[English] 日本語
Yorodumi
- PDB-4qq4: CW-type zinc finger of MORC3 in complex with the amino terminus o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qq4
TitleCW-type zinc finger of MORC3 in complex with the amino terminus of histone H3
Components
  • Histone H3.3H3F3A
  • 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 interferon-beta production / maintenance of protein location in nucleus / nucleosomal DNA binding / antiviral innate immune response / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / negative regulation of fibroblast proliferation / methylated histone binding / Inhibition of DNA recombination at telomere / telomere organization ...negative regulation of interferon-beta production / maintenance of protein location in nucleus / nucleosomal DNA binding / antiviral innate immune response / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / negative regulation of fibroblast proliferation / methylated histone binding / Inhibition of DNA recombination at telomere / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / post-embryonic development / DNA methylation / Condensation of Prophase Chromosomes / 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 / 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 / PML body / Meiotic recombination / Pre-NOTCH Transcription and Translation / nuclear matrix / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / positive regulation of cellular senescence / nucleosome / protein-macromolecule adaptor activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / protein stabilization / RNA polymerase II cis-regulatory region sequence-specific DNA 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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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 / H3F3A


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

-
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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more