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- PDB-8fik: APOBEC3A E72A inactive mutant in complex with ATTC-hairpin DNA su... -

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Basic information

Entry
Database: PDB / ID: 8fik
TitleAPOBEC3A E72A inactive mutant in complex with ATTC-hairpin DNA substrate
Components
  • DNA (5'-D(P*CP*CP*CP*AP*TP*CP*AP*TP*TP*CP*GP*AP*TP*GP*GP*G)-3')
  • DNA dC->dU-editing enzyme APOBEC-3A
KeywordsDNA BINDING PROTEIN/DNA / APOBEC / APOBEC3A / A3A / cancer / DNA / mutation / cytidine deaminase / hairpin DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / retrotransposon silencing ...mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / retrotransposon silencing / DNA demethylation / negative regulation of viral genome replication / P-body / defense response to virus / innate immune response / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
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
INOSITOL HEXAKISPHOSPHATE / PHOSPHATE ION / DNA / DNA (> 10) / DNA dC->dU-editing enzyme APOBEC-3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.912 Å
AuthorsHarjes, S. / Jameson, G.B. / Harjes, E. / Filichev, V.V. / Kurup, H.M.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council (HRC)20/1355 New Zealand
CitationJournal: To Be Published
Title: DNA-based inhibitors restrict mutagenic activity of APOBEC3 in cells
Authors: Harjes, S. / Kurup, H.M. / Filichev, V. / Harjes, E. / Jameson, G.B.
History
DepositionDec 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release

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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-3A
B: DNA dC->dU-editing enzyme APOBEC-3A
D: DNA (5'-D(P*CP*CP*CP*AP*TP*CP*AP*TP*TP*CP*GP*AP*TP*GP*GP*G)-3')
H: DNA (5'-D(P*CP*CP*CP*AP*TP*CP*AP*TP*TP*CP*GP*AP*TP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,86112
Polymers55,7144
Non-polymers1,1478
Water2,828157
1
A: DNA dC->dU-editing enzyme APOBEC-3A
D: DNA (5'-D(P*CP*CP*CP*AP*TP*CP*AP*TP*TP*CP*GP*AP*TP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7136
Polymers27,8572
Non-polymers8564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-64 kcal/mol
Surface area12390 Å2
MethodPISA
2
B: DNA dC->dU-editing enzyme APOBEC-3A
H: DNA (5'-D(P*CP*CP*CP*AP*TP*CP*AP*TP*TP*CP*GP*AP*TP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1486
Polymers27,8572
Non-polymers2914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-63 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.001, 57.229, 92.752
Angle α, β, γ (deg.)90.000, 106.478, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32D
42H

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGASNASNAA10 - 19610 - 196
211ARGARGASNASNBB10 - 19610 - 196
322DCDCDGDGDC-8 - 62 - 16
422DCDCDGDGHD-8 - 62 - 16

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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Components

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Protein / DNA chain , 2 types, 4 molecules ABDH

#1: Protein DNA dC->dU-editing enzyme APOBEC-3A / A3A / Phorbolin-1


Mass: 22982.979 Da / Num. of mol.: 2 / Mutation: E72A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3A / Plasmid: pETite / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P31941, single-stranded DNA cytosine deaminase
#2: DNA chain DNA (5'-D(P*CP*CP*CP*AP*TP*CP*AP*TP*TP*CP*GP*AP*TP*GP*GP*G)-3')


Mass: 4874.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 165 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.55 Å3/Da / Density % sol: 51.72 % / Description: Flattened needle
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: A3A-E72A (50 mM MES pH 6.0, 100 mM NaCl, 1 mM TCEP, 0.2 mM EDTA) was mixed with oligonucleotides (10 mM Tris/HCl pH 7.9, 1 mM EDTA) at 0.85 mM and 1.7 mM respectively. Dilution was done with ...Details: A3A-E72A (50 mM MES pH 6.0, 100 mM NaCl, 1 mM TCEP, 0.2 mM EDTA) was mixed with oligonucleotides (10 mM Tris/HCl pH 7.9, 1 mM EDTA) at 0.85 mM and 1.7 mM respectively. Dilution was done with protein buffer. The mixture was added to crystallization liquid 1 to 1 and the mixture was pipetted on siliconized glass disks and sealed on top of a reservoir of crystallization liquid for hanging drop crystallization at 12 degrees Celsius. The crystallization liquid has the following composition: 100 mM Bicine at pH 6.6, 200 mM NaCl, 20 mM putrescine, 1 mM TCEP, 1 mM inositol hex phosphate (phytic acid) and 45 % pentaerythritol propoxylate (5/4 PO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953739 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2021 / Details: 1 vertical and 2 horizontal focussing mirrors
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953739 Å / Relative weight: 1
ReflectionResolution: 1.91→48.173 Å / Num. obs: 42309 / % possible obs: 98.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 26.3 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.057 / Net I/σ(I): 7.5
Reflection shellResolution: 1.91→1.96 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.913 / Mean I/σ(I) obs: 1 / Num. unique obs: 2706 / CC1/2: 0.471 / Rpim(I) all: 0.589 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
JBluIce-EPICSdata collection
Aimlessdata scaling
pointlessdata scaling
MOLREPphasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KEG

5keg


Resolution: 1.912→48.173 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.19 / SU B: 9.215 / SU ML: 0.128 / Average fsc free: 0.867 / Average fsc work: 0.876 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.142
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 2103 4.972 %RANDOM
Rwork0.2001 40190 --
all0.202 ---
obs-42293 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.801 Å2
Baniso -1Baniso -2Baniso -3
1-1.559 Å20 Å20.376 Å2
2---0.657 Å20 Å2
3----0.957 Å2
Refinement stepCycle: LAST / Resolution: 1.912→48.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 614 55 157 3857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123948
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153198
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.665508
X-RAY DIFFRACTIONr_angle_other_deg1.3851.5767351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7155392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70920.914197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82815494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8321527
X-RAY DIFFRACTIONr_chiral_restr0.1070.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024133
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02975
X-RAY DIFFRACTIONr_nbd_refined0.2140.2741
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2150.22862
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21763
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21594
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2149
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1050.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2310.219
X-RAY DIFFRACTIONr_nbd_other0.2110.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.214
X-RAY DIFFRACTIONr_mcbond_it2.5382.6951544
X-RAY DIFFRACTIONr_mcbond_other2.5372.6931543
X-RAY DIFFRACTIONr_mcangle_it3.9624.0181944
X-RAY DIFFRACTIONr_mcangle_other3.9624.0211945
X-RAY DIFFRACTIONr_scbond_it3.4093.342404
X-RAY DIFFRACTIONr_scbond_other3.3993.3262401
X-RAY DIFFRACTIONr_scangle_it5.5044.953564
X-RAY DIFFRACTIONr_scangle_other5.4984.943562
X-RAY DIFFRACTIONr_lrange_it7.39931.5874582
X-RAY DIFFRACTIONr_lrange_other7.39931.6154583
X-RAY DIFFRACTIONr_ncsr_local_group_10.1020.056028
X-RAY DIFFRACTIONr_ncsr_local_group_20.1450.051241
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.101970.05007
12BX-RAY DIFFRACTIONLocal ncs0.101970.05007
23DX-RAY DIFFRACTIONLocal ncs0.145250.05008
24HX-RAY DIFFRACTIONLocal ncs0.145250.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.912-1.9620.3011590.312840X-RAY DIFFRACTION94.9952
1.962-2.0150.3191390.2992869X-RAY DIFFRACTION98.2685
2.015-2.0740.2771450.2642805X-RAY DIFFRACTION98.1044
2.074-2.1380.2461320.2562721X-RAY DIFFRACTION98.21
2.138-2.2080.2641410.2512616X-RAY DIFFRACTION97.1459
2.208-2.2850.2821290.2272513X-RAY DIFFRACTION97.3471
2.285-2.3710.251270.2072463X-RAY DIFFRACTION97.9206
2.371-2.4680.241340.1932373X-RAY DIFFRACTION99.0909
2.468-2.5780.2041150.192303X-RAY DIFFRACTION99.4652
2.578-2.7030.2191380.1912176X-RAY DIFFRACTION99.6555
2.703-2.8490.2391090.1982113X-RAY DIFFRACTION99.7307
2.849-3.0220.265830.1892025X-RAY DIFFRACTION99.3402
3.022-3.230.2411000.1961856X-RAY DIFFRACTION99.542
3.23-3.4890.243970.1931722X-RAY DIFFRACTION99.1821
3.489-3.8210.183900.1661590X-RAY DIFFRACTION98.6494
3.821-4.2710.174750.1621461X-RAY DIFFRACTION99.3532
4.271-4.930.196600.1421310X-RAY DIFFRACTION99.1317
4.93-6.0340.209620.1971085X-RAY DIFFRACTION99.2215
6.034-8.5130.343340.214865X-RAY DIFFRACTION98.5746
8.513-48.1730.211340.235483X-RAY DIFFRACTION98.1025
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)
10.56730.1003-0.32090.63870.19160.6892-0.0162-0.1158-0.036-0.04630.0383-0.0261-0.03550.1175-0.02210.0241-0.0072-0.01510.0370.00320.031-0.7180.10742.517
20.56330.1105-0.04880.9141-0.10570.81460.0425-0.049-0.00670.035-0.0019-0.0295-0.03410.022-0.04060.0372-0.0129-0.02740.00940.0060.027325.876-9.8812.527
32.3871-0.19530.01872.3111-0.22533.04910.06370.49530.4215-0.47440.1428-0.0495-0.08890.3692-0.20650.1877-0.09010.01550.20530.0890.1448-1.21811.50919.938
42.11782.38930.47956.52120.86232.102-0.1727-0.2978-0.0304-0.15260.23130.53620.3167-0.3678-0.05860.1225-0.05140.01080.19760.10620.14834.748-23.62512.452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA10 - 196
2X-RAY DIFFRACTION2ALLB10 - 196
3X-RAY DIFFRACTION3ALLD-8 - 6
4X-RAY DIFFRACTION4ALLH-8 - 6

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