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- PDB-3vm8: Crystal structure of the human APOBEC3C having HIV-1 Vif-binding ... -

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Basic information

Entry
Database: PDB / ID: 3vm8
TitleCrystal structure of the human APOBEC3C having HIV-1 Vif-binding interface
ComponentsProbable DNA dC->dU-editing enzyme APOBEC-3C
KeywordsHYDROLASE / APOBEC3C / SIVagm / metal-binding / single domain / Z2 / antiviral defense / host-virus interaction / HIV / HIV-1 Vif / Bet
Function / homology
Function and homology information


mRNA Editing: C to U Conversion / Formation of the Editosome / cytidine deamination / 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 ...mRNA Editing: C to U Conversion / Formation of the Editosome / cytidine deamination / 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 / : / retrotransposon silencing / negative regulation of viral genome replication / P-body / defense response to virus / innate immune response / RNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
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-3C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKitamura, S. / Suzuki, A. / Watanabe, N. / Iwatani, Y.
CitationJournal: To be Published
Title: Crystal structure of the human APOBEC3C having HIV-1 Vif-binding interface
Authors: Kitamura, S. / Ode, H. / Nakashima, M. / Imahashi, M. / Naganawa, Y. / Ibe, S. / Yokomaku, Y. / Watanabe, N. / Suzuki, A. / Sugiura, W. / Iwatani, Y.
History
DepositionDec 9, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _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: Probable DNA dC->dU-editing enzyme APOBEC-3C
B: Probable DNA dC->dU-editing enzyme APOBEC-3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8354
Polymers45,7042
Non-polymers1312
Water0
1
A: Probable DNA dC->dU-editing enzyme APOBEC-3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9172
Polymers22,8521
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable DNA dC->dU-editing enzyme APOBEC-3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9172
Polymers22,8521
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.419, 104.419, 74.502
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Probable DNA dC->dU-editing enzyme APOBEC-3C / APOBEC1-like / Phorbolin I


Mass: 22851.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3C, APOBEC1L, PBI / Plasmid: pET41a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS
References: UniProt: Q9NRW3, 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

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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: 2.57 Å3/Da / Density % sol: 52.05 % / Mosaicity: 0.92 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Bicine, PEG 6000, L-Arginine HCl, pH 9.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: May 27, 2011
RadiationMonochromator: Confocal Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→1000 Å / Num. all: 9105 / Num. obs: 9105 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Rmerge(I) obs: 0.108 / Χ2: 1.579 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.0510.90.5224581.6331100
3.05-3.1110.90.4644661.6371100
3.11-3.1710.90.3874751.5951100
3.17-3.23110.2954511.5551100
3.23-3.310.90.2744671.5961100
3.3-3.3810.90.2564791.6511100
3.38-3.468.90.2344512.6411100
3.46-3.5610.80.1974811.8441100
3.56-3.667.40.1853592.241179.6
3.66-3.787.20.1544162.138186.5
3.78-3.9160.1733892.438184.6
3.91-4.079.10.114251.627192
4.07-4.26110.0954701.4331100
4.26-4.48110.0754611.311100
4.48-4.7610.90.0684871.3491100
4.76-5.1311.10.0674651.3291100
5.13-5.65110.0754661.3011100
5.65-6.46110.0754801.3281100
6.46-8.1410.80.0644771.2281100
8.14-100010.10.054821.04196.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IR2

3ir2


Resolution: 3→90.43 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.833 / WRfactor Rfree: 0.2847 / WRfactor Rwork: 0.2166 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7549 / SU B: 23.717 / SU ML: 0.441 / SU Rfree: 0.5663 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.566 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3023 427 4.7 %RANDOM
Rwork0.228 ---
all0.2315 9042 --
obs0.2315 9042 96.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.26 Å2 / Biso mean: 58.0914 Å2 / Biso min: 30.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å2-0.52 Å20 Å2
2---1.04 Å20 Å2
3---1.56 Å2
Refinement stepCycle: LAST / Resolution: 3→90.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3174 0 2 0 3176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.023278
X-RAY DIFFRACTIONr_angle_refined_deg0.9921.9164448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5475372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63423.187182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.71715534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7611526
X-RAY DIFFRACTIONr_chiral_restr0.0740.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212594
LS refinement shellResolution: 2.998→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 34 -
Rwork0.275 611 -
all-645 -
obs-611 97.14 %

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