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- PDB-8edj: Crystal structure of rA3G-ssRNA-GA -

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Basic information

Entry
Database: PDB / ID: 8edj
TitleCrystal structure of rA3G-ssRNA-GA
Components
  • DNA dC->dU-editing enzyme APOBEC-3G
  • RNA (5'-R(P*UP*GP*AP*UP*UP*U)-3')
KeywordsHYDROLASE/RNA / Deaminase / APOBEC / HYDROLASE / HYDROLASE-RNA 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 / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / zinc ion binding / nucleus
Similarity search - Function
Novel AID APOBEC clade 2 / : / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / 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: 1.83 Å
AuthorsPacheco, J. / Yang, H.J. / Li, S.-X. / Chen, X.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI150524 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis of sequence-specific RNA recognition by the antiviral factor APOBEC3G.
Authors: Yang, H. / Kim, K. / Li, S. / Pacheco, J. / Chen, X.S.
History
DepositionSep 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Structure summary / Category: audit_author / chem_comp_atom / chem_comp_bond / Item: _audit_author.name
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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
R: RNA (5'-R(P*UP*GP*AP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4505
Polymers48,2232
Non-polymers2273
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-107 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.305, 68.058, 129.312
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 45144.473 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: RNA chain RNA (5'-R(P*UP*GP*AP*UP*UP*U)-3')


Mass: 3078.780 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.18 M Na2SO4, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 83087 / % possible obs: 99.94 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08526 / Net I/σ(I): 21.01
Reflection shellResolution: 1.83→50 Å / Num. unique obs: 4301 / CC1/2: 0.953

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7UU4

7uu4


Resolution: 1.83→42.027 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1921 2461 2.96 %
Rwork0.1681 80626 -
obs0.1689 83087 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.12 Å2 / Biso mean: 37.9933 Å2 / Biso min: 18 Å2
Refinement stepCycle: final / Resolution: 1.83→42.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 125 7 330 3566
Biso mean--27.56 44.67 -
Num. residues----379
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.83-1.86520.3141330.25644421
1.8652-1.90330.28481390.24014546
1.9033-1.94470.29891370.24474411
1.9447-1.98990.23431400.21164519
1.9899-2.03970.21231390.18654489
2.0397-2.09480.20091360.18814424
2.0948-2.15650.21561430.17724507
2.1565-2.22610.17351320.1714486
2.2261-2.30560.19731350.18184514
2.3056-2.39790.22461350.17734447
2.3979-2.5070.21611430.17814515
2.507-2.63920.23251330.18514442
2.6392-2.80450.18931320.17524479
2.8045-3.0210.20591400.18324504
3.021-3.32490.17541400.16034464
3.3249-3.80570.18771380.14974505
3.8057-4.79380.13411290.13084467
4.7938-42.0270.18411370.16084486
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.85030.10730.28461.84090.95322.60080.0060.067-0.0231-0.1896-0.03660.1439-0.059-0.11660.03020.18980.01-0.01890.21810.010.2328-9.221217.4064-50.4879
20.76260.231-0.63651.0781-0.88342.09710.0788-0.06960.05810.250.02610.0886-0.2781-0.0331-0.10180.2443-0.01460.00140.2174-0.01090.2543-9.040613.4698-19.4952
33.03980.4577-1.48234.55910.28192.60680.13570.30230.1963-0.1779-0.14710.3478-0.1767-0.1914-0.08510.25520.0332-0.01010.2803-0.04120.3093-7.93934.6261-40.5981
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 140 )A4 - 140
2X-RAY DIFFRACTION2chain 'A' and (resid 141 through 380 )A141 - 380
3X-RAY DIFFRACTION3chain 'R' and (resid 4 through 9 )R4 - 9

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