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- PDB-7uu3: Crystal structure of APOBEC3G complex with 3'overhangs RNA-Complex -

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Basic information

Entry
Database: PDB / ID: 7uu3
TitleCrystal structure of APOBEC3G complex with 3'overhangs RNA-Complex
Components
  • DNA dC->dU-editing enzyme APOBEC-3G
  • RNA (5'-R(*CP*CP*CP*AP*CP*GP*GP*GP*AP*AP*U)-3')
  • RNA (5'-R(*CP*CP*CP*GP*UP*GP*GP*GP*AP*AP*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 / 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: 3.099 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
B: DNA dC->dU-editing enzyme APOBEC-3G
C: RNA (5'-R(*CP*CP*CP*AP*CP*GP*GP*GP*AP*AP*U)-3')
D: RNA (5'-R(*CP*CP*CP*GP*UP*GP*GP*GP*AP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4158
Polymers99,1534
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-164 kcal/mol
Surface area39610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.709, 67.192, 79.624
Angle α, β, γ (deg.)98.290, 108.720, 112.660
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 60 or resid 65...
21(chain B and (resid 8 through 60 or resid 65...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 8 through 60 or resid 65...A8 - 60
121(chain A and (resid 8 through 60 or resid 65...A65 - 71
131(chain A and (resid 8 through 60 or resid 65...A73 - 194
141(chain A and (resid 8 through 60 or resid 65...A196
151(chain A and (resid 8 through 60 or resid 65...A330
161(chain A and (resid 8 through 60 or resid 65...A330 - 806
211(chain B and (resid 8 through 60 or resid 65...B8 - 60
221(chain B and (resid 8 through 60 or resid 65...B65 - 71
231(chain B and (resid 8 through 60 or resid 65...B73 - 194
241(chain B and (resid 8 through 60 or resid 65...B196
251(chain B and (resid 8 through 60 or resid 65...B330
261(chain B and (resid 8 through 60 or resid 65...B330 - 806

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Components

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


Mass: 45144.473 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(*CP*CP*CP*AP*CP*GP*GP*GP*AP*AP*U)-3')


Mass: 4423.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(*CP*CP*CP*GP*UP*GP*GP*GP*AP*AP*U)-3')


Mass: 4440.651 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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 0.1 M MES, pH 6.3, 12% PEG 20K

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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: Dec 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.099→50 Å / Num. obs: 61081 / % possible obs: 98.24 % / Redundancy: 3.3 % / CC1/2: 0.99 / Net I/σ(I): 8.89
Reflection shellResolution: 3.099→3.21 Å / Redundancy: 2.4 % / Num. unique obs: 4248 / CC1/2: 0.557 / % possible all: 93.7

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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: 3.099→45.695 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 24.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2099 1868 10.01 %
Rwork0.1698 16800 -
obs0.1739 18668 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.74 Å2 / Biso mean: 94.3458 Å2 / Biso min: 41.2 Å2
Refinement stepCycle: final / Resolution: 3.099→45.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6138 465 4 0 6607
Biso mean--83.97 --
Num. residues----761
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3550X-RAY DIFFRACTION5.912TORSIONAL
12B3550X-RAY DIFFRACTION5.912TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.099-3.18260.36631360.295122492
3.1826-3.27620.29031400.2774126498
3.2762-3.38190.34061460.2391130998
3.3819-3.50270.24471400.2172126499
3.5027-3.64290.23761450.2129129799
3.6429-3.80860.23771460.1995132099
3.8086-4.00930.23321450.2034129599
4.0093-4.26030.2021440.1648129499
4.2603-4.5890.18221460.1446132099
4.589-5.05030.18121460.1397131199
5.0503-5.77980.2111430.1558128799
5.7798-7.27720.22661460.1662130999
7.2772-45.6950.14751450.1202130699
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)
11.01110.2002-0.28790.97030.02071.248-0.08870.1013-0.1153-0.4426-0.17530.07550.70760.1005-00.75190.08140.04110.5803-0.05890.680122.1863-31.6582-39.6608
20.8487-0.4731-0.86822.47280.70641.12250.04620.01410.0325-0.2188-0.18680.21870.0977-0.0681-00.43430.0322-0.03430.38720.03570.469915.7644-14.2558-29.221
31.51540.3191-0.192.99150.48231.36120.2078-0.01080.11130.3815-0.20240.1886-0.18020.1866-0.00010.4175-0.02160.06660.4882-0.00070.53278.17353.8895-15.6662
40.42480.67920.18590.79520.250.74310.1190.31120.1142-0.363-0.1169-0.0214-0.1701-0.26410.00010.5234-0.0272-0.00020.673-0.00210.502755.7859-39.821-11.6669
50.69810.26080.2411.0869-0.16230.00530.01260.0241-0.4481-0.0517-0.0079-0.3213-0.12070.05500.4368-0.05130.02410.57470.07940.576364.2926-49.7825-4.7083
61.6510.14530.22892.19710.57970.13610.0189-0.13470.1187-0.08570.0488-0.2154-0.14580.0452-00.5398-0.00150.01470.57280.04850.438459.6143-35.5362-2.4984
70.1330.2521-0.1920.24820.26810.40810.4455-0.4019-0.05910.8778-0.0641-0.3097-0.31690.18790.00010.8835-0.1729-0.02680.823-0.12730.775466.5974-18.727214.3535
81.68510.59760.31762.5523-0.36131.4483-0.0203-0.34460.24170.38350.025-0.1648-0.57570.1636-00.9273-0.0342-0.09940.6897-0.15270.582658.9417-13.632615.2606
9-0.0223-0.22370.50710.2339-0.08990.35050.34960.0495-0.2258-0.07680.6504-0.44320.6310.33760.00050.80170.0759-0.19751.09670.05731.114835.3768-22.0662-20.2289
10-0.0632-0.17130.3092-0.0054-0.22560.2646-0.10180.70860.1579-0.2387-0.53180.8451-0.4487-0.5493-0.00020.82340.1698-0.17091.14740.07420.93641.7458-28.406-9.4071
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 80 )A8 - 80
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 287 )A81 - 287
3X-RAY DIFFRACTION3chain 'A' and (resid 288 through 380 )A288 - 380
4X-RAY DIFFRACTION4chain 'B' and (resid 7 through 41 )B7 - 41
5X-RAY DIFFRACTION5chain 'B' and (resid 42 through 109 )B42 - 109
6X-RAY DIFFRACTION6chain 'B' and (resid 110 through 193 )B110 - 193
7X-RAY DIFFRACTION7chain 'B' and (resid 194 through 228 )B194 - 228
8X-RAY DIFFRACTION8chain 'B' and (resid 229 through 380 )B229 - 380
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 11 )C1 - 11
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 11 )D1 - 11

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