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- PDB-6p3z: Crystal Structure of Full Length APOBEC3G E/Q (pH 5.2) -

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Basic information

Entry
Database: PDB / ID: 6p3z
TitleCrystal Structure of Full Length APOBEC3G E/Q (pH 5.2)
ComponentsApolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
KeywordsRNA BINDING PROTEIN / APOBEC3G / HIV / Cytidine Deaminases
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
DNA dC->dU-editing enzyme APOBEC-3G
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.844 Å
AuthorsYang, H.J. / Li, S.X. / Chen, X.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM087986 United States
CitationJournal: Nat Commun / Year: 2020
Title: Understanding the structural basis of HIV-1 restriction by the full length double-domain APOBEC3G.
Authors: Yang, H. / Ito, F. / Wolfe, A.D. / Li, S. / Mohammadzadeh, N. / Love, R.P. / Yan, M. / Zirkle, B. / Gaba, A. / Chelico, L. / Chen, X.S.
History
DepositionMay 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _audit_author.name / _database_2.pdbx_DOI ..._audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
B: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5064
Polymers90,3752
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-88 kcal/mol
Surface area36340 Å2
2
A: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2532
Polymers45,1871
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2532
Polymers45,1871
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.788, 153.513, 67.800
Angle α, β, γ (deg.)90.000, 114.140, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 23 or resid 25...
21(chain B and (resid 4 through 23 or resid 25...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNASNASN(chain A and (resid 4 through 23 or resid 25...AA4 - 2311 - 30
12PROPROTHRTHR(chain A and (resid 4 through 23 or resid 25...AA25 - 4132 - 48
13ASPASPGLYGLY(chain A and (resid 4 through 23 or resid 25...AA43 - 19050 - 193
14LEULEULEULEU(chain A and (resid 4 through 23 or resid 25...AA192 - 193195 - 196
15HISHISHISHIS(chain A and (resid 4 through 23 or resid 25...AA195 - 328198 - 331
16ASPASPGLYGLY(chain A and (resid 4 through 23 or resid 25...AA330 - 372333 - 375
17LEULEUZNZN(chain A and (resid 4 through 23 or resid 25...AA - C374 - 701377
21GLNGLNASNASN(chain B and (resid 4 through 23 or resid 25...BB4 - 2311 - 30
22PROPROTHRTHR(chain B and (resid 4 through 23 or resid 25...BB25 - 4132 - 48
23ASPASPGLYGLY(chain B and (resid 4 through 23 or resid 25...BB43 - 19050 - 193
24LEULEULEULEU(chain B and (resid 4 through 23 or resid 25...BB192 - 193195 - 196
25GLNGLNZNZN(chain B and (resid 4 through 23 or resid 25...BB - D4 - 70111
26ASPASPGLYGLY(chain B and (resid 4 through 23 or resid 25...BB330 - 372333 - 375
27LEULEUZNZN(chain B and (resid 4 through 23 or resid 25...BB - D374 - 701377

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Components

#1: Protein Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G


Mass: 45187.430 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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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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: 3.76 Å3/Da / Density % sol: 67.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 50 mM MES, pH 5.2 1.7 M lithium sulfate 10 mM MgCl2

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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: Jun 5, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 27992 / % possible obs: 94.3 % / Redundancy: 6.7 % / Net I/σ(I): 8.6
Reflection shellResolution: 2.85→2.95 Å / Num. unique obs: 2278

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.844→48.171 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 2012 7.2 %
Rwork0.2041 25951 -
obs0.2071 27963 94.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.55 Å2 / Biso mean: 44.3038 Å2 / Biso min: 9.04 Å2
Refinement stepCycle: final / Resolution: 2.844→48.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6042 0 2 0 6044
Biso mean--35.64 --
Num. residues----724
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2112X-RAY DIFFRACTION1.555TORSIONAL
12B2112X-RAY DIFFRACTION1.555TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8445-2.91560.30831140.29351420153474
2.9156-2.99440.35591180.2891597171581
2.9944-3.08250.33511320.26821713184586
3.0825-3.1820.25411370.24321782191992
3.182-3.29570.29021390.23531858199796
3.2957-3.42760.25491470.21741893204096
3.4276-3.58360.27361510.20721929208098
3.5836-3.77240.25361570.19231949210699
3.7724-4.00870.24391490.18219592108100
4.0087-4.3180.19461520.167419432095100
4.318-4.75220.22231540.152619652119100
4.7522-5.4390.19721500.165819732123100
5.439-6.84950.23891530.226519942147100
6.8495-48.17790.22691590.21121976213599
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)
11.50390.7354-0.47063.2121-0.29671.8037-0.10520.0482-0.2666-0.53590.0770.21840.37620.09880.03250.28330.0471-0.01180.1543-0.0350.1506-4.8825-18.9241.7988
21.92760.6478-1.68982.3159-0.2554.6145-0.0975-0.0053-0.0955-0.0645-0.0171-0.0750.35020.26220.050.4130.0360.06020.3025-0.02640.1603-7.5838-4.661932.4082
32.41210.68590.1724.1588-0.38471.1516-0.04720.17030.5251-0.57110.16590.7825-0.1652-0.11880.01650.33240.0755-0.02320.19390.04490.3361-1.55123.0204-6.508
41.25490.6740.14823.4899-0.30361.2967-0.0365-0.11080.3077-0.46050.07790.2397-0.2246-0.0194-0.01610.18230.0324-0.04670.1458-0.02470.15485.582617.8332-2.6948
55.53640.11890.01642.239-0.35621.4119-0.0872-0.13910.2780.08080.0570.138-0.0379-0.11850.01540.17670.017-0.03580.2682-0.00830.362332.6675.03296.3535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 4 through 193 )B4 - 193
2X-RAY DIFFRACTION2chain 'B' and (resid 194 through 383 )B194 - 383
3X-RAY DIFFRACTION3chain 'A' and (resid 4 through 57 )A4 - 57
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 193 )A58 - 193
5X-RAY DIFFRACTION5chain 'A' and (resid 194 through 383 )A194 - 383

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