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

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Basic information

Entry
Database: PDB / ID: 8fii
TitleWild type APOBEC3A in complex with TT(FdZ)-hairpin inhibitor (crystal form 1)
Components
  • DNA (5'-D(P*GP*CP*GP*CP*TP*TP*(UFP)P*GP*CP*GP*C)-3')
  • DNA dC->dU-editing enzyme APOBEC-3A
KeywordsDNA BINDING PROTEIN / APOBEC / APOBEC3A / A3A / cancer / DNA / 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 / DNA cytosine deamination / cytidine to uridine editing / clearance of foreign intracellular DNA / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / 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 / DNA cytosine deamination / cytidine to uridine editing / clearance of foreign intracellular DNA / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / 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: 2.94 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
E: DNA (5'-D(P*GP*CP*GP*CP*TP*TP*(UFP)P*GP*CP*GP*C)-3')
F: DNA (5'-D(P*GP*CP*GP*CP*TP*TP*(UFP)P*GP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,56813
Polymers52,7724
Non-polymers7969
Water00
1
A: DNA dC->dU-editing enzyme APOBEC-3A
F: DNA (5'-D(P*GP*CP*GP*CP*TP*TP*(UFP)P*GP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7366
Polymers26,3862
Non-polymers3504
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-52 kcal/mol
Surface area10930 Å2
MethodPISA
2
B: DNA dC->dU-editing enzyme APOBEC-3A
E: DNA (5'-D(P*GP*CP*GP*CP*TP*TP*(UFP)P*GP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8317
Polymers26,3862
Non-polymers4455
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-56 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.323, 57.197, 91.422
Angle α, β, γ (deg.)90.000, 99.370, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12E
22F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGASNASNAA10 - 19610 - 196
21ARGARGASNASNBB10 - 19610 - 196
12DGDGDCDCEC-6 - 41 - 11
22DGDGDCDCFD-6 - 41 - 11

NCS ensembles :
ID
1
2

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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(P*GP*CP*GP*CP*TP*TP*(UFP)P*GP*CP*GP*C)-3')


Mass: 3345.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
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: 2.63 Å3/Da / Density % sol: 53.2 % / Description: Flattened needle
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: A3A (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 (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 hexa 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: 2.94→49.05 Å / Num. obs: 11619 / % possible obs: 99 % / Redundancy: 3.9 % / Biso Wilson estimate: 42.3 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.094 / Net I/σ(I): 5.8
Reflection shellResolution: 2.94→3.12 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1817 / CC1/2: 0.918 / Rpim(I) all: 0.338 / % possible all: 97.1

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Processing

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

Resolution: 2.94→48.35 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.851 / SU B: 64.922 / SU ML: 0.589 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.515 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITION
RfactorNum. reflection% reflectionSelection details
Rfree0.3103 567 4.9 %RANDOM
Rwork0.2512 ---
obs0.2542 11041 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.02 Å2 / Biso mean: 54.095 Å2 / Biso min: 34.27 Å2
Baniso -1Baniso -2Baniso -3
1-7.43 Å20 Å26.32 Å2
2---5.56 Å2-0 Å2
3----3.76 Å2
Refinement stepCycle: final / Resolution: 2.94→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 448 37 0 3377
Biso mean--82.66 --
Num. residues----379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123504
X-RAY DIFFRACTIONr_bond_other_d0.0030.0152891
X-RAY DIFFRACTIONr_angle_refined_deg1.781.6564847
X-RAY DIFFRACTIONr_angle_other_deg1.41.5866595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3615352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43120.973185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.63815446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6621525
X-RAY DIFFRACTIONr_chiral_restr0.0990.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023715
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02885
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A52650.16
12B52650.16
21E7690.24
22F7690.24
LS refinement shellResolution: 2.943→3.019 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 46 -
Rwork0.376 754 -
all-800 -
obs--93.79 %
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)
11.0442-0.20290.28640.6625-0.15211.1782-0.04760.06170.04520.03530.0769-0.0488-0.01410.0738-0.02940.2213-0.00740.11820.0213-0.01090.07494.809-0.23641.67
20.73550.16650.21930.92450.24231.0825-0.0219-0.0917-0.03520.00120.0084-0.00550.0494-0.04610.01350.2142-0.00440.11690.02120.00090.064526.591-13.61412.899
30.21710.725-0.61193.3975-2.17781.74940.0112-0.0146-0.02130.0582-0.0378-0.0158-0.05760.04660.02650.08960.0271-0.03560.0275-0.0450.096816.923-6.79828.003
42.14071.7590.67194.82310.36450.6395-0.0792-0.27030.0013-0.04310.11950.17730.137-0.2268-0.04020.1484-0.03430.05070.12330.05080.08656.604-24.50515.99
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 196
2X-RAY DIFFRACTION2B10 - 196
3X-RAY DIFFRACTION3D-6 - 4
4X-RAY DIFFRACTION4E-6 - 4

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