[English] 日本語
Yorodumi
- PDB-5sww: Crystal Structure of Human APOBEC3A complexed with ssDNA -

+
Open data


ID or keywords:

Loading...

-
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 / 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
APOBEC-like C-terminal domain / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: NaF, PEG3350

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more