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- PDB-8fij: Wild type APOBEC3A in complex with TT(FdZ)-hairpin inhibitor (cry... -

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Basic information

Entry
Database: PDB / ID: 8fij
TitleWild type APOBEC3A in complex with TT(FdZ)-hairpin inhibitor (crystal form 2)
Components
  • DNA (5'-D(*GP*CP*GP*CP*TP*TP*(UFP)P*GP*CP*GP*CP*T)-3')
  • DNA dC->dU-editing enzyme APOBEC-3A
KeywordsDNA BINDING PROTEIN / APOBEC / APOBEC3A / A3A / cancer / DNA / mutation / cytidine deaminase / hairpin DNA inhibitor
Function / homology
Function and homology information


mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / DNA cytosine deamination / cytidine to uridine editing / clearance of foreign intracellular DNA / cytidine deaminase activity / transposable element silencing / positive regulation of gene expression via chromosomal CpG island demethylation ...mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / DNA cytosine deamination / cytidine to uridine editing / clearance of foreign intracellular DNA / cytidine deaminase activity / transposable element silencing / positive regulation of gene expression via chromosomal CpG island 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
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: 2.799 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: Nat Commun / Year: 2023
Title: Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A.
Authors: Harjes, S. / Kurup, H.M. / Rieffer, A.E. / Bayarjargal, M. / Filitcheva, J. / Su, Y. / Hale, T.K. / Filichev, V.V. / Harjes, E. / Harris, R.S. / Jameson, G.B.
History
DepositionDec 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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(*GP*CP*GP*CP*TP*TP*(UFP)P*GP*CP*GP*CP*T)-3')
E: DNA (5'-D(*GP*CP*GP*CP*TP*TP*(UFP)P*GP*CP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,08112
Polymers53,3814
Non-polymers7018
Water362
1
A: DNA dC->dU-editing enzyme APOBEC-3A
D: DNA (5'-D(*GP*CP*GP*CP*TP*TP*(UFP)P*GP*CP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0416
Polymers26,6902
Non-polymers3504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA dC->dU-editing enzyme APOBEC-3A
E: DNA (5'-D(*GP*CP*GP*CP*TP*TP*(UFP)P*GP*CP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0416
Polymers26,6902
Non-polymers3504
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.943, 56.365, 90.113
Angle α, β, γ (deg.)90.000, 104.985, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 10 - 196 / Label seq-ID: 10 - 196

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Global NCS restraints between domains: 1 2)
NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.123951, 0.042222, 0.99139), (0.015743, -0.999052, 0.04058), (0.992163, 0.010578, -0.124498)6.47408, 13.41176, -6.2209
3given(1), (1), (1)
4given(0.079336, 0.036307, 0.996187), (-0.066188, -0.996939, 0.041606), (0.994648, -0.069236, -0.07669)8.08412, 16.440611, -5.73424

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Components

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


Mass: 23041.016 Da / Num. of mol.: 2
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(*GP*CP*GP*CP*TP*TP*(UFP)P*GP*CP*GP*CP*T)-3')


Mass: 3649.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46.65 % / Description: Flattened needle
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
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 hexaphosphate (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 23, 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: 2.799→48.291 Å / Num. obs: 11861 / % possible obs: 97.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 57 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.118 / Net I/σ(I): 4.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.157 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1629 / CC1/2: 0.466 / Rpim(I) all: 0.735 / % possible all: 92.8

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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: 2.799→48.291 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.834 / WRfactor Rfree: 0.313 / WRfactor Rwork: 0.251 / SU B: 67.886 / SU ML: 0.581 / Average fsc free: 0.7681 / Average fsc work: 0.7885 / Cross valid method: THROUGHOUT / ESU R Free: 0.5
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.3182 623 5.256 %RANDOM
Rwork0.2577 11229 --
all0.261 ---
obs-11852 97.724 %-
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: 60.975 Å2
Baniso -1Baniso -2Baniso -3
1-4.278 Å2-0 Å21.154 Å2
2---2.679 Å2-0 Å2
3----1.939 Å2
Refinement stepCycle: LAST / Resolution: 2.799→48.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 404 32 2 3362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123478
X-RAY DIFFRACTIONr_bond_other_d0.0030.0152908
X-RAY DIFFRACTIONr_angle_refined_deg1.641.6544800
X-RAY DIFFRACTIONr_angle_other_deg1.3521.5856630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1445362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61220.778180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8615453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0421526
X-RAY DIFFRACTIONr_chiral_restr0.0870.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023700
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02866
X-RAY DIFFRACTIONr_nbd_refined0.2260.2726
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2360.22720
X-RAY DIFFRACTIONr_nbtor_refined0.1920.21588
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.21549
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2150.27
X-RAY DIFFRACTIONr_metal_ion_refined0.070.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.227
X-RAY DIFFRACTIONr_nbd_other0.2880.2105
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1010.23
X-RAY DIFFRACTIONr_mcbond_it3.0984.8281463
X-RAY DIFFRACTIONr_mcbond_other3.0854.8271462
X-RAY DIFFRACTIONr_mcangle_it5.0977.2291820
X-RAY DIFFRACTIONr_mcangle_other5.0967.2311821
X-RAY DIFFRACTIONr_scbond_it3.1315.1792015
X-RAY DIFFRACTIONr_scbond_other3.0565.1211992
X-RAY DIFFRACTIONr_scangle_it5.2217.7342980
X-RAY DIFFRACTIONr_scangle_other5.1697.6482945
X-RAY DIFFRACTIONr_lrange_it10.49588.413838
X-RAY DIFFRACTIONr_lrange_other10.4488.33613833
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: tight positional; tight thermal / Rms dev Biso : 5.13109 Å2 / Rms dev position: 0.27737 Å / Weight Biso : 0.5 / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.799-2.8710.432310.356719X-RAY DIFFRACTION86.3061
2.871-2.950.406320.365846X-RAY DIFFRACTION99.0971
2.95-3.0350.294490.353753X-RAY DIFFRACTION98.164
3.035-3.1290.312330.339793X-RAY DIFFRACTION98.2164
3.129-3.2310.41330.329731X-RAY DIFFRACTION98.3269
3.231-3.3440.388410.292725X-RAY DIFFRACTION97.8289
3.344-3.4710.353380.255682X-RAY DIFFRACTION98.6301
3.471-3.6120.32460.234676X-RAY DIFFRACTION99.8617
3.612-3.7720.308410.225635X-RAY DIFFRACTION99.2658
3.772-3.9560.252380.22621X-RAY DIFFRACTION99.0977
3.956-4.170.295360.22588X-RAY DIFFRACTION99.5215
4.17-4.4220.239500.201529X-RAY DIFFRACTION98.3022
4.422-4.7260.293220.197531X-RAY DIFFRACTION99.1039
4.726-5.1040.289270.231496X-RAY DIFFRACTION98.8658
5.104-5.5890.289300.242441X-RAY DIFFRACTION98.3299
5.589-6.2450.429300.28405X-RAY DIFFRACTION98.6395
6.245-7.2050.392180.283360X-RAY DIFFRACTION98.6945
7.205-8.810.38150.272306X-RAY DIFFRACTION97.8659
8.81-12.3960.2260.249251X-RAY DIFFRACTION96.9811
12.396-48.2910.42770.311141X-RAY DIFFRACTION94.2675
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)
11.1818-0.32350.87510.7485-0.11132.16550.0208-0.00310.0215-0.06660.1035-0.03060.0287-0.03-0.12430.2501-0.01830.16670.0177-0.0050.127214.540.38531.282
21.4640.32140.34511.1541-0.04291.34270.09060.10890.13070.06080.01860.0989-0.0357-0.1277-0.10920.18450.00630.17350.02740.01960.171237.96313.9013.052
31.54592.2626-0.38793.7958-1.1260.7461-0.03030.2628-0.11970.1288-0.1343-0.3028-0.10810.49530.16460.223-0.07960.11750.53560.12230.198734.68-7.36230.45
41.7711-0.42120.7518.73914.9094.33130.0479-0.59880.20450.49920.092-0.37450.1716-0.4153-0.13990.23810.01840.10820.381-0.08230.11739.82524.18823.726
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA10 - 196
2X-RAY DIFFRACTION2ALLB10 - 196
3X-RAY DIFFRACTION3ALLD-4 - 3
4X-RAY DIFFRACTION4ALLE-6 - 5

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