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- PDB-6p40: Crystal Structure of Full Length APOBEC3G FKL -

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Basic information

Entry
Database: PDB / ID: 6p40
TitleCrystal Structure of Full Length APOBEC3G FKL
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: 2.452 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)88,6326
Polymers88,3702
Non-polymers2624
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-173 kcal/mol
Surface area34390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.067, 86.423, 90.158
Angle α, β, γ (deg.)90.000, 101.380, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ZN / End label comp-ID: ZN / Auth seq-ID: 7 - 702 / Label seq-ID: 14

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA - D
2chain BBB - F

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Components

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


Mass: 44185.164 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.: 4 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 0.1 M MES, pH 6.9 8% 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: Mar 17, 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: 2.47→50 Å / Num. obs: 34058 / % possible obs: 99.5 % / Redundancy: 3.9 % / Net I/σ(I): 15.3
Reflection shellResolution: 2.47→2.51 Å / Num. unique obs: 1678

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.452→46.695 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2284 3837 5.87 %
Rwork0.1729 61505 -
obs0.1761 65342 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.07 Å2 / Biso mean: 50.0238 Å2 / Biso min: 18.87 Å2
Refinement stepCycle: final / Resolution: 2.452→46.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6040 0 4 111 6155
Biso mean--46.97 47.02 -
Num. residues----728
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2204X-RAY DIFFRACTION1.128TORSIONAL
12B2204X-RAY DIFFRACTION1.128TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.452-2.48310.3511170.26281830194778
2.4831-2.51570.35211360.25392203233994
2.5157-2.55020.30851380.26112241237996
2.5502-2.58660.36571450.26942319246497
2.5866-2.62520.35351360.26622198233496
2.6252-2.66620.33691420.23382337247997
2.6662-2.70990.32331430.22192275241898
2.7099-2.75670.19791380.20812224236297
2.7567-2.80680.30561460.21482363250998
2.8068-2.86080.27311410.21322289243098
2.8608-2.91920.31581450.20312315246098
2.9192-2.98260.27031450.21162335248098
2.9826-3.0520.23991440.20782279242398
3.052-3.12830.26521480.19432347249598
3.1283-3.21290.25741390.1982260239997
3.2129-3.30740.30031420.19112287242998
3.3074-3.41410.22041430.17352278242198
3.4141-3.53610.23481430.16752307245098
3.5361-3.67760.20991430.15842325246898
3.6776-3.84490.21721410.15262263240498
3.8449-4.04750.18951460.14292323246999
4.0475-4.30090.15211440.14012343248798
4.3009-4.63270.20661460.12922306245299
4.6327-5.09840.17841460.12912341248799
5.0984-5.8350.21291440.162298244299
5.835-7.34680.18941510.16562317246898
7.3468-46.70310.17811450.14982302244798
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)
11.279-0.3019-0.19751.19420.08391.2173-0.05740.08410.1068-0.0662-0.0724-0.0701-0.128-0.0971-0.00360.23790.0078-0.02980.2438-0.01040.20726.09726.65832.128
20.6245-0.3978-0.14551.63080.68531.9420.0042-0.00110.0341-0.1721-0.0263-0.3161-0.15150.06970.00120.1704-0.05680.00150.19420.02910.19729.5976.28321.747
30.44870.28880.240.42710.15780.5799-0.0257-0.14410.15170.03850.3089-0.35050.13660.24430.01890.34-0.06260.13590.2422-0.03890.476436.929-8.88814.176
40.47740.1514-0.17731.68420.74621.24910.06350.0812-0.07020.0339-0.1181-0.08320.1596-0.0157-0.03850.2668-0.01320.00980.1851-0.02840.235124.8-32.30313.097
50.707-0.3825-0.11321.1727-0.019-0.05760.0070.0639-0.11760.0743-0.11020.25880.0708-0.0593-0.0020.2542-0.08110.02130.3084-0.08660.29911.776-12.31724.315
60.40450.0296-0.06580.5595-0.32790.29420.0831-0.0363-0.27790.06360.02250.5311-0.2549-0.0520.01310.32-0.04580.09620.4306-0.13080.5263-6.6093.71927.649
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 7:173 )A7 - 173
2X-RAY DIFFRACTION2( CHAIN A AND RESID 174:350 )A174 - 350
3X-RAY DIFFRACTION3( CHAIN A AND ( RESID 351:382 OR RESID 701:702 ) )A351 - 382
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 351:382 OR RESID 701:702 ) )A701 - 702
5X-RAY DIFFRACTION4( CHAIN B AND RESID 7:173 )B7 - 173
6X-RAY DIFFRACTION5( CHAIN B AND RESID 174:350 )B174 - 350
7X-RAY DIFFRACTION6( CHAIN B AND ( RESID 351:382 OR RESID 701:702 ) )B351 - 382
8X-RAY DIFFRACTION6( CHAIN B AND ( RESID 351:382 OR RESID 701:702 ) )B701 - 702

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