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- PDB-5svx: MORC3 CW in complex with histone H3K4me3 -

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Basic information

Entry
Database: PDB / ID: 5svx
TitleMORC3 CW in complex with histone H3K4me3
Components
  • H3K4me3
  • 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 / Chromatin modifying enzymes / negative regulation of fibroblast proliferation / : / antiviral innate immune response / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication ...negative regulation of interferon-beta production / maintenance of protein location in nucleus / Chromatin modifying enzymes / negative regulation of fibroblast proliferation / : / antiviral innate immune response / 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 / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / post-embryonic development / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / PML body / 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 / nuclear matrix / Transcriptional regulation of granulopoiesis / HCMV Early Events / positive regulation of cellular senescence / structural constituent of chromatin / nucleosome / nucleosome assembly / peptidyl-serine phosphorylation / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / protein-macromolecule adaptor activity / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / protein stabilization / protein phosphorylation / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin / negative regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity / DNA binding / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane
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 / Histidine kinase/HSP90-like ATPase superfamily ...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 / Histidine kinase/HSP90-like ATPase superfamily / Histone H3 signature 1. / 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
Histone H3.1 / MORC family CW-type zinc finger protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.56 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
Revision 1.1Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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: H3K4me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2063
Polymers7,1412
Non-polymers651
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-3 kcal/mol
Surface area4210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.250, 68.550, 26.530
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
11B-108-

HOH

21B-109-

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: 5847.418 Da / Num. of mol.: 1 / Fragment: unp residues 407-454
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 H3K4me3


Mass: 1293.516 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
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: 1.98 Å3/Da / Density % sol: 37.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.5 M (NH4)SO4, 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: 1.28 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Sep 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.56→34.32 Å / Num. obs: 15728 / % possible obs: 100 % / Redundancy: 17.6 % / Net I/σ(I): 24.3
Reflection shellResolution: 1.56→1.6 Å / Redundancy: 15 % / Rmerge(I) obs: 0.18 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.56→34.275 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.84
RfactorNum. reflection% reflection
Rfree0.178 771 4.9 %
Rwork0.1429 --
obs0.1446 15728 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.56→34.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms497 0 0 103 600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004508
X-RAY DIFFRACTIONf_angle_d1.009690
X-RAY DIFFRACTIONf_dihedral_angle_d17.797197
X-RAY DIFFRACTIONf_chiral_restr0.03968
X-RAY DIFFRACTIONf_plane_restr0.00492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5581-1.65570.18371280.1362485X-RAY DIFFRACTION100
1.6557-1.78350.16561220.13452503X-RAY DIFFRACTION100
1.7835-1.9630.17371290.13072486X-RAY DIFFRACTION100
1.963-2.2470.15731340.1292498X-RAY DIFFRACTION100
2.247-2.83080.18491290.14622490X-RAY DIFFRACTION100
2.8308-34.28330.18861290.15812495X-RAY DIFFRACTION100

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