[English] 日本語
Yorodumi
- PDB-6btf: DNA Polymerase Beta I260Q Ternary Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6btf
TitleDNA Polymerase Beta I260Q Ternary Complex
Components
  • DNA Downstream Strand
  • DNA Primer Strand
  • DNA Template Strand
  • DNA polymerase beta
KeywordsTRANSFERASE / LYASE/DNA / Lyase / DNA complex / LYASE-DNA complex
Function / homology
Function and homology information


Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity ...Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair, gap-filling / response to gamma radiation / base-excision repair / spindle microtubule / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / response to ethanol / microtubule / in utero embryonic development / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / Ub-specific processing proteases / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family ...DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsEckenroth, B.E. / Doublie, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA080830 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: I260Q DNA polymerase beta highlights precatalytic conformational rearrangements critical for fidelity.
Authors: Liptak, C. / Mahmoud, M.M. / Eckenroth, B.E. / Moreno, M.V. / East, K. / Alnajjar, K.S. / Huang, J. / Towle-Weicksel, J.B. / Doublie, S. / Loria, J.P. / Sweasy, J.B.
History
DepositionDec 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase beta
T: DNA Template Strand
P: DNA Primer Strand
D: DNA Downstream Strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6899
Polymers47,1284
Non-polymers5605
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-72 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.610, 79.879, 55.382
Angle α, β, γ (deg.)90.000, 107.400, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase beta


Mass: 38256.645 Da / Num. of mol.: 1 / Mutation: I260Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 DE3
References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

-
DNA chain , 3 types, 3 molecules TPD

#2: DNA chain DNA Template Strand


Mass: 4274.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA Primer Strand


Mass: 3061.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA Downstream Strand


Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 4 types, 342 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18-20% PEG 3350, 175-250 mM sodium acetate, 50 mM HEPES pH 7.5, 2 mM TCEP, 1% tert-butanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 11, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.75→38 Å / Num. obs: 82376 / % possible obs: 99.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 22.76 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.053 / Rrim(I) all: 0.098 / Net I/σ(I): 12
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 8164 / CC1/2: 0.524 / Rpim(I) all: 0.301 / Rrim(I) all: 0.539 / % possible all: 99.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.59 Å31.32 Å
Translation1.59 Å31.32 Å

-
Processing

Software
NameVersionClassification
PHENIXv1.9-1692refinement
SAINTv2016.9-0data reduction
SADABSv2016.9-0data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FMS

2fms


Resolution: 1.75→37.551 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.94
RfactorNum. reflection% reflection
Rfree0.2138 8300 10.08 %
Rwork0.1749 --
obs0.1788 82376 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.03 Å2 / Biso mean: 31.3994 Å2 / Biso min: 12.1 Å2
Refinement stepCycle: final / Resolution: 1.75→37.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 596 32 337 3430
Biso mean--25.11 40.11 -
Num. residues----346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063216
X-RAY DIFFRACTIONf_angle_d0.9614472
X-RAY DIFFRACTIONf_chiral_restr0.039497
X-RAY DIFFRACTIONf_plane_restr0.004470
X-RAY DIFFRACTIONf_dihedral_angle_d19.4361224
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.76990.40032800.36022378265897
1.7699-1.79070.33873030.32292446274998
1.7907-1.81250.32812910.31632466275799
1.8125-1.83550.32462390.2752473271299
1.8355-1.85960.27542550.258525732828100
1.8596-1.88510.25452850.226924902775100
1.8851-1.9120.25092720.214825032775100
1.912-1.94060.23192830.208524782761100
1.9406-1.97090.27272800.20925392819100
1.9709-2.00320.23283010.20424272728100
2.0032-2.03780.24382720.193225692841100
2.0378-2.07480.23323060.193424322738100
2.0748-2.11470.25072990.187725322831100
2.1147-2.15790.21062820.184524782760100
2.1579-2.20480.23172860.176525292815100
2.2048-2.25610.22592830.178324542737100
2.2561-2.31250.20542870.171425362823100
2.3125-2.3750.22112480.177225042752100
2.375-2.44490.23252570.173125032760100
2.4449-2.52380.22862710.165125462817100
2.5238-2.6140.21972970.180524742771100
2.614-2.71860.22422790.178324812760100
2.7186-2.84230.21882910.179725072798100
2.8423-2.99210.21892600.173925262786100
2.9921-3.17940.20252720.171125292801100
3.1794-3.42480.19682620.15912465272799
3.4248-3.76910.16642870.14152474276199
3.7691-4.31380.16092670.1262410267797
4.3138-5.43240.19382360.14332377261394
5.4324-37.55960.20692690.17591977224680
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)
12.53840.87970.89454.31390.81822.76610.07890.08610.0046-0.0818-0.0157-0.23670.05240.0641-0.03370.17630.02410.00730.197-0.03370.17053.5913-3.141864.8972
21.4517-0.372-0.01422.42321.24131.80010.1021-0.0052-0.0706-0.0070.1209-0.31870.2180.2868-0.23890.18980.023-0.01970.20280.01640.19816.516-4.537570.8331
35.56982.10671.25782.4835-0.38152.02380.1218-0.64010.07940.2999-0.0518-0.3855-0.0738-0.0037-0.08910.13970.0265-0.01990.2032-0.05520.2098-6.82188.12683.5518
41.6435-0.03380.45291.84480.09362.7773-0.0267-0.07410.12390.01580.02870.1907-0.1803-0.3657-0.00860.10410.02170.01070.17870.01510.1544-23.173411.841371.1789
51.45030.0149-0.22941.85890.03322.86140.01890.08450.023-0.1801-0.0285-0.0553-0.11830.02080.01840.0938-0.0014-0.00750.12480.01010.1445-15.36278.492863.0545
62.3770.4364-0.59534.4076-1.18423.4976-0.12820.432-0.0494-0.63740.0016-0.0740.145-0.31060.09230.31480.0023-0.03340.2959-0.01940.1772-16.02285.329348.9238
70.6976-0.07250.03741.2593-0.95220.7316-0.0660.14590.412-0.211-0.046-0.6005-0.27570.2834-0.02910.2487-0.06910.04390.23610.00970.39390.925219.706264.4405
81.5403-0.29470.02818.46060.19591.96550.004-0.2320.3029-0.8789-0.1972-0.527-0.199-0.04760.17160.2668-0.02150.02390.1651-0.05370.3024-0.433223.156868.5808
91.05410.8858-0.61253.6116-2.01122.82780.12540.78890.3223-1.10290.2137-0.34070.29520.15260.09850.5642-0.07640.34210.72080.01810.31458.90620.513749.6911
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 47 )A11 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 126 )A48 - 126
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 151 )A127 - 151
4X-RAY DIFFRACTION4chain 'A' and (resid 152 through 239 )A152 - 239
5X-RAY DIFFRACTION5chain 'A' and (resid 240 through 300 )A240 - 300
6X-RAY DIFFRACTION6chain 'A' and (resid 301 through 335 )A301 - 335
7X-RAY DIFFRACTION7chain 'T' and (resid 3 through 16 )T3 - 16
8X-RAY DIFFRACTION8chain 'P' and (resid 1 through 10 )P1 - 10
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 5 )D1 - 5

+
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://pdbjlvh1.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