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- PDB-6o5w: Crystal structure of MORC3 CW domain fused with viral influenza A... -

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Basic information

Entry
Database: PDB / ID: 6o5w
TitleCrystal structure of MORC3 CW domain fused with viral influenza A NS1 peptide
ComponentsNS1-linked peptide,MORC family CW-type zinc finger protein 3
KeywordsTRANSCRIPTION / MORC3 / ATPase / NS1 / virus / histone / CW / chromatin
Function / homology
Function and homology information


negative regulation of interferon-beta production / maintenance of protein location in nucleus / antiviral innate immune response / negative regulation of fibroblast proliferation / methylated histone binding / post-embryonic development / PML body / nuclear matrix / positive regulation of cellular senescence / protein-macromolecule adaptor activity ...negative regulation of interferon-beta production / maintenance of protein location in nucleus / antiviral innate immune response / negative regulation of fibroblast proliferation / methylated histone binding / post-embryonic development / PML body / nuclear matrix / positive regulation of cellular senescence / protein-macromolecule adaptor activity / peptidyl-serine phosphorylation / protein stabilization / protein phosphorylation / chromatin / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
MICRORCHIDIA ATPase family / Morc, S5 domain 2-like / Morc6 ribosomal protein S5 domain 2-like / Herpes Virus-1 - #100 / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / Herpes Virus-1 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily ...MICRORCHIDIA ATPase family / Morc, S5 domain 2-like / Morc6 ribosomal protein S5 domain 2-like / Herpes Virus-1 - #100 / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / Herpes Virus-1 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MORC family CW-type zinc finger protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.412 Å
AuthorsAhn, J. / Zhang, Y. / Vann, K.R. / Kutateleadze, T.
CitationJournal: Structure / Year: 2019
Title: MORC3 Is a Target of the Influenza A Viral Protein NS1.
Authors: Zhang, Y. / Ahn, J. / Green, K.J. / Vann, K.R. / Black, J. / Brooke, C.B. / Kutateladze, T.G.
History
DepositionMar 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NS1-linked peptide,MORC family CW-type zinc finger protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8582
Polymers6,7921
Non-polymers651
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.912, 37.424, 50.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NS1-linked peptide,MORC family CW-type zinc finger protein 3 / Nuclear matrix protein 2 / Zinc finger CW-type coiled-coil domain protein 3


Mass: 6792.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NS1-linked peptide (225-230) Linker(403-406) MORC Family CW-Type Zinc Finger 3(407-455)
Source: (gene. exp.) Homo sapiens (human) / Gene: MORC3, KIAA0136, NXP2, ZCWCC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14149
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.14 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM HEPES pH 7.5 and 1.4M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.28 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.41→50 Å / Num. obs: 71940 / % possible obs: 99.2 % / Redundancy: 11 % / Rsym value: 0.08 / Net I/σ(I): 92.4
Reflection shellResolution: 1.41→1.43 Å / Num. unique obs: 554

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
SCALEPACKdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD
Starting model: 5SVX

5svx


Resolution: 1.412→26.338 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 14.04
RfactorNum. reflection% reflection
Rfree0.1687 2140 10 %
Rwork0.1528 --
obs0.1544 21392 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.412→26.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms456 0 1 135 592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005494
X-RAY DIFFRACTIONf_angle_d0.948673
X-RAY DIFFRACTIONf_dihedral_angle_d14.695194
X-RAY DIFFRACTIONf_chiral_restr0.09364
X-RAY DIFFRACTIONf_plane_restr0.00793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4119-1.44470.15161360.14751244X-RAY DIFFRACTION95
1.4447-1.48080.17691440.14821276X-RAY DIFFRACTION98
1.4808-1.52090.16261430.14361289X-RAY DIFFRACTION100
1.5209-1.56560.1531460.14611281X-RAY DIFFRACTION98
1.5656-1.61610.16961420.1351302X-RAY DIFFRACTION100
1.6161-1.67390.1571430.14031290X-RAY DIFFRACTION100
1.6739-1.74090.18931480.15881300X-RAY DIFFRACTION100
1.7409-1.82010.1711390.15351277X-RAY DIFFRACTION100
1.8201-1.91610.15951450.14431299X-RAY DIFFRACTION100
1.9161-2.03610.15931450.15541302X-RAY DIFFRACTION100
2.0361-2.19320.18251440.14431314X-RAY DIFFRACTION100
2.1932-2.41380.19191360.15281278X-RAY DIFFRACTION100
2.4138-2.76270.17411450.17451278X-RAY DIFFRACTION99
2.7627-3.47950.1881420.15751301X-RAY DIFFRACTION99
3.4795-26.34280.13891420.15251221X-RAY DIFFRACTION95

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