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- PDB-5sww: Crystal Structure of Human APOBEC3A complexed with ssDNA -

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Basic information

Entry
Database: PDB / ID: 5sww
TitleCrystal Structure of Human APOBEC3A complexed with ssDNA
Components
  • DNA 15-Mer
  • DNA dC->dU-editing enzyme APOBEC-3A
KeywordsHydrolase/DNA / APOBEC3A / Cytidine deaminase / Hydrolase-DNA complex
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
: / APOBEC3, cytosine deaminase domain / : / 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 / DNA (> 10) / DNA dC->dU-editing enzyme APOBEC-3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.151 Å
AuthorsShi, K. / Banerjee, S. / Kurahashi, K. / Aihara, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118000 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B.
Authors: Shi, K. / Carpenter, M.A. / Banerjee, S. / Shaban, N.M. / Kurahashi, K. / Salamango, D.J. / McCann, J.L. / Starrett, G.J. / Duffy, J.V. / Demir, O. / Amaro, R.E. / Harki, D.A. / Harris, R.S. / Aihara, H.
History
DepositionAug 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: DNA dC->dU-editing enzyme APOBEC-3A
D: DNA dC->dU-editing enzyme APOBEC-3A
E: DNA 15-Mer
F: DNA 15-Mer
G: DNA 15-Mer
H: DNA 15-Mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,17716
Polymers112,5478
Non-polymers6308
Water28816
1
A: DNA dC->dU-editing enzyme APOBEC-3A
E: DNA 15-Mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2944
Polymers28,1372
Non-polymers1582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-44 kcal/mol
Surface area10680 Å2
MethodPISA
2
B: DNA dC->dU-editing enzyme APOBEC-3A
F: DNA 15-Mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4786
Polymers28,1372
Non-polymers3424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-42 kcal/mol
Surface area10430 Å2
MethodPISA
3
C: DNA dC->dU-editing enzyme APOBEC-3A
G: DNA 15-Mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2023
Polymers28,1372
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-41 kcal/mol
Surface area11010 Å2
MethodPISA
4
D: DNA dC->dU-editing enzyme APOBEC-3A
H: DNA 15-Mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2023
Polymers28,1372
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-40 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.148, 90.199, 167.257
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

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


Mass: 23468.553 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3A / Production host: Escherichia coli (E. coli)
References: UniProt: P31941, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: DNA chain
DNA 15-Mer


Mass: 4668.103 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.02 Å3/Da / Density % sol: 59.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: NaF, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 24189 / % possible obs: 100 % / Redundancy: 5.5 % / Rsym value: 0.191 / Net I/σ(I): 8.4
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.44 / CC1/2: 0.69 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(dev_2499: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XXO Chain A

4xxo


Resolution: 3.151→47.424 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.263 2017 8.35 %
Rwork0.2097 --
obs0.2141 24164 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.151→47.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6085 468 28 16 6597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026821
X-RAY DIFFRACTIONf_angle_d0.4559317
X-RAY DIFFRACTIONf_dihedral_angle_d16.7893849
X-RAY DIFFRACTIONf_chiral_restr0.039946
X-RAY DIFFRACTIONf_plane_restr0.0031130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1511-3.22990.38381380.30571543X-RAY DIFFRACTION99
3.2299-3.31720.32271410.28441542X-RAY DIFFRACTION100
3.3172-3.41480.3651390.27921549X-RAY DIFFRACTION100
3.4148-3.5250.29981390.24131548X-RAY DIFFRACTION99
3.525-3.65090.28451460.2311590X-RAY DIFFRACTION100
3.6509-3.7970.2471410.22591568X-RAY DIFFRACTION100
3.797-3.96980.27111420.20481574X-RAY DIFFRACTION100
3.9698-4.17890.24531410.19661550X-RAY DIFFRACTION100
4.1789-4.44060.22961460.16151573X-RAY DIFFRACTION100
4.4406-4.78310.21891430.16541590X-RAY DIFFRACTION100
4.7831-5.26390.26411470.16911589X-RAY DIFFRACTION100
5.2639-6.02430.24831460.19691609X-RAY DIFFRACTION100
6.0243-7.5850.24991490.22921620X-RAY DIFFRACTION100
7.585-47.42960.25091590.21261702X-RAY DIFFRACTION99
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)
17.4888-0.01322.77467.2179-3.68973.4342-0.44340.65710.07030.45750.04160.02720.28340.66380.40090.60950.00180.05020.3554-0.08280.389847.746105.494918.8631
27.503-1.5208-5.28321.60041.16023.7567-1.3327-1.5261-0.59970.54110.5828-0.23070.68521.5123-0.20121.36460.08320.23320.1531-0.21330.586255.7896.055129.4831
37.2006-3.58455.77448.0038-1.9435.24730.88180.8482-1.9558-0.79170.82710.87321.6588-0.3948-0.99141.5497-0.50.05170.7999-0.14080.885733.090394.372511.3406
41.5331.1587-0.56190.94540.26727.41740.0076-0.3515-0.4341-0.4434-0.3216-0.48751.79220.89120.11481.3786-0.04680.06590.2572-0.11150.482647.838292.190328.6585
54.4377-0.118-0.2381.53680.00253.4098-0.2345-0.00260.0695-0.07970.15720.20951.0398-0.285-0.01170.7931-0.157-0.01130.2269-0.02920.405441.62104.234827.7938
65.23495.9344-4.77618.112-5.01584.40950.0352-0.04610.33930.9843-0.00690.665-0.9276-0.66950.02150.45550.1027-0.05770.5421-0.10010.579836.9471115.614132.3417
77.8785-2.3366-4.1266.84623.55518.96560.19670.29720.20.5627-0.4625-0.09420.37860.26930.18340.1929-0.0575-0.09870.56210.03570.448474.8657132.678923.0465
80.6723-0.50061.18883.9561-5.79188.87980.08860.0052-0.4542-0.5019-0.8603-0.56542.0691.17690.02490.2768-0.0058-0.06931.08450.08710.703384.3191124.535412.3602
96.6967-1.1052-0.29622.9889-0.48953.73390.56410.39381.40640.590.4027-1.1902-0.36321.6929-0.36020.4617-0.4365-0.21031.4347-0.00030.53887.6682142.142725.0848
102.84132.34921.86072.7652-0.88548.7727-0.61350.214-0.4393-0.25030.4533-0.56341.15971.88790.10760.45370.0342-0.04491.23080.00380.447387.0931130.14569.1647
111.6845-0.03820.31445.0356-0.21453.55670.17740.00560.16820.046-0.1687-0.0059-0.30550.9032-0.04580.2134-0.145-0.06020.7304-0.01260.355776.118138.754814.0094
124.02793.5238-5.59656.1431-3.92478.58330.33710.8650.36070.1388-0.3254-0.0531-0.9245-1.5876-0.06510.5750.0744-0.09250.555-0.00540.448664.7766143.53739.4297
136.96732.25184.57482.03770.91137.42130.27790.3548-0.0891-0.0210.7549-0.32940.92541.61840.21370.63590.4113-0.13672.3249-0.01010.325282.6101134.32753.4762
144.60630.79450.11490.362-0.30846.15640.0601-0.6081-0.45050.16690.4326-0.3843-0.02362.2793-0.52810.53510.0618-0.02871.0285-0.13640.394672.2678133.349552.414
159.7776-7.6351-6.58316.01935.19734.7532-0.5685-2.51572.14610.70671.7549-1.4861-0.5222.3181-1.24790.9573-0.2016-0.09631.1881-0.35890.825471.7597143.396962.679
163.67221.1371-3.2297.62263.26165.9507-0.0149-0.5294-2.32053.09520.5594-0.62120.93231.558-0.31390.87550.2643-0.34821.02080.1961.234370.011115.345359.7167
173.17041.38520.36515.76411.74275.5641-0.1045-0.32220.37090.53450.23960.30760.28961.1177-0.0420.32570.0360.05220.5309-0.04180.412763.44134.12854.9218
180.023-0.11350.0110.5601-0.03150.0061-0.0007-0.5950.66-0.17410.7218-0.643-0.86482.0499-0.47220.5713-0.52180.17892.4138-0.30140.371183.4862139.424144.2213
199.03780.3891-5.20392.38550.27233.0391-0.32921.34870.6583-0.5370.22120.47350.015-0.10710.19530.481-0.1246-0.02890.5043-0.04260.454261.5474135.328238.2985
200.6226-0.87371.04226.5841.38033.08930.3356-0.14460.55690.70280.1151-0.2858-2.68140.3027-0.41611.3989-0.19370.09310.5135-0.00520.559146.7008166.742411.0845
214.96844.4081-5.0926.569-3.27767.26951.295-0.24240.95840.8862-0.14380.8826-2.5698-0.7154-1.00530.96880.32490.07060.82120.04720.543536.0396162.059221.2451
222.16993.2938-3.81227.5836-4.64887.352.0224-2.2567-0.36511.1289-1.2078-1.3395-1.05621.6065-0.76590.9605-0.2635-0.10840.9171-0.15720.814365.1571160.153717.8336
234.169-0.9937-0.55923.7291-0.46233.2670.4121-0.4334-0.17130.2669-0.20990.4983-1.47750.1794-0.07640.70030.03390.07380.30520.01050.378445.6117156.025711.8706
242.9538-2.77431.71674.046-4.6077.09530.5640.5713-0.2563-0.8192-0.79790.92880.3359-0.32930.20410.44970.1260.10050.468-0.07760.468645.0285151.8395-3.4657
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 70 )
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 96 )
5X-RAY DIFFRACTION5chain 'A' and (resid 97 through 178 )
6X-RAY DIFFRACTION6chain 'A' and (resid 179 through 305 )
7X-RAY DIFFRACTION7chain 'B' and (resid 10 through 39 )
8X-RAY DIFFRACTION8chain 'B' and (resid 40 through 56 )
9X-RAY DIFFRACTION9chain 'B' and (resid 57 through 82 )
10X-RAY DIFFRACTION10chain 'B' and (resid 83 through 96 )
11X-RAY DIFFRACTION11chain 'B' and (resid 97 through 178 )
12X-RAY DIFFRACTION12chain 'B' and (resid 179 through 305 )
13X-RAY DIFFRACTION13chain 'C' and (resid 8 through 21 )
14X-RAY DIFFRACTION14chain 'C' and (resid 22 through 40 )
15X-RAY DIFFRACTION15chain 'C' and (resid 41 through 56 )
16X-RAY DIFFRACTION16chain 'C' and (resid 57 through 70 )
17X-RAY DIFFRACTION17chain 'C' and (resid 71 through 165 )
18X-RAY DIFFRACTION18chain 'C' and (resid 166 through 178 )
19X-RAY DIFFRACTION19chain 'C' and (resid 179 through 305 )
20X-RAY DIFFRACTION20chain 'D' and (resid 8 through 40 )
21X-RAY DIFFRACTION21chain 'D' and (resid 41 through 56 )
22X-RAY DIFFRACTION22chain 'D' and (resid 57 through 70 )
23X-RAY DIFFRACTION23chain 'D' and (resid 71 through 178 )
24X-RAY DIFFRACTION24chain 'D' and (resid 179 through 305 )

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