[English] 日本語
Yorodumi
- PDB-5ofb: Crystal structure of human MORC2 (residues 1-603) with spinal mus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ofb
TitleCrystal structure of human MORC2 (residues 1-603) with spinal muscular atrophy mutation S87L
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


constitutive heterochromatin formation / transposable element silencing by heterochromatin formation / Fatty acyl-CoA biosynthesis / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / heterochromatin / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / fatty acid metabolic process / nuclear matrix / chromatin remodeling / DNA damage response ...constitutive heterochromatin formation / transposable element silencing by heterochromatin formation / Fatty acyl-CoA biosynthesis / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / heterochromatin / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / fatty acid metabolic process / nuclear matrix / chromatin remodeling / DNA damage response / chromatin binding / magnesium ion binding / protein homodimerization activity / ATP hydrolysis activity / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / ATPase MORC2, chromo domain-like / 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
ADENOSINE-5'-TRIPHOSPHATE / ATPase MORC2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsDouse, C.H. / Liu, Y. / 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 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation_author / pdbx_related_exp_data_set
Item: _citation_author.identifier_ORCID / _pdbx_related_exp_data_set.data_reference
Revision 1.3May 1, 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
B: MORC family CW-type zinc finger protein 2
A: MORC family CW-type zinc finger protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,3089
Polymers140,0902
Non-polymers1,2187
Water5,477304
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering, gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-58 kcal/mol
Surface area50150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.850, 124.680, 80.360
Angle α, β, γ (deg.)90.00, 97.73, 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: 70045.078 Da / Num. of mol.: 2 / Mutation: S87L
Source method: isolated from a genetically manipulated source
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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.4 Å3/Da / Density % sol: 48 % / Description: Plates
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M bicine/Trizma pH 8.5 10.2% PEG 4k 20.4% 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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.975999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975999 Å / Relative weight: 1
ReflectionResolution: 2.018→79.629 Å / Num. obs: 82175 / % possible obs: 91.9 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.042 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) all% possible allMean I/σ(I) obs
2.018-2.0533.70.64843310.80.52996.7
5.478-79.6293.80.03145070.9980.02598.928.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Wild-type human MORC2

Resolution: 2.02→79.63 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 8.481 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22764 4183 5.1 %RANDOM
Rwork0.19789 ---
obs0.1994 77992 91.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.952 Å2
Baniso -1Baniso -2Baniso -3
1-2.48 Å20 Å21.07 Å2
2---1.7 Å20 Å2
3----1.03 Å2
Refinement stepCycle: 1 / Resolution: 2.02→79.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8713 0 67 304 9084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198953
X-RAY DIFFRACTIONr_bond_other_d0.0030.028358
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.97212069
X-RAY DIFFRACTIONr_angle_other_deg1.135319359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.36851068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53923.176444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.445151639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3191591
X-RAY DIFFRACTIONr_chiral_restr0.1270.21291
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219833
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021916
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7994.4374293
X-RAY DIFFRACTIONr_mcbond_other2.84.4364292
X-RAY DIFFRACTIONr_mcangle_it4.2766.6315354
X-RAY DIFFRACTIONr_mcangle_other4.2756.6325355
X-RAY DIFFRACTIONr_scbond_it3.4284.9424660
X-RAY DIFFRACTIONr_scbond_other3.4284.9424661
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4917.226716
X-RAY DIFFRACTIONr_long_range_B_refined10.127132753
X-RAY DIFFRACTIONr_long_range_B_other10.127132688
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.018→2.071 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 310 -
Rwork0.289 6088 -
obs--97.09 %
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)
10.12350.0081-0.01370.2002-0.01580.3673-0.01310.01150.0555-0.00550.0307-0.0319-0.0013-0.0166-0.01760.0032-0.0036-0.00310.0697-0.00940.0338-12.2804-13.0656-26.0624
20.2232-0.05370.04840.14450.03910.102-0.0071-0.0791-0.02780.0164-0.006-0.0350.0777-0.00960.01310.07740.0180.03170.06610.02350.0334-18.6904-41.4063-8.7669
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 591
2X-RAY DIFFRACTION2A1 - 591

+
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