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- PDB-2x5y: Human ZC3HAV1 (ARTD13), C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2x5y
TitleHuman ZC3HAV1 (ARTD13), C-terminal domain
ComponentsZINC FINGER CCCH-TYPE ANTIVIRAL PROTEIN 1
KeywordsIMMUNE SYSTEM / ANTIVIRAL DEFENSE / TRANSFERASE
Function / homology
Function and homology information


positive regulation of RIG-I signaling pathway / positive regulation of mRNA catabolic process / negative regulation of viral genome replication / positive regulation of interferon-alpha production / positive regulation of type I interferon production / positive regulation of interferon-beta production / response to virus / Signaling by BRAF and RAF1 fusions / late endosome / positive regulation of canonical NF-kappaB signal transduction ...positive regulation of RIG-I signaling pathway / positive regulation of mRNA catabolic process / negative regulation of viral genome replication / positive regulation of interferon-alpha production / positive regulation of type I interferon production / positive regulation of interferon-beta production / response to virus / Signaling by BRAF and RAF1 fusions / late endosome / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / lysosome / cadherin binding / innate immune response / RNA binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
ZAP, zinc finger / ZAP, helix turn helix N-terminal domain / Zap helix turn helix N-terminal domain / Zinc-finger antiviral protein (ZAP) zinc finger domain 3 / : / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Zinc finger, CCCH-type ...ZAP, zinc finger / ZAP, helix turn helix N-terminal domain / Zap helix turn helix N-terminal domain / Zinc-finger antiviral protein (ZAP) zinc finger domain 3 / : / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Zinc finger CCCH-type antiviral protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsKarlberg, T. / Schutz, P. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Karlberg, T. / Schutz, P. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kallas, A. / Kotenyova, T. / Kraulis, P. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Siponen, M.I. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wisniewska, M. / Schuler, H.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for Lack of Adp-Ribosyltransferase Activity in Poly(Adp-Ribose) Polymerase-13/Zinc Finger Antiviral Protein.
Authors: Karlberg, T. / Klepsch, M. / Thorsell, A. / Andersson, C.D. / Linusson, A. / Schuler, H.
History
DepositionFeb 11, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references / Structure summary
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ZINC FINGER CCCH-TYPE ANTIVIRAL PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)20,3091
Polymers20,3091
Non-polymers00
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.858, 54.103, 69.284
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 ZINC FINGER CCCH-TYPE ANTIVIRAL PROTEIN 1 / ZINC FINGER CCCH DOMAIN-CONTAINING PROTEIN 2 / ZINC FINGER ANTIVIRAL PROTEIN / ZAP


Mass: 20309.092 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN RESIDUES 724-896
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) R3 PRARE / References: UniProt: Q7Z2W4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHR851ILE EXISTS AS A NATUARL VARIANT.

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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: 2.23 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: 20 % PEG 3350, 0.2M NA-FLUORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 20, 2009 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.05→35 Å / Num. obs: 80468 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.7
Reflection shellResolution: 1.05→1.08 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.9 / % possible all: 70.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PQF

2pqf


Resolution: 1.05→31.84 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.557 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.14927 4027 5 %RANDOM
Rwork0.13026 ---
obs0.1312 76504 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.122 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.05→31.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1421 0 0 259 1680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221544
X-RAY DIFFRACTIONr_bond_other_d0.0040.021079
X-RAY DIFFRACTIONr_angle_refined_deg1.9341.9472103
X-RAY DIFFRACTIONr_angle_other_deg1.01632656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5945198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.74924.74478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72315289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.845154
X-RAY DIFFRACTIONr_chiral_restr0.1210.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021723
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02324
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_it2.021.5899
X-RAY DIFFRACTIONr_mcbond_other0.6471.5353
X-RAY DIFFRACTIONr_mcangle_it3.10221481
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9673645
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6764.5608
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.61932623
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 218 -
Rwork0.158 4135 -
obs--100 %

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