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- PDB-3u9g: Crystal structure of the Zinc finger antiviral protein -

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Basic information

Entry
Database: PDB / ID: 3u9g
TitleCrystal structure of the Zinc finger antiviral protein
ComponentsZinc finger CCCH-type antiviral protein 1
KeywordsANTIVIRAL PROTEIN / zinc finger protein
Function / homology
Function and homology information


: / positive regulation of RIG-I signaling pathway / positive regulation of mRNA catabolic process / regulation of defense response to virus by host / negative regulation of viral genome replication / cellular response to exogenous dsRNA / positive regulation of type I interferon production / positive regulation of interferon-alpha production / positive regulation of interferon-beta production / response to virus ...: / positive regulation of RIG-I signaling pathway / positive regulation of mRNA catabolic process / regulation of defense response to virus by host / negative regulation of viral genome replication / cellular response to exogenous dsRNA / positive regulation of type I interferon production / positive regulation of interferon-alpha production / positive regulation of interferon-beta production / response to virus / cellular response to virus / late endosome / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / lysosome / innate immune response / RNA binding / identical protein binding / nucleus / metal ion binding / 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 / Zinc finger C3H1-type profile. ...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. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Zinc finger CCCH-type antiviral protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å
AuthorsChen, S. / Xu, Y. / Zhang, K. / Wang, X. / Sun, J. / Gao, G. / Liu, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structure of N-terminal domain of ZAP indicates how a zinc-finger protein recognizes complex RNA.
Authors: Chen, S. / Xu, Y. / Zhang, K. / Wang, X. / Sun, J. / Gao, G. / Liu, Y.
History
DepositionOct 18, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2105
Polymers25,9481
Non-polymers2624
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Zinc finger CCCH-type antiviral protein 1
hetero molecules

A: Zinc finger CCCH-type antiviral protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,41910
Polymers51,8962
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1970 Å2
ΔGint-13 kcal/mol
Surface area24310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.894, 52.894, 138.275
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-363-

HOH

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Components

#1: Protein Zinc finger CCCH-type antiviral protein 1 / Zinc finger antiviral protein / ZAP / rZAP


Mass: 25948.029 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Zc3hav1, Zap / Production host: Escherichia coli (E. coli) / References: UniProt: Q8K3Y6
#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% (w/v) PEG 3350, 0.06M magnesium formate dehydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.25 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 21576 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 19.7 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 30.4 / Num. unique all: 1079 / Rsym value: 0.324 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.801→32.491 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 20.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 2063 5.15 %RANDOM
Rwork0.1911 ---
obs0.1929 21522 99.83 %-
all-21576 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.442 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.1012 Å20 Å2-0 Å2
2--3.1012 Å20 Å2
3----6.2023 Å2
Refinement stepCycle: LAST / Resolution: 1.801→32.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 4 200 1938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061763
X-RAY DIFFRACTIONf_angle_d0.9382374
X-RAY DIFFRACTIONf_dihedral_angle_d15.715676
X-RAY DIFFRACTIONf_chiral_restr0.062264
X-RAY DIFFRACTIONf_plane_restr0.004312
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8008-1.84270.29121480.21972539100
1.8427-1.88880.26351350.20612563100
1.8888-1.93980.2651450.20152462100
1.9398-1.99690.26451550.19632546100
1.9969-2.06130.2511660.18732487100
2.0613-2.1350.2271490.18692533100
2.135-2.22050.22611300.17782540100
2.2205-2.32150.25591310.1962531100
2.3215-2.44390.20121470.18522519100
2.4439-2.59690.25741170.20092569100
2.5969-2.79730.22711670.18832525100
2.7973-3.07860.21741280.18562518100
3.0786-3.52370.21811390.17752565100
3.5237-4.43760.19351010.1772553100
4.4376-32.49610.21491050.2002251598

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