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- PDB-5of9: Crystal structure of human MORC2 (residues 1-603) -

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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


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
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

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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 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

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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


Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.38 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

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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

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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 )

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