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- PDB-7uu4: Crystal structure of APOBEC3G complex with ssRNA -

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Basic information

Entry
Database: PDB / ID: 7uu4
TitleCrystal structure of APOBEC3G complex with ssRNA
Components
  • DNA dC->dU-editing enzyme APOBEC-3G
  • RNA (5'-R(P*UP*AP*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 to uridine editing / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / retrotransposon silencing / P-body / defense response to virus ...Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / retrotransposon silencing / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / RNA binding / 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
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: 2.1 Å
AuthorsYang, H. / Li, S. / 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
DepositionApr 28, 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*AP*AP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4345
Polymers48,2072
Non-polymers2273
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-105 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.225, 67.976, 126.768
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*AP*AP*UP*UP*U)-3')


Mass: 3062.780 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.: 231 / 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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.22 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-B / Wavelength: 1.03318 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 51798 / % possible obs: 97.92 % / Redundancy: 12.9 % / CC1/2: 0.998 / Net I/σ(I): 14.9
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 2400 / CC1/2: 0.922

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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: 6P3X

6p3x


Resolution: 2.1→46.358 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2041 2847 5.5 %
Rwork0.1842 48950 -
obs0.1853 51797 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.24 Å2 / Biso mean: 45.215 Å2 / Biso min: 22.2 Å2
Refinement stepCycle: final / Resolution: 2.1→46.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 124 7 231 3466
Biso mean--40.48 45.01 -
Num. residues----379
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.13620.30461190.2642203982
2.1362-2.17510.3041370.2611230391
2.1751-2.21690.25211380.2346240697
2.2169-2.26210.24721470.2354247598
2.2621-2.31130.26741390.2257243399
2.3113-2.36510.25681490.2245251799
2.3651-2.42420.321400.218243699
2.4242-2.48980.22431470.2089249599
2.4898-2.5630.25111450.21432493100
2.563-2.64580.24011450.2066247099
2.6458-2.74030.22091490.19512471100
2.7403-2.850.25141430.2078249599
2.85-2.97970.24161450.2082501100
2.9797-3.13680.20131410.20722462100
3.1368-3.33320.20981460.19142513100
3.3332-3.59050.16681390.16582484100
3.5905-3.95170.16181480.16562492100
3.9517-4.52310.17331440.13892500100
4.5231-5.6970.16411410.14752482100
5.697-46.3580.1771450.1725248399
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)
11.93720.49420.7212.95821.48293.73420.00180.1558-0.0774-0.3045-0.04290.16990.0442-0.13720.04390.2425-0.0005-0.00640.18670.01990.2153-9.090517.7631-49.327
20.91180.2327-0.74381.7488-1.29342.97320.0167-0.10730.05990.41470.09850.1953-0.2978-0.1559-0.10390.31880.01610.01160.2281-0.00680.2944-8.783313.9281-18.5075
35.4620.1355-0.03635.12550.27074.2735-0.22760.23060.4002-0.3242-0.06470.21510.1219-0.1830.27290.4344-0.0240.04760.3129-0.0240.4331-8.019535.1969-40.0904
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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