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- PDB-8tvc: Crystal structure of rA3G-ssDNA-AA -

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Basic information

Entry
Database: PDB / ID: 8tvc
TitleCrystal structure of rA3G-ssDNA-AA
Components
  • DNA 21-mer
  • DNA dC->dU-editing enzyme APOBEC-3G
KeywordsHYDROLASE/DNA / DEAMINASE / APOBEC / HYDROLASE / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / DNA cytosine deamination / cytidine deaminase activity / transposable element silencing / negative regulation of viral genome replication / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / zinc ion binding / nucleus
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
PHOSPHATE ION / DNA / DNA (> 10) / DNA dC->dU-editing enzyme APOBEC-3G
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsYang, H. / Pacheco, J.I. / Chen, X.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2024
Title: Molecular mechanism for regulating APOBEC3G DNA editing function by the non-catalytic domain.
Authors: Yang, H. / Pacheco, J. / Kim, K. / Bokani, A. / Ito, F. / Ebrahimi, D. / Chen, X.S.
History
DepositionAug 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA dC->dU-editing enzyme APOBEC-3G
B: DNA 21-mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7975
Polymers51,5712
Non-polymers2263
Water4,810267
1
A: DNA dC->dU-editing enzyme APOBEC-3G
hetero molecules

B: DNA 21-mer


Theoretical massNumber of molelcules
Total (without water)51,7975
Polymers51,5712
Non-polymers2263
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y+1/2,-z-1/21
Buried area970 Å2
ΔGint-94 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.429, 68.461, 126.735
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein DNA dC->dU-editing enzyme APOBEC-3G / Deoxycytidine deaminase


Mass: 45199.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: APOBEC3G / Production host: Escherichia coli (E. coli)
References: UniProt: M1GSK9, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: DNA chain DNA 21-mer


Mass: 6371.105 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.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 3350, 0.1 M Bis-Tris Propane pH 7.3, 0.2 M Sodium/Potassium Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.93→43.08 Å / Num. obs: 36833 / % possible obs: 99.28 % / Redundancy: 5.9 % / Biso Wilson estimate: 28.88 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.07828 / Rrim(I) all: 0.0858 / Net I/σ(I): 10.8
Reflection shellResolution: 1.93→1.999 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.5008 / Mean I/σ(I) obs: 0.88 / Num. unique obs: 3472 / CC1/2: 0.937 / CC star: 0.983 / Rrim(I) all: 0.5662 / % possible all: 94.69

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
JBluIce-EPICS201x.ydata collection
PHASERphasing
xia2data scaling
xia2data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→43.08 Å / SU ML: 0.2117 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.907
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2084 1792 4.87 %
Rwork0.1776 34997 -
obs0.1792 36789 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.06 Å2
Refinement stepCycle: LAST / Resolution: 1.93→43.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3111 85 7 267 3470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773314
X-RAY DIFFRACTIONf_angle_d0.86944515
X-RAY DIFFRACTIONf_chiral_restr0.0561454
X-RAY DIFFRACTIONf_plane_restr0.0083568
X-RAY DIFFRACTIONf_dihedral_angle_d10.4074452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.37081300.3532499X-RAY DIFFRACTION93.46
1.98-2.040.29621290.28952634X-RAY DIFFRACTION99
2.04-2.110.29521390.2562650X-RAY DIFFRACTION99.79
2.11-2.180.25281450.2142654X-RAY DIFFRACTION99.71
2.18-2.270.24311400.19412699X-RAY DIFFRACTION99.93
2.27-2.370.22971440.18292667X-RAY DIFFRACTION99.93
2.37-2.50.21351260.18472689X-RAY DIFFRACTION99.75
2.5-2.650.20161410.18282696X-RAY DIFFRACTION99.89
2.65-2.860.24251290.18282703X-RAY DIFFRACTION99.79
2.86-3.150.21781620.17812691X-RAY DIFFRACTION99.79
3.15-3.60.19341370.1612737X-RAY DIFFRACTION99.97
3.6-4.540.16411290.13452777X-RAY DIFFRACTION100
4.54-43.080.16951410.16212901X-RAY DIFFRACTION99.87
Refinement TLS params.Method: refined / Origin x: 8.79006919052 Å / Origin y: -16.0086671915 Å / Origin z: -30.253686282 Å
111213212223313233
T0.168973048487 Å2-0.000180006153148 Å20.00392507851428 Å2-0.169160914146 Å20.0136648587217 Å2--0.205099942961 Å2
L0.410923864957 °2-0.0665962150215 °20.0892995996888 °2-1.47664129379 °20.564020889833 °2--1.31814004859 °2
S-0.00183383917481 Å °-0.0112543356685 Å °0.0137079312434 Å °0.115998917053 Å °0.0197078140698 Å °-0.120449353931 Å °0.105673345263 Å °0.0500814840892 Å °-0.0117799264324 Å °
Refinement TLS groupSelection details: all

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