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- PDB-3vow: Crystal Structure of the Human APOBEC3C having HIV-1 Vif-binding ... -

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Basic information

Entry
Database: PDB / ID: 3vow
TitleCrystal Structure of the Human APOBEC3C having HIV-1 Vif-binding Interface
ComponentsProbable DNA dC->dU-editing enzyme APOBEC-3C
KeywordsHYDROLASE / APOBEC3C / APOBEC3 / antiviral deffense / host-virus interaction / metal-binding / HIV-1 Vif / Bet / single domain / SIVagm / Z2 / HIV
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 / clearance of foreign intracellular DNA / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / transposable element silencing ...mRNA Editing: C to U Conversion / Formation of the Editosome / cytidine deamination / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / clearance of foreign intracellular DNA / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / transposable element silencing / positive regulation of gene expression via chromosomal CpG island demethylation / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsKitamura, S. / Suzuki, A. / Watanabe, N. / Iwatani, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: The APOBEC3C crystal structure and the interface for HIV-1 Vif binding.
Authors: Kitamura, S. / Ode, H. / Nakashima, M. / Imahashi, M. / Naganawa, Y. / Kurosawa, T. / Yokomaku, Y. / Yamane, T. / Watanabe, N. / Suzuki, A. / Sugiura, W. / Iwatani, Y.
History
DepositionFeb 22, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Oct 24, 2012Group: Structure summary
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Nov 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETEMINATED

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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)45,8705
Polymers45,7042
Non-polymers1663
Water1,62190
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
Water181
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)22,9533
Polymers22,8521
Non-polymers1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.042, 105.042, 70.046
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.44 Å3/Da / Density % sol: 49.61 % / Mosaicity: 0.364 °
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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2012
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.15→105.05 Å / Num. all: 24043 / Num. obs: 24043 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.3 % / Rmerge(I) obs: 0.054 / Χ2: 1.834 / Net I/σ(I): 20.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.1922.60.33811881.2861100
2.19-2.2322.50.30711821.2961100
2.23-2.2722.60.26212021.3441100
2.27-2.3222.60.22211761.3291100
2.32-2.3722.60.21412001.3281100
2.37-2.4222.60.17412171.3421100
2.42-2.4822.60.15211741.3821100
2.48-2.5522.60.13311921.4121100
2.55-2.6222.60.11412071.4611100
2.62-2.7122.60.0912061.5271100
2.71-2.8122.60.08112181.5651100
2.81-2.9222.60.06912011.6581100
2.92-3.0522.50.05911901.7131100
3.05-3.2122.50.0511831.8831100
3.21-3.4122.40.04712272.0961100
3.41-3.6822.20.04711942.6731100
3.68-4.0521.80.04812103.2021100
4.05-4.6321.60.04312133.1031100
4.63-5.8420.90.03612252.5331100
5.84-105.0520.90.03712382.702198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3ir2


Resolution: 2.15→90.97 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2715 / WRfactor Rwork: 0.2184 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.791 / SU B: 6.15 / SU ML: 0.161 / SU R Cruickshank DPI: 0.2726 / SU Rfree: 0.2181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.273 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 1228 5.1 %RANDOM
Rwork0.2137 ---
all0.2162 24011 --
obs0.2162 24011 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.36 Å2 / Biso mean: 45.5565 Å2 / Biso min: 20.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20.29 Å20 Å2
2--0.59 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.15→90.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3158 0 3 90 3251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023296
X-RAY DIFFRACTIONr_angle_refined_deg1.391.9184483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6955382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08523.261184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.68515539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.51526
X-RAY DIFFRACTIONr_chiral_restr0.0990.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212618
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 83 -
Rwork0.262 1608 -
all-1691 -
obs-1608 99.3 %

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