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- PDB-5ofb: Crystal structure of human MORC2 (residues 1-603) with spinal mus... -

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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 / cytosol / cytoplasm
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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: 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

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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: 2.4 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

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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

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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

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