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- PDB-4row: The crystal structure of novel APOBEC3G CD2 head-to-tail dimer su... -

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Basic information

Entry
Database: PDB / ID: 4row
TitleThe crystal structure of novel APOBEC3G CD2 head-to-tail dimer suggests the binding mode of full-length APOBEC3G to HIV-1 ssDNA
ComponentsDNA dC->dU-editing enzyme APOBEC-3G
KeywordsHYDROLASE / Zinc Finger / DNA deamination / DNA Binding / deamination
Function / homology
Function and homology information


apolipoprotein B mRNA editing enzyme complex / dCTP deaminase activity / cytidine deamination / base conversion or substitution editing / single-stranded DNA cytosine deaminase / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / negative regulation of viral process ...apolipoprotein B mRNA editing enzyme complex / dCTP deaminase activity / cytidine deamination / base conversion or substitution editing / single-stranded DNA cytosine deaminase / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / negative regulation of viral process / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / retrotransposon silencing / negative regulation of viral genome replication / APOBEC3G mediated resistance to HIV-1 infection / positive regulation of defense response to virus by host / Vif-mediated degradation of APOBEC3G / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / RNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
APOBEC-like C-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-3G
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLu, X. / Zhang, T. / Xu, Z. / Liu, S. / Zhao, B. / Lan, W. / Wang, C. / Ding, J. / Cao, C.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal structure of DNA cytidine deaminase ABOBEC3G catalytic deamination domain suggests a binding mode of full-length enzyme to single-stranded DNA
Authors: Lu, X. / Zhang, T. / Xu, Z. / Liu, S. / Zhao, B. / Lan, W. / Wang, C. / Ding, J. / Cao, C.
History
DepositionOct 29, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: 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_asym_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_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,2512
Polymers23,1851
Non-polymers651
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.308, 70.007, 82.347
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-598-

HOH

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Components

#1: Protein DNA dC->dU-editing enzyme APOBEC-3G / APOBEC-related cytidine deaminase / APOBEC-related protein / ARCD / APOBEC-related protein 9 / ARP- ...APOBEC-related cytidine deaminase / APOBEC-related protein / ARCD / APOBEC-related protein 9 / ARP-9 / CEM-15 / CEM15 / Deoxycytidine deaminase / A3G


Mass: 23185.182 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, UNP residues 193-384 / Mutation: D370A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3G, MDS019 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HC16, 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.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.6
Details: 0.1M sodium citrate tribasic dehydrate pH 5.6, 20% v/v 2-propanol, 20% w/v polyethylene glycol 4000, VAPOR DIFFUSION, temperature 291.0K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 15, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 22865 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 29.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 5.8 / % possible all: 97.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→35.31 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.02 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18769 1168 5.1 %RANDOM
Rwork0.14727 ---
obs0.1494 21647 98.68 %-
all-20479 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.359 Å2
Baniso -1Baniso -2Baniso -3
1-2.9 Å20 Å20 Å2
2--1.73 Å20 Å2
3----4.63 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1573 0 1 190 1764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191642
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9122227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5045196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12123.06888
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53515267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8571513
X-RAY DIFFRACTIONr_chiral_restr0.0930.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211299
X-RAY DIFFRACTIONr_rigid_bond_restr2.77731641
X-RAY DIFFRACTIONr_sphericity_free19.665565
X-RAY DIFFRACTIONr_sphericity_bonded12.91151717
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 96 -
Rwork0.164 1522 -
obs--95.63 %
Refinement TLS params.Method: refined / Origin x: 36.4509 Å / Origin y: 83.9104 Å / Origin z: 15.5962 Å
111213212223313233
T0.0222 Å2-0.0014 Å20.0014 Å2-0.0174 Å2-0.0003 Å2--0.0005 Å2
L0 °20 °20 °2-0 °20 °2--0.0001 °2
S-0.0003 Å °-0 Å °-0.0001 Å °0.0002 Å °0.0004 Å °-0 Å °-0.0012 Å °0.0007 Å °-0.0001 Å °

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