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- PDB-5svi: MORC3 CW domain in complex with unmodified histone H3 -

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Basic information

Entry
Database: PDB / ID: 5svi
TitleMORC3 CW domain in complex with unmodified histone H3
Components
  • ALA-ARG-THR-LYS-GLN-THR-ALA-ARG
  • MORC family CW-type zinc finger protein 3
KeywordsTRANSCRIPTION / Histone reader / chromatin / posttranslational modifications / Zinc finger / CW domain
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 / Resolution: 1.613 Å
AuthorsTong, Q. / Andrews, F.H. / Kutateladze, T.G.
CitationJournal: Cell Rep / Year: 2016
Title: Multivalent Chromatin Engagement and Inter-domain Crosstalk Regulate MORC3 ATPase.
Authors: Andrews, F.H. / Tong, Q. / Sullivan, K.D. / Cornett, E.M. / Zhang, Y. / Ali, M. / Ahn, J. / Pandey, A. / Guo, A.H. / Strahl, B.D. / Costello, J.C. / Espinosa, J.M. / Rothbart, S.B. / Kutateladze, T.G.
History
DepositionAug 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 2.0Feb 19, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_entity_id / _atom_site.label_seq_id ..._atom_site.label_entity_id / _atom_site.label_seq_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_src_syn.entity_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_asym.entity_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 3
B: MORC family CW-type zinc finger protein 3
C: ALA-ARG-THR-LYS-GLN-THR-ALA-ARG
D: ALA-ARG-THR-LYS-GLN-THR-ALA-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3436
Polymers14,2124
Non-polymers1312
Water2,720151
1
A: MORC family CW-type zinc finger protein 3
C: ALA-ARG-THR-LYS-GLN-THR-ALA-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1713
Polymers7,1062
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-3 kcal/mol
Surface area3890 Å2
MethodPISA
2
B: MORC family CW-type zinc finger protein 3
D: ALA-ARG-THR-LYS-GLN-THR-ALA-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1713
Polymers7,1062
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-4 kcal/mol
Surface area4480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.500, 31.060, 36.090
Angle α, β, γ (deg.)107.81, 93.44, 90.21
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 6171.794 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MORC3, KIAA0136, NXP2, ZCWCC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14149
#2: Protein/peptide ALA-ARG-THR-LYS-GLN-THR-ALA-ARG


Mass: 934.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 R 300K / Detector: PIXEL / Date: Mar 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→34.29 Å / Num. obs: 12165 / % possible obs: 86 % / Redundancy: 2 % / Net I/σ(I): 9.2

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.613→34.29 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 2.19 / Phase error: 24.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2213 1212 9.96 %
Rwork0.1828 --
obs0.1865 12165 86.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.613→34.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms937 0 2 151 1090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007945
X-RAY DIFFRACTIONf_angle_d1.111280
X-RAY DIFFRACTIONf_dihedral_angle_d15.999366
X-RAY DIFFRACTIONf_chiral_restr0.081125
X-RAY DIFFRACTIONf_plane_restr0.006172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6127-1.67730.2756470.2521396X-RAY DIFFRACTION29
1.6773-1.75370.21731140.21161092X-RAY DIFFRACTION76
1.7537-1.84610.22671490.19461322X-RAY DIFFRACTION94
1.8461-1.96180.23491400.18511335X-RAY DIFFRACTION95
1.9618-2.11320.23891530.18161355X-RAY DIFFRACTION95
2.1132-2.32580.26011520.18891328X-RAY DIFFRACTION96
2.3258-2.66230.22981490.19961361X-RAY DIFFRACTION96
2.6623-3.35370.2051500.18291380X-RAY DIFFRACTION97
3.3537-34.29820.1971580.15971384X-RAY DIFFRACTION99

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