[English] 日本語
Yorodumi
- PDB-5of9: Crystal structure of human MORC2 (residues 1-603) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5of9
TitleCrystal structure of human MORC2 (residues 1-603)
ComponentsMORC family CW-type zinc finger protein 2
KeywordsNUCLEAR PROTEIN / GHKL ATPase / chromatin remodeler / epigenetic silencing / transcriptional repressor / coiled-coil / CW domain / DNA binding protein / Charcot-Marie-Tooth disease / spinal muscular atrophy
Function / homology
Function and homology information


positive regulation of DNA methylation-dependent heterochromatin formation / Fatty acyl-CoA biosynthesis / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of gene expression, epigenetic / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / heterochromatin / fatty acid metabolic process / nuclear matrix / chromatin remodeling / DNA damage response ...positive regulation of DNA methylation-dependent heterochromatin formation / Fatty acyl-CoA biosynthesis / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of gene expression, epigenetic / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / heterochromatin / fatty acid metabolic process / nuclear matrix / chromatin remodeling / DNA damage response / chromatin binding / magnesium ion binding / ATP hydrolysis activity / protein homodimerization activity / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Morc, S5 domain 2-like / Morc6 ribosomal protein S5 domain 2-like / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ATPase MORC2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.807 Å
AuthorsDouse, C.H. / Shamin, M. / Modis, Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust101908/Z/13/Z United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/N011791/1 United Kingdom
Citation
Journal: Nat Commun / Year: 2018
Title: Neuropathic MORC2 mutations perturb GHKL ATPase dimerization dynamics and epigenetic silencing by multiple structural mechanisms.
Authors: Douse, C.H. / Bloor, S. / Liu, Y. / Shamin, M. / Tchasovnikarova, I.A. / Timms, R.T. / Lehner, P.J. / Modis, Y.
#1: Journal: Nat. Genet. / Year: 2017
Title: Hyperactivation of HUSH complex function by Charcot-Marie-Tooth disease mutation in MORC2.
Authors: Tchasovnikarova, I.A. / Timms, R.T. / Douse, C.H. / Roberts, R.C. / Dougan, G. / Kingston, R.E. / Modis, Y. / Lehner, P.J.
History
DepositionJul 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MORC family CW-type zinc finger protein 2
B: MORC family CW-type zinc finger protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,2308
Polymers140,0382
Non-polymers1,1926
Water12,989721
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering, Dimer detected by multi-angle light scattering (MALS) and size-exclusion chromatography, gel filtration, homology, Homology to MORC3 dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-44 kcal/mol
Surface area50390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.170, 127.930, 80.190
Angle α, β, γ (deg.)90.00, 101.22, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 70019.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Step tagged was removed by cleavage with PreScission protein to generate product starting with sequence GPRMAFT...
Source: (gene. exp.) Homo sapiens (human) / Gene: MORC2, KIAA0852, ZCWCC1
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
References: UniProt: Q9Y6X9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.38 Å3/Da / Density % sol: 48.33 % / Description: Pyramidal
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M bicine/Trizma pH 8.5 9% PEG 4000 18% glycerol 0.02 M each of the following: 1,6-hexanediol; 1-butanol; RS-1,2 propanediol; 2-propanol; 1,4-butanediol; 1,3-propanediol Based on Morpheus crystal screen

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.972636 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972636 Å / Relative weight: 1
ReflectionResolution: 1.807→78.658 Å / Num. obs: 118149 / % possible obs: 98.9 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.049 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.3 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
1.807-1.8380.9012.159480.6840.55598.3
4.905-78.6580.05328.859940.9960.03298.5

-
Processing

Software
NameVersionClassification
PHENIX(1.12rc2_2821: ???)refinement
XDS1.1.7data reduction
Aimless1.1.7data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IX2

5ix2


Resolution: 1.807→64.906 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.08
RfactorNum. reflection% reflection
Rfree0.188 5844 4.95 %
Rwork0.161 --
obs0.1624 118137 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.807→64.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8700 0 66 721 9487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128950
X-RAY DIFFRACTIONf_angle_d1.10812066
X-RAY DIFFRACTIONf_dihedral_angle_d17.8275475
X-RAY DIFFRACTIONf_chiral_restr0.0671292
X-RAY DIFFRACTIONf_plane_restr0.0071562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8069-1.82740.39841860.33773805X-RAY DIFFRACTION99
1.8274-1.84890.30651880.30353664X-RAY DIFFRACTION99
1.8489-1.87150.3141700.27233702X-RAY DIFFRACTION97
1.8715-1.89520.28791920.25893689X-RAY DIFFRACTION98
1.8952-1.92010.24911940.23833763X-RAY DIFFRACTION99
1.9201-1.94640.25351840.22183775X-RAY DIFFRACTION99
1.9464-1.97420.23871700.20263742X-RAY DIFFRACTION100
1.9742-2.00370.22271820.19853801X-RAY DIFFRACTION99
2.0037-2.0350.23311800.18763729X-RAY DIFFRACTION100
2.035-2.06840.19761990.17653789X-RAY DIFFRACTION100
2.0684-2.1040.2291800.17553713X-RAY DIFFRACTION99
2.104-2.14230.19921940.17043791X-RAY DIFFRACTION99
2.1423-2.18350.19732040.16563730X-RAY DIFFRACTION99
2.1835-2.22810.18172040.15753699X-RAY DIFFRACTION98
2.2281-2.27650.20342130.15743641X-RAY DIFFRACTION97
2.2765-2.32950.19571940.15383743X-RAY DIFFRACTION99
2.3295-2.38770.17791820.1533777X-RAY DIFFRACTION100
2.3877-2.45230.20161970.15113778X-RAY DIFFRACTION100
2.4523-2.52450.19422160.14613742X-RAY DIFFRACTION99
2.5245-2.6060.18482090.1493739X-RAY DIFFRACTION99
2.606-2.69910.18642060.15433746X-RAY DIFFRACTION99
2.6991-2.80720.19042020.15193733X-RAY DIFFRACTION99
2.8072-2.93490.2241700.15873719X-RAY DIFFRACTION97
2.9349-3.08970.20741850.16113757X-RAY DIFFRACTION99
3.0897-3.28320.17062000.15793798X-RAY DIFFRACTION100
3.2832-3.53670.20111860.15473754X-RAY DIFFRACTION99
3.5367-3.89260.16052150.14563786X-RAY DIFFRACTION99
3.8926-4.45570.15332080.12923641X-RAY DIFFRACTION97
4.4557-5.61330.15872180.13453777X-RAY DIFFRACTION100
5.6133-64.94760.17642160.17993770X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8584-0.05230.22681.0990.04011.3180.0114-0.14230.08560.0475-0.0039-0.0605-0.14610.0846-0.01160.1414-0.00620.00720.2161-0.02740.1811-6.0112-26.7053-7.69
21.63771.841-3.54671.7529-3.64987.4389-0.0839-0.211-0.21270.0219-0.1454-0.09420.20050.32990.22330.40190.12360.01760.5284-0.02820.515-44.4282-39.08050.9518
30.76690.02150.20171.5150.06881.49330.03790.07440.2733-0.3623-0.08880.1068-0.46560.00440.03490.3770.0619-0.01150.19750.02150.2903-19.7136-11.017-28.2978
41.28890.19430.11661.62270.41871.86620.015-0.1543-0.08170.0835-0.0281-0.1470.11990.10920.02970.1570.0182-0.00070.17440.02510.2092-10.6919-46.0333-13.4627
51.36780.3746-0.19690.651-0.36391.4057-0.0538-0.0122-0.2331-0.11960.009-0.09710.26930.00270.05190.22810.00760.00840.1473-0.00780.2281-17.584-56.3525-24.0248
67.1798-5.80915.52195.1846-3.81964.5281-0.4604-0.24210.10240.7950.1029-0.2746-0.5456-0.11270.20710.3343-0.0230.01560.37610.03630.296423.2559-55.7121-13.2671
71.6884-1.59981.79832.5618-0.54053.1992-0.01850.1267-0.0736-0.359-0.0513-0.06880.7264-0.1928-0.00910.2151-0.05020.01840.35280.07040.372222.3906-67.8782-9.0159
81.9380.3845-0.5521.0820.76533.7857-0.06350.44810.1322-0.28680.01720.061-0.2191-0.07420.05710.2560.00290.01370.28910.04360.2025-3.7522-38.0207-45.3037
92.10231.1151-0.73942.2584-1.39372.1133-0.33420.5978-0.6076-0.76350.1336-0.33510.7762-0.00630.18410.795-0.02370.19170.5992-0.17310.5308-5.0227-58.1807-52.3071
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 281 )
2X-RAY DIFFRACTION2chain 'A' and (resid 282 through 361 )
3X-RAY DIFFRACTION3chain 'A' and (resid 362 through 551 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 42 )
5X-RAY DIFFRACTION5chain 'B' and (resid 43 through 281 )
6X-RAY DIFFRACTION6chain 'B' and (resid 282 through 319 )
7X-RAY DIFFRACTION7chain 'B' and (resid 320 through 361 )
8X-RAY DIFFRACTION8chain 'B' and (resid 362 through 482 )
9X-RAY DIFFRACTION9chain 'B' and (resid 483 through 551 )

+
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