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- PDB-9kql: The crystal structure of MORC2_CC3 domain at 3.1 Angstroms resolution -

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Basic information

Entry
Database: PDB / ID: 9kql
TitleThe crystal structure of MORC2_CC3 domain at 3.1 Angstroms resolution
ComponentsATPase MORC2
KeywordsDNA BINDING PROTEIN / dimer / regulation
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsZhang, Y.S. / Xu, W.Y. / Huang, C.D. / Wang, C.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: The crystal structure of MORC2_CC3 domain at 3.1 Angstroms resolution
Authors: Zhang, Y.S. / Xu, W.Y. / Huang, C.D. / Wang, C.
History
DepositionNov 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATPase MORC2
B: ATPase MORC2


Theoretical massNumber of molelcules
Total (without water)24,7462
Polymers24,7462
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-53 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.253, 130.253, 40.895
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein ATPase MORC2 / MORC family CW-type zinc finger protein 2 / Zinc finger CW-type coiled-coil domain protein 1


Mass: 12372.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MORC2, KIAA0852, ZCWCC1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9Y6X9, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.52 Å3/Da / Density % sol: 65.04 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M Citric acid(pH 3.5) 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 6774 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.033 / Rrim(I) all: 0.117 / Χ2: 0.906 / Net I/σ(I): 8.7 / Num. measured all: 85583
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.05-3.110.51.2143330.7030.9090.3881.2750.952100
3.1-3.16121.1673470.7920.940.3471.2180.961100
3.16-3.2212.70.9393210.8840.9690.2720.9780.902100
3.22-3.2913.40.8043310.9170.9780.2270.8360.935100
3.29-3.3613.40.6623490.9420.9850.1870.6880.951100
3.36-3.4313.10.5393310.9540.9880.1550.5610.94100
3.43-3.52130.4273320.9690.9920.1220.4450.993100
3.52-3.6212.40.3473290.9750.9940.1020.3620.94100
3.62-3.7212.20.2473410.9740.9930.0740.2590.98100
3.72-3.8412.30.193290.9840.9960.0570.1990.986100
3.84-3.9813.20.1513350.9920.9980.0430.1570.963100
3.98-4.1413.40.123430.9960.9990.0340.1250.94499.4
4.14-4.3313.20.1093270.9960.9990.0310.1131.004100
4.33-4.5613.30.0863430.9960.9990.0240.0890.901100
4.56-4.8412.20.0763310.9970.9990.0220.0790.906100
4.84-5.2112.50.0663480.9970.9990.0190.0690.762100
5.21-5.7413.50.0713430.9970.9990.020.0740.738100
5.74-6.5713.10.063470.9970.9990.0170.0630.655100
6.57-8.2711.90.0473460.99910.0140.0490.635100
8.27-5011.60.0623680.9970.9990.0190.0651.09199.7

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→32.56 Å / SU ML: 0.33 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 349 5.43 %
Rwork0.1981 --
obs0.2008 6429 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→32.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 0 2 1669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041691
X-RAY DIFFRACTIONf_angle_d0.6272271
X-RAY DIFFRACTIONf_dihedral_angle_d3.776225
X-RAY DIFFRACTIONf_chiral_restr0.039255
X-RAY DIFFRACTIONf_plane_restr0.006293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.90.27261790.23832992X-RAY DIFFRACTION100
3.9-32.560.23271700.17613088X-RAY DIFFRACTION100

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