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- PDB-6bux: CRYSTAL STRUCTURE OF APOBEC3G CATALYTIC DOMAIN COMPLEX WITH SUBST... -

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Basic information

Entry
Database: PDB / ID: 6bux
TitleCRYSTAL STRUCTURE OF APOBEC3G CATALYTIC DOMAIN COMPLEX WITH SUBSTRATE SSDNA
Components
  • Apolipoprotein B mRNA editing enzyme catalytic subunit 3G catalytic domain
  • DNA (5'-D(*AP*AP*TP*CP*CP*CP*AP*AP*A)-3')
KeywordsHYDROLASE/DNA / HYDROLASE / ANTIVIRAL DEFENCE / DNA CYTIDINE DEAMINASE / HYDROLASE-DNA complex
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 / DNA dC->dU-editing enzyme APOBEC-3G
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.856 Å
AuthorsMaiti, A. / Matsuo, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM118474 United States
CitationJournal: Nat Commun / Year: 2018
Title: Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA.
Authors: Maiti, A. / Myint, W. / Kanai, T. / Delviks-Frankenberry, K. / Sierra Rodriguez, C. / Pathak, V.K. / Schiffer, C.A. / Matsuo, H.
History
DepositionDec 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apolipoprotein B mRNA editing enzyme catalytic subunit 3G catalytic domain
B: DNA (5'-D(*AP*AP*TP*CP*CP*CP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9124
Polymers25,7552
Non-polymers1582
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-47 kcal/mol
Surface area11160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.413, 47.237, 51.462
Angle α, β, γ (deg.)90.00, 103.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Apolipoprotein B mRNA editing enzyme catalytic subunit 3G catalytic domain


Mass: 23062.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HC16*PLUS
#2: DNA chain DNA (5'-D(*AP*AP*TP*CP*CP*CP*AP*AP*A)-3')


Mass: 2692.815 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% PEG6000, 50 mM di-Sodium L-Malate; pH5.0, 30 mM CaCl2, Vapor Diffusion, Sitting Drop, Temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.856→50 Å / Num. obs: 18860 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.989 / Rsym value: 0.083 / Net I/σ(I): 24.16
Reflection shellResolution: 1.856→1.93 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 6.3 / Num. unique obs: 1861 / CC1/2: 0.957 / Rsym value: 0.328 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IR2 (Chain A)

3ir2


Resolution: 1.856→38.608 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.88
RfactorNum. reflection% reflection
Rfree0.2111 958 5.08 %
Rwork0.1789 --
obs0.1805 18843 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.9 Å2
Refinement stepCycle: LAST / Resolution: 1.856→38.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1547 179 7 154 1887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061805
X-RAY DIFFRACTIONf_angle_d0.7622476
X-RAY DIFFRACTIONf_dihedral_angle_d12.8251391
X-RAY DIFFRACTIONf_chiral_restr0.05255
X-RAY DIFFRACTIONf_plane_restr0.006291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8564-1.95430.23231340.19182471X-RAY DIFFRACTION98
1.9543-2.07670.22591540.18912529X-RAY DIFFRACTION100
2.0767-2.2370.24931530.18742537X-RAY DIFFRACTION100
2.237-2.46210.25481180.19562578X-RAY DIFFRACTION100
2.4621-2.81830.23221250.20492555X-RAY DIFFRACTION100
2.8183-3.55040.22921370.18342575X-RAY DIFFRACTION100
3.5504-38.61630.17141370.15892640X-RAY DIFFRACTION100

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