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- PDB-4qq4: CW-type zinc finger of MORC3 in complex with the amino terminus o... -

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Basic information

Entry
Database: PDB / ID: 4qq4
TitleCW-type zinc finger of MORC3 in complex with the amino terminus of histone H3
Components
  • Histone H3.3
  • MORC family CW-type zinc finger protein 3
KeywordsMETAL BINDING PROTEIN / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / negative regulation of interferon-beta production / pericentric heterochromatin formation / inner kinetochore / maintenance of protein location in nucleus / muscle cell differentiation / oocyte maturation / nucleus organization ...negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / negative regulation of interferon-beta production / pericentric heterochromatin formation / inner kinetochore / maintenance of protein location in nucleus / muscle cell differentiation / oocyte maturation / nucleus organization / spermatid development / subtelomeric heterochromatin formation / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / negative regulation of fibroblast proliferation / antiviral innate immune response / nucleosomal DNA binding / Inhibition of DNA recombination at telomere / telomere organization / embryo implantation / methylated histone binding / RNA Polymerase I Promoter Opening / post-embryonic development / 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 / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / 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 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / multicellular organism growth / PML body / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear matrix / positive regulation of cellular senescence / Transcriptional regulation of granulopoiesis / osteoblast differentiation / male gonad development / structural constituent of chromatin / nucleosome / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / protein-macromolecule adaptor activity / Senescence-Associated Secretory Phenotype (SASP) / peptidyl-serine phosphorylation / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cell population proliferation / chromosome, telomeric region / protein stabilization / protein heterodimerization activity / protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / 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 / 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 / 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 H3.3 / MORC family CW-type zinc finger protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsLiu, Y. / Tempel, W. / Dong, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Family-wide Characterization of Histone Binding Abilities of Human CW Domain-containing Proteins.
Authors: Liu, Y. / Tempel, W. / Zhang, Q. / Liang, X. / Loppnau, P. / Qin, S. / Min, J.
History
DepositionJun 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Structure summary
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3May 18, 2016Group: Database references
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MORC family CW-type zinc finger protein 3
B: MORC family CW-type zinc finger protein 3
C: Histone H3.3
D: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,23516
Polymers17,9684
Non-polymers26712
Water1,60389
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-104 kcal/mol
Surface area7280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.622, 64.860, 36.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-2003-

UNX

21A-2118-

HOH

DetailsTHE BIOLOGICAL UNIT HAS NOT BEEN DETERMINED AS PART OF THIS STUDY

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 7378.121 Da / Num. of mol.: 2 / Fragment: unp residues 400-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0136, MORC3, ZCWCC3 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q14149
#2: Protein/peptide Histone H3.3


Mass: 1605.885 Da / Num. of mol.: 2 / Fragment: unp residues 2-16 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243

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Non-polymers , 4 types, 101 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.02 Å3/Da / Density % sol: 39.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG-3350, 0.2 M ammonium chloride, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791521 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791521 Å / Relative weight: 1
ReflectionResolution: 1.75→45.05 Å / Num. obs: 15427 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.75-1.787.10.9582.3592983899.9
9.09-45.054.90.04728.469214098.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.3.6data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4o62

4o62


Resolution: 1.75→45.05 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2115 / WRfactor Rwork: 0.169 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8363 / SU B: 2.519 / SU ML: 0.078 / SU R Cruickshank DPI: 0.1028 / SU Rfree: 0.1071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ARP/WARP was used for phase improvement and automated model building. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 928 6 %THIN SHELLS (SFTOOLS)
Rwork0.1804 ---
obs0.1828 15390 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.76 Å2 / Biso mean: 28.654 Å2 / Biso min: 8.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å2-0 Å20 Å2
2--1.95 Å2-0 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.75→45.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms920 0 12 89 1021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02971
X-RAY DIFFRACTIONr_bond_other_d0.0010.02885
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.9641323
X-RAY DIFFRACTIONr_angle_other_deg0.81432045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7955110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.81824.3453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99415155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9411510
X-RAY DIFFRACTIONr_chiral_restr0.0990.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211093
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02221
X-RAY DIFFRACTIONr_mcbond_it3.6692.799451
X-RAY DIFFRACTIONr_mcbond_other3.6652.803452
X-RAY DIFFRACTIONr_mcangle_it5.6674.153560
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 119 -
Rwork0.248 1013 -
all-1132 -
obs--99.91 %

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