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- PDB-7uu5: Crystal structure of APOBEC3G complex with 5'-Overhang dsRNA -

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Basic information

Entry
Database: PDB / ID: 7uu5
TitleCrystal structure of APOBEC3G complex with 5'-Overhang dsRNA
Components
  • DNA dC->dU-editing enzyme APOBEC-3G
  • RNA (5'-R(P*UP*AP*AP*CP*CP*GP*CP*AP*GP*CP*G)-3')
  • RNA (5'-R(P*UP*AP*AP*CP*GP*CP*UP*GP*CP*GP*G)-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 / RNA (> 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: 2.9 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

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Assembly

Deposited unit
A: DNA dC->dU-editing enzyme APOBEC-3G
B: DNA dC->dU-editing enzyme APOBEC-3G
M: RNA (5'-R(P*UP*AP*AP*CP*GP*CP*UP*GP*CP*GP*G)-3')
N: RNA (5'-R(P*UP*AP*AP*CP*CP*GP*CP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8328
Polymers101,5704
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.305, 71.559, 72.710
Angle α, β, γ (deg.)119.390, 111.000, 90.080
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 14 or resid 16...
21(chain B and (resid 3 through 14 or resid 16...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 14 or resid 16...A3 - 14
121(chain A and (resid 3 through 14 or resid 16...A16 - 58
131(chain A and (resid 3 through 14 or resid 16...A60 - 98
141(chain A and (resid 3 through 14 or resid 16...A100 - 172
151(chain A and (resid 3 through 14 or resid 16...A1 - 383
161(chain A and (resid 3 through 14 or resid 16...A255 - 3
171(chain A and (resid 3 through 14 or resid 16...A320 - 354
181(chain A and (resid 3 through 14 or resid 16...A1 - 383
191(chain A and (resid 3 through 14 or resid 16...A356 - 383
1101(chain A and (resid 3 through 14 or resid 16...A800 - 900
211(chain B and (resid 3 through 14 or resid 16...B3 - 14
221(chain B and (resid 3 through 14 or resid 16...B16 - 58
231(chain B and (resid 3 through 14 or resid 16...B60 - 98
241(chain B and (resid 3 through 14 or resid 16...B100 - 172
251(chain B and (resid 3 through 14 or resid 16...B174 - 215
261(chain B and (resid 3 through 14 or resid 16...B0
271(chain B and (resid 3 through 14 or resid 16...B1 - 383
281(chain B and (resid 3 through 14 or resid 16...B320 - 354
291(chain B and (resid 3 through 14 or resid 16...B356 - 3
2101(chain B and (resid 3 through 14 or resid 16...B356 - 383
2111(chain B and (resid 3 through 14 or resid 16...B800 - 900

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Components

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


Mass: 45130.379 Da / Num. of mol.: 2
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*CP*GP*CP*UP*GP*CP*GP*G)-3')


Mass: 5663.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(P*UP*AP*AP*CP*CP*GP*CP*AP*GP*CP*G)-3')


Mass: 5646.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.8 M Na/K phosphate, pH 6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 21497 / % possible obs: 98.2 % / Redundancy: 3.3 % / CC1/2: 0.994 / Net I/σ(I): 11.56
Reflection shellResolution: 2.9→3.004 Å / Num. unique obs: 2116 / CC1/2: 0.845

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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: 2.9→46.508 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2428 1335 6.26 %
Rwork0.187 20006 -
obs0.1907 21341 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 250.37 Å2 / Biso mean: 86.8796 Å2 / Biso min: 32.4 Å2
Refinement stepCycle: final / Resolution: 2.9→46.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6296 471 4 0 6771
Biso mean--113.64 --
Num. residues----780
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3441X-RAY DIFFRACTION12.946TORSIONAL
12B3441X-RAY DIFFRACTION12.946TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9-3.00360.39471390.2965184392
3.0036-3.12390.31871320.2574200798
3.1239-3.2660.28551260.231200999
3.266-3.43820.32961420.2175201399
3.4382-3.65350.25591320.1945203299
3.6535-3.93540.23391460.1803198199
3.9354-4.33120.23251260.1694203099
4.3312-4.95730.22831360.1538200899
4.9573-6.24330.21421250.1852205999
6.2433-46.5080.20221310.1707202499
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)
14.5612-0.8205-1.45362.850.86352.28780.09740.10460.2114-0.085-0.20680.3538-0.2566-0.33450.09920.4386-0.0318-0.07480.4335-0.02460.3709-42.16.010824.8174
24.0274-1.2030.6381.45530.08131.24720.18880.2046-0.1232-0.0555-0.0367-0.26120.1654-0.0386-0.16970.5178-0.00660.01490.44760.02150.5556-13.3212-8.26825.1593
33.93290.2281-1.42343.0246-0.61912.30970.18350.08960.1912-0.0541-0.1637-0.37-0.24280.1645-0.03190.43740.022-0.04580.487-0.06740.361-16.06744.5335-19.8691
44.12780.76540.92211.3887-0.1841.10150.0845-0.1617-0.11240.1116-0.03910.38060.1659-0.0269-0.06590.48920.00770.00210.4257-0.08080.5616-46.7534-8.4703-20.565
55.553-1.949-0.47575.8904-1.47443.00640.37950.21291.8982-1.31440.6976-0.7272-2.0308-0.4415-1.06351.76820.06020.41591.24320.30911.0893-28.319817.25111.7125
66.04451.07230.0567.84373.74893.20740.3704-0.36911.98551.3280.48680.5995-1.39220.6681-0.92031.561-0.08870.37161.3345-0.22541.1158-29.520117.2583.0656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 141 )A1 - 141
2X-RAY DIFFRACTION2chain 'A' and (resid 142 through 383 )A142 - 383
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 164 )B1 - 164
4X-RAY DIFFRACTION4chain 'B' and (resid 165 through 383 )B165 - 383
5X-RAY DIFFRACTION5chain 'M' and (resid 2 through 12 )M2 - 12
6X-RAY DIFFRACTION6chain 'N' and (resid 2 through 12 )N2 - 12

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