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- PDB-3wus: Crystal Structure of the Vif-Binding Domain of Human APOBEC3F -

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Basic information

Entry
Database: PDB / ID: 3wus
TitleCrystal Structure of the Vif-Binding Domain of Human APOBEC3F
ComponentsDNA dC->dU-editing enzyme APOBEC-3F
KeywordsHYDROLASE / APOBEC3F / A3F / Zinc binding / antiviral enzyme / CYTIDINE DEAMINASE / DNA binding / HIV-1 VIF / single-stranded polynucleotide
Function / homology
Function and homology information


apolipoprotein B mRNA editing enzyme complex / base conversion or substitution editing / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / : / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of viral process ...apolipoprotein B mRNA editing enzyme complex / base conversion or substitution editing / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / : / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of viral process / retrotransposon silencing / : / negative regulation of viral genome replication / positive regulation of defense response to virus by host / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / RNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
APOBEC-like N-terminal domain / Novel AID APOBEC clade 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like
Similarity search - Domain/homology
DNA dC->dU-editing enzyme APOBEC-3F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsNakashima, M. / Kawamura, T. / Ode, H. / Watanabe, N. / Iwatani, Y.
CitationJournal: J.Virol. / Year: 2015
Title: Structural Insights into HIV-1 Vif-APOBEC3F Interaction.
Authors: Nakashima, M. / Ode, H. / Kawamura, T. / Kitamura, S. / Naganawa, Y. / Awazu, H. / Tsuzuki, S. / Matsuoka, K. / Nemoto, M. / Hachiya, A. / Sugiura, W. / Yokomaku, Y. / Watanabe, N. / Iwatani, Y.
History
DepositionMay 2, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

Downloads & links

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Assembly

Deposited unit
A: DNA dC->dU-editing enzyme APOBEC-3F
B: DNA dC->dU-editing enzyme APOBEC-3F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8684
Polymers45,7382
Non-polymers1312
Water1267
1
A: DNA dC->dU-editing enzyme APOBEC-3F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9342
Polymers22,8691
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA dC->dU-editing enzyme APOBEC-3F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9342
Polymers22,8691
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.294, 117.294, 78.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein DNA dC->dU-editing enzyme APOBEC-3F / Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3F / A3F


Mass: 22868.834 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, UNP RESIDUES 187-373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3F / Plasmid: PET41A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3)PLYSS
References: UniProt: Q8IUX4, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.43 Å3/Da / Density % sol: 64.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 8.5% PEG 20000, 2% Dioxane, 300mM L-Arginine HCl, 85mM Na BICINE, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2012
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→101.58 Å / Num. obs: 20935 / % possible obs: 99.9 % / Redundancy: 10.9 % / Rsym value: 0.107 / Net I/σ(I): 36.1
Reflection shellResolution: 2.54→2.58 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
REFMAC5.8.0069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VOW

3vow


Resolution: 2.54→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.912 / SU B: 9.709 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25648 1069 5.1 %RANDOM
Rwork0.19979 ---
obs0.20266 19812 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.789 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20.69 Å20 Å2
2--1.39 Å2-0 Å2
3----4.5 Å2
Refinement stepCycle: LAST / Resolution: 2.54→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3130 0 2 7 3139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193248
X-RAY DIFFRACTIONr_bond_other_d0.0010.022832
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.9114416
X-RAY DIFFRACTIONr_angle_other_deg0.89536522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.535366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51523.556180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.56715506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9651516
X-RAY DIFFRACTIONr_chiral_restr0.1070.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02870
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_it4.5655.1751470
X-RAY DIFFRACTIONr_mcbond_other4.5625.1721469
X-RAY DIFFRACTIONr_mcangle_it7.0227.7521834
X-RAY DIFFRACTIONr_mcangle_other7.0237.7561835
X-RAY DIFFRACTIONr_scbond_it5.3015.7141778
X-RAY DIFFRACTIONr_scbond_other5.2935.7071775
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2118.372581
X-RAY DIFFRACTIONr_long_range_B_refined11.13542.5043793
X-RAY DIFFRACTIONr_long_range_B_other11.13442.5143793
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.544→2.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 57 -
Rwork0.315 1454 -
obs--98.37 %

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