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- PDB-6bwy: DNA substrate selection by APOBEC3G -

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Basic information

Entry
Database: PDB / ID: 6bwy
TitleDNA substrate selection by APOBEC3G
Components
  • DNA (30-MER)
  • Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
KeywordsHYDROLASE / Deaminase / DNA binding / complex
Function / homology
Function and homology information


apolipoprotein B mRNA editing enzyme complex / dCTP deaminase activity / telomere cap complex / cytidine deamination / chromosome, telomeric repeat region / telomerase inhibitor activity / base conversion or substitution editing / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing ...apolipoprotein B mRNA editing enzyme complex / dCTP deaminase activity / telomere cap complex / cytidine deamination / chromosome, telomeric repeat region / telomerase inhibitor activity / base conversion or substitution editing / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / cytidine deaminase activity / shelterin complex / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of viral process / regulation of telomere maintenance via telomerase / retrotransposon silencing / nuclear telomere cap complex / G-rich strand telomeric DNA binding / single-stranded telomeric DNA binding / telomere capping / DNA demethylation / negative regulation of viral genome replication / APOBEC3G mediated resistance to HIV-1 infection / positive regulation of defense response to virus by host / telomere maintenance / P-body / Vif-mediated degradation of APOBEC3G / defense response to virus / ribonucleoprotein complex / innate immune response / RNA binding / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
APOBEC-like C-terminal domain / Protection of telomeres protein 1, ssDNA-binding domain / ssDNA-binding domain of telomere protection protein / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 / Novel AID APOBEC clade 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. ...APOBEC-like C-terminal domain / Protection of telomeres protein 1, ssDNA-binding domain / ssDNA-binding domain of telomere protection protein / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 / 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 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / Protection of telomeres protein 1 / DNA dC->dU-editing enzyme APOBEC-3G
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZiegler, S.J. / Buzovetsky, O.
CitationJournal: PLoS ONE / Year: 2018
Title: Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies.
Authors: Ziegler, S.J. / Liu, C. / Landau, M. / Buzovetsky, O. / Desimmie, B.A. / Zhao, Q. / Sasaki, T. / Burdick, R.C. / Pathak, V.K. / Anderson, K.S. / Xiong, Y.
History
DepositionDec 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

Downloads & links

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Assembly

Deposited unit
I: DNA (30-MER)
C: DNA (30-MER)
D: DNA (30-MER)
F: DNA (30-MER)
A: Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
B: Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
E: Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
G: Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,98027
Polymers205,2948
Non-polymers1,68619
Water1,02757
1
I: DNA (30-MER)
A: Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7697
Polymers51,3232
Non-polymers4455
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-56 kcal/mol
Surface area18300 Å2
MethodPISA
2
C: DNA (30-MER)
G: Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7697
Polymers51,3232
Non-polymers4455
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-12 kcal/mol
Surface area18330 Å2
MethodPISA
3
D: DNA (30-MER)
B: Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6746
Polymers51,3232
Non-polymers3504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-55 kcal/mol
Surface area18420 Å2
MethodPISA
4
F: DNA (30-MER)
E: Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7697
Polymers51,3232
Non-polymers4455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-24 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.072, 79.072, 266.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22E
13A
23G
14B
24E
15B
25G
16E
26G

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 30 - 381 / Label seq-ID: 7 - 358

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AE
21BF
12AE
22EG
13AE
23GH
14BF
24EG
15BF
25GH
16EG
26GH

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: DNA chain
DNA (30-MER)


Mass: 9357.086 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein
Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion / APOBEC-related cytidine deaminase / ARCD / APOBEC-related protein 9 / ARP-9 / CEM-15 / CEM15 / ...APOBEC-related cytidine deaminase / ARCD / APOBEC-related protein 9 / ARP-9 / CEM-15 / CEM15 / Deoxycytidine deaminase / A3G


Mass: 41966.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast), (gene. exp.) Homo sapiens (human)
Strain: 972 / ATCC 24843 / Gene: pot1, SPAC26H5.06, APOBEC3G, MDS019 / Production host: Escherichia coli (E. coli)
References: UniProt: O13988, UniProt: Q9HC16, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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

Crystal growTemperature: 298 K / Method: batch mode
Details: 100 mM HEPES pH7, 200 mM LiCl, and 20% (w/v) Polyethylene glycol (PEG) 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.501
11-H, K, -L20.499
ReflectionResolution: 2.9→44.19 Å / Num. obs: 35772 / % possible obs: 97.5 % / Redundancy: 3.3 % / CC1/2: 0.7 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.064 / Net I/σ(I): 5.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3545 / Rpim(I) all: 0.539

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IR2, 1QZH

3ir2

1qzh


Resolution: 2.9→44.19 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.923 / SU B: 27.433 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.109
RfactorNum. reflection% reflectionSelection details
Rfree0.28692 1737 5 %RANDOM
Rwork0.23394 ---
obs0.23665 32909 96.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 88.213 Å2
Baniso -1Baniso -2Baniso -3
1-65 Å20 Å20 Å2
2--65 Å20 Å2
3----130 Å2
Refinement stepCycle: 1 / Resolution: 2.9→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11169 577 79 57 11882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01912166
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.89416625
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60851374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40624.144584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.126151913
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8881573
X-RAY DIFFRACTIONr_chiral_restr0.1210.21743
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0219149
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.5816.585520
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.7869.8616886
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.5456.4536646
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined15.64561.16349433
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A108940.1
12B108940.1
21A111180.08
22E111180.08
31A112340.07
32G112340.07
41B110020.1
42E110020.1
51B109400.1
52G109400.1
61E110620.08
62G110620.08
LS refinement shellResolution: 2.901→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 127 -
Rwork0.3 2374 -
obs--94.81 %
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)
10.17850.10230.24751.60230.87232.3093-0.0134-0.1171-0.02720.00140.08640.1369-0.1899-0.0175-0.0730.0221-0.00040.00190.09840.01890.4949151.008168.3825-50.7332
20.77440.3091.37550.73331.12183.612-0.0179-0.03570.01340.0984-0.10280.20030.5123-0.23670.12070.335-0.07090.04770.15940.02740.4517131.858272.4026-20.06
30.3011-0.2696-0.38440.8012-0.16522.63390.10990.1613-0.01870.0281-0.1032-0.1662-0.2622-0.0499-0.00660.07350.07330.00830.1210.01580.449286.712468.4038-2.8963
41.1833-0.43620.5451.0191-0.60821.7609-0.0424-0.1499-0.08450.0611-0.1235-0.11750.2280.11920.16590.05920.01730.03520.06440.06350.5172105.349273.7056-33.1456
50.2712-0.38230.27690.813-0.38412.7702-0.0140.07790.05480.01380.0386-0.1703-0.04430.0592-0.02460.0019-0.00680.01760.1029-0.02430.5066125.5652108.14217.2217
61.5009-0.33911.67351.3882-0.52612.13430.0335-0.0476-0.06170.1064-0.1182-0.10560.1540.09410.08470.10340.01170.06030.16260.02420.4798144.7422112.7116-23.0597
70.25590.29340.03370.9686-0.58932.29220.0694-0.16310.0159-0.0185-0.04650.1648-0.29070.0996-0.02290.1263-0.12590.01170.1842-0.02750.4204110.8425107.8178-40.489
81.1031-0.09670.28651.16080.51323.0302-0.13860.1926-0.1162-0.0019-0.09880.20660.5649-0.02380.23750.1539-0.03150.05670.0422-0.07020.530592.2958112.5379-9.9506
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 194
2X-RAY DIFFRACTION1I1 - 7
3X-RAY DIFFRACTION2A195 - 381
4X-RAY DIFFRACTION3B30 - 194
5X-RAY DIFFRACTION3D1 - 7
6X-RAY DIFFRACTION4B195 - 381
7X-RAY DIFFRACTION5E30 - 194
8X-RAY DIFFRACTION5F1 - 7
9X-RAY DIFFRACTION6E195 - 381
10X-RAY DIFFRACTION7G30 - 194
11X-RAY DIFFRACTION7C1 - 7
12X-RAY DIFFRACTION8G195 - 381

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