[English] 日本語
Yorodumi
- PDB-6bwy: DNA substrate selection by APOBEC3G -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bwy
TitleDNA substrate selection by APOBEC3G
Components
  • DNA (30-MER)
  • Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
KeywordsHYDROLASE / Deaminase / DNA binding / complex
Function / homology
Function and homology information


: / apolipoprotein B mRNA editing enzyme complex / telomere cap complex / dCTP deaminase activity / chromosome, telomeric repeat region / base conversion or substitution editing / 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 ...: / apolipoprotein B mRNA editing enzyme complex / telomere cap complex / dCTP deaminase activity / chromosome, telomeric repeat region / base conversion or substitution editing / 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 / negative regulation of viral process / cytidine deaminase activity / telomerase inhibitor activity / regulation of telomere maintenance via telomerase / shelterin complex / transposable element silencing / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping / negative regulation of viral genome replication / APOBEC3G mediated resistance to HIV-1 infection / positive regulation of defense response to virus by host / telomere maintenance / antiviral innate immune response / P-body / Vif-mediated degradation of APOBEC3G / defense response to virus / ribonucleoprotein complex / innate immune response / RNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Protection of telomeres protein 1, ssDNA-binding domain / ssDNA-binding domain of telomere protection protein / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 / APOBEC3, cytosine deaminase domain / : / APOBEC/CMP deaminase, zinc-binding ...: / Protection of telomeres protein 1, ssDNA-binding domain / ssDNA-binding domain of telomere protection protein / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 / 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 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / Protection of telomeres protein 1 / DNA dC->dU-editing enzyme APOBEC-3G
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZiegler, S.J. / Buzovetsky, O.
CitationJournal: PLoS ONE / Year: 2018
Title: Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies.
Authors: Ziegler, S.J. / Liu, C. / Landau, M. / Buzovetsky, O. / Desimmie, B.A. / Zhao, Q. / Sasaki, T. / Burdick, R.C. / Pathak, V.K. / Anderson, K.S. / Xiong, Y.
History
DepositionDec 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
I: DNA (30-MER)
C: DNA (30-MER)
D: DNA (30-MER)
F: DNA (30-MER)
A: Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
B: Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
E: Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
G: Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,98027
Polymers205,2948
Non-polymers1,68619
Water1,02757
1
I: DNA (30-MER)
A: Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7697
Polymers51,3232
Non-polymers4455
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-56 kcal/mol
Surface area18300 Å2
MethodPISA
2
C: DNA (30-MER)
G: Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7697
Polymers51,3232
Non-polymers4455
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-12 kcal/mol
Surface area18330 Å2
MethodPISA
3
D: DNA (30-MER)
B: Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6746
Polymers51,3232
Non-polymers3504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-55 kcal/mol
Surface area18420 Å2
MethodPISA
4
F: DNA (30-MER)
E: Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7697
Polymers51,3232
Non-polymers4455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-24 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.072, 79.072, 266.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
12A
22E
13A
23G
14B
24E
15B
25G
16E
26G

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 30 - 381 / Label seq-ID: 7 - 358

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AE
21BF
12AE
22EG
13AE
23GH
14BF
24EG
15BF
25GH
16EG
26GH

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: DNA chain
DNA (30-MER)


Mass: 9357.086 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein
Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion / APOBEC-related cytidine deaminase / ARCD / APOBEC-related protein 9 / ARP-9 / CEM-15 / CEM15 / ...APOBEC-related cytidine deaminase / ARCD / APOBEC-related protein 9 / ARP-9 / CEM-15 / CEM15 / Deoxycytidine deaminase / A3G


Mass: 41966.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast), (gene. exp.) Homo sapiens (human)
Strain: 972 / ATCC 24843 / Gene: pot1, SPAC26H5.06, APOBEC3G, MDS019 / Production host: Escherichia coli (E. coli)
References: UniProt: O13988, UniProt: Q9HC16, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 298 K / Method: batch mode
Details: 100 mM HEPES pH7, 200 mM LiCl, and 20% (w/v) Polyethylene glycol (PEG) 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.501
11-H, K, -L20.499
ReflectionResolution: 2.9→44.19 Å / Num. obs: 35772 / % possible obs: 97.5 % / Redundancy: 3.3 % / CC1/2: 0.7 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.064 / Net I/σ(I): 5.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3545 / Rpim(I) all: 0.539

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IR2, 1QZH

3ir2

1qzh


Resolution: 2.9→44.19 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.923 / SU B: 27.433 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.109
RfactorNum. reflection% reflectionSelection details
Rfree0.28692 1737 5 %RANDOM
Rwork0.23394 ---
obs0.23665 32909 96.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 88.213 Å2
Baniso -1Baniso -2Baniso -3
1-65 Å20 Å20 Å2
2--65 Å20 Å2
3----130 Å2
Refinement stepCycle: 1 / Resolution: 2.9→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11169 577 79 57 11882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01912166
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.89416625
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60851374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40624.144584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.126151913
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8881573
X-RAY DIFFRACTIONr_chiral_restr0.1210.21743
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0219149
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.5816.585520
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.7869.8616886
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.5456.4536646
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined15.64561.16349433
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A108940.1
12B108940.1
21A111180.08
22E111180.08
31A112340.07
32G112340.07
41B110020.1
42E110020.1
51B109400.1
52G109400.1
61E110620.08
62G110620.08
LS refinement shellResolution: 2.901→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 127 -
Rwork0.3 2374 -
obs--94.81 %
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)
10.17850.10230.24751.60230.87232.3093-0.0134-0.1171-0.02720.00140.08640.1369-0.1899-0.0175-0.0730.0221-0.00040.00190.09840.01890.4949151.008168.3825-50.7332
20.77440.3091.37550.73331.12183.612-0.0179-0.03570.01340.0984-0.10280.20030.5123-0.23670.12070.335-0.07090.04770.15940.02740.4517131.858272.4026-20.06
30.3011-0.2696-0.38440.8012-0.16522.63390.10990.1613-0.01870.0281-0.1032-0.1662-0.2622-0.0499-0.00660.07350.07330.00830.1210.01580.449286.712468.4038-2.8963
41.1833-0.43620.5451.0191-0.60821.7609-0.0424-0.1499-0.08450.0611-0.1235-0.11750.2280.11920.16590.05920.01730.03520.06440.06350.5172105.349273.7056-33.1456
50.2712-0.38230.27690.813-0.38412.7702-0.0140.07790.05480.01380.0386-0.1703-0.04430.0592-0.02460.0019-0.00680.01760.1029-0.02430.5066125.5652108.14217.2217
61.5009-0.33911.67351.3882-0.52612.13430.0335-0.0476-0.06170.1064-0.1182-0.10560.1540.09410.08470.10340.01170.06030.16260.02420.4798144.7422112.7116-23.0597
70.25590.29340.03370.9686-0.58932.29220.0694-0.16310.0159-0.0185-0.04650.1648-0.29070.0996-0.02290.1263-0.12590.01170.1842-0.02750.4204110.8425107.8178-40.489
81.1031-0.09670.28651.16080.51323.0302-0.13860.1926-0.1162-0.0019-0.09880.20660.5649-0.02380.23750.1539-0.03150.05670.0422-0.07020.530592.2958112.5379-9.9506
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 194
2X-RAY DIFFRACTION1I1 - 7
3X-RAY DIFFRACTION2A195 - 381
4X-RAY DIFFRACTION3B30 - 194
5X-RAY DIFFRACTION3D1 - 7
6X-RAY DIFFRACTION4B195 - 381
7X-RAY DIFFRACTION5E30 - 194
8X-RAY DIFFRACTION5F1 - 7
9X-RAY DIFFRACTION6E195 - 381
10X-RAY DIFFRACTION7G30 - 194
11X-RAY DIFFRACTION7C1 - 7
12X-RAY DIFFRACTION8G195 - 381

+
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