-domain Crosstalk Regulate MORC3 ATPase.
Authors: Andrews, F.H. / Tong, Q. / Sullivan, K.D. / Cornett, E.M. / Zhang, Y. / Ali, M. / Ahn, J. / Pandey, A. / Guo, A.H. / Strahl, B.D. / Costello, J.C. / Espinosa, J.M. / Rothbart, S.B. / Kutateladze, T.G.
History
DepositionAug 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MORC family CW-type zinc finger protein 3
B: H3K4me1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3654
Polymers7,2412
Non-polymers1242
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-1 kcal/mol
Surface area4450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.990, 70.660, 26.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

21A-625-

HOH

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Components

#1: Protein/peptide MORC family CW-type zinc finger protein 3 / Nuclear matrix protein 2 / Zinc finger CW-type coiled-coil domain protein 3


Mass: 5976.532 Da / Num. of mol.: 1 / Fragment: unp residues 407-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MORC3, KIAA0136, NXP2, ZCWCC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14149
#2: Protein/peptide H3K4me1 /


Mass: 1264.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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 Å3/Da / Density % sol: 38.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.5 M (NH4)2SO4, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Sep 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→35.33 Å / Num. obs: 60514 / % possible obs: 96.4 % / Redundancy: 1.9 % / Net I/σ(I): 23.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.05→35.33 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 11.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1465 1540 2.99 %
Rwork0.1228 --
obs0.1234 51495 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.05→35.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms503 0 5 108 616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011601
X-RAY DIFFRACTIONf_angle_d1.334828
X-RAY DIFFRACTIONf_dihedral_angle_d17.646254
X-RAY DIFFRACTIONf_chiral_restr0.08781
X-RAY DIFFRACTIONf_plane_restr0.008117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.08390.15871230.16213992X-RAY DIFFRACTION87
1.0839-1.12270.15421400.12954535X-RAY DIFFRACTION98
1.1227-1.16760.09861460.11414632X-RAY DIFFRACTION99
1.1676-1.22080.14591370.124559X-RAY DIFFRACTION99
1.2208-1.28510.12671400.11614595X-RAY DIFFRACTION99
1.2851-1.36560.14821420.11414602X-RAY DIFFRACTION100
1.3656-1.47110.13491410.11394634X-RAY DIFFRACTION100
1.4711-1.61910.11931440.10284600X-RAY DIFFRACTION100
1.6191-1.85340.10161410.10514603X-RAY DIFFRACTION100
1.8534-2.3350.14661390.11644604X-RAY DIFFRACTION100
2.335-35.350.18981470.14274599X-RAY DIFFRACTION99

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