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- PDB-7uxd: Crystal structure of APOBEC3G Catalytic domain complex with ssDNA... -

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Basic information

Entry
Database: PDB / ID: 7uxd
TitleCrystal structure of APOBEC3G Catalytic domain complex with ssDNA containing 2'-deoxy Zebularine.
Components
  • DNA (5'-D(*AP*AP*TP*CP*CP*(DDN)P*AP*AP*A)-3')
  • DNA dC->dU-editing enzyme APOBEC-3G
KeywordsHYDROLASE/DNA / DNA CYTIDINE DEAMINASE / APOBEC / APOBEC- inhibitor COMPLEX / Zebularine / 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 / deoxycytidine deaminase activity / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate ...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 / deoxycytidine deaminase activity / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of viral process / retrotransposon silencing / DNA demethylation / negative regulation of viral genome replication / APOBEC3G mediated resistance to HIV-1 infection / positive regulation of defense response to virus by host / P-body / Vif-mediated degradation of APOBEC3G / defense response to virus / ribonucleoprotein complex / innate immune response / RNA binding / zinc ion binding / identical protein binding / nucleus / cytosol / 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 / DNA dC->dU-editing enzyme APOBEC-3G
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMaiti, A. / Matsuo, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)75N91019D00024 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI150478 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structure of the catalytically active APOBEC3G bound to a DNA oligonucleotide inhibitor reveals tetrahedral geometry of the transition state.
Authors: Maiti, A. / Hedger, A.K. / Myint, W. / Balachandran, V. / Watts, J.K. / Schiffer, C.A. / Matsuo, H.
History
DepositionMay 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
B: DNA (5'-D(*AP*AP*TP*CP*CP*(DDN)P*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8813
Polymers25,8162
Non-polymers651
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: MicroScale Thermophoresis (MST)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-10 kcal/mol
Surface area11140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.489, 47.121, 52.042
Angle α, β, γ (deg.)90.000, 103.180, 90.000
Int Tables number4
Space group name H-MP1211

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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: 23120.125 Da / Num. of mol.: 1
Mutation: P200A, L234K, N236A, C243A, P247K, F310K, Q318K, C321A, Q322A, C356A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3G, MDS019 / Variant: UNP Residues 191-384 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HC16, single-stranded DNA cytosine deaminase
#2: DNA chain DNA (5'-D(*AP*AP*TP*CP*CP*(DDN)P*AP*AP*A)-3')


Mass: 2695.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% PEG6000, 50 mM di-Sodium L-Malate; pH5.0, 30 mM CACL2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 33649 / % possible obs: 93.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.058 / Rrim(I) all: 0.104 / Χ2: 0.844 / Net I/σ(I): 7.7 / Num. measured all: 106388
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.553.20.46835660.7520.3060.5610.39598.9
1.55-1.623.40.35835170.8370.2270.4260.46399
1.62-1.693.40.27235500.8880.1740.3240.57398.6
1.69-1.783.30.20234600.9340.1320.2420.68497.4
1.78-1.893.10.15734730.9530.1060.190.86196
1.89-2.042.90.13132200.9590.090.161.2189.7
2.04-2.243.10.10831700.9710.0730.1311.1788.1
2.24-2.562.80.08830370.9740.0630.1091.23284.6
2.56-3.233.20.07635620.9740.0520.0921.03698.2
3.23-503.10.07930940.9670.0530.0951.16483.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BUX (Chain A)

6bux


Resolution: 1.5→34.506 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1944 1655 4.92 %
Rwork0.1725 31979 -
obs0.1736 33634 93.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.38 Å2 / Biso mean: 36.7548 Å2 / Biso min: 15.57 Å2
Refinement stepCycle: final / Resolution: 1.5→34.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 179 1 212 1911
Biso mean--27.57 44.23 -
Num. residues----199
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.54410.26261570.2308277798
1.5441-1.59390.24491390.2108283499
1.5939-1.65090.18721390.1958277799
1.6509-1.7170.21611510.1895280498
1.717-1.79510.1961590.1787274497
1.7951-1.88980.20131530.1757270796
1.8898-2.00810.20731400.1778247488
2.0081-2.16320.21091260.1784285999
2.1632-2.38080.1937970.1729204671
2.3808-2.72520.2191280.1806272395
2.7252-3.4330.21320.1759287199
3.433-34.50.16751340.1526236381
Refinement TLS params.Method: refined / Origin x: 10.3286 Å / Origin y: -4.9278 Å / Origin z: 13.0935 Å
111213212223313233
T0.1481 Å20.0127 Å20.0001 Å2-0.1759 Å2-0.0122 Å2--0.1605 Å2
L2.378 °2-0.3013 °20.4459 °2-2.4152 °20.0313 °2--2.8906 °2
S-0.0061 Å °0.0892 Å °-0.0582 Å °-0.0927 Å °0.0035 Å °0.2297 Å °-0.1381 Å °-0.3952 Å °0.0146 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA194 - 383
2X-RAY DIFFRACTION1allA390
3X-RAY DIFFRACTION1allB-5 - 3
4X-RAY DIFFRACTION1allS1 - 235

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