[English] 日本語
Yorodumi
- PDB-9icg: DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9icg
TitleDNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DCTP (1 MILLIMOLAR) AND ZNCL2 (1 MILLIMOLAR)
Components
  • DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3')
  • DNA (5'-D(*TP*CP*TP*AP*AP*TP*G)-3')
  • PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7))
KeywordsTRANSFERASE/DNA / DNA-DIRECTED DNA POLYMERASE / DNA REPLICATION / DNA REPAIR / NUCLEOTIDYLTRANSFERASE / COMPLEX (NUCLEOTIDYLTRANSFERASE-DNA / TRANSFERASE-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 / 5'-deoxyribose-5-phosphate lyase activity / POLB-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair ...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 / 5'-deoxyribose-5-phosphate lyase activity / POLB-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / PCNA-Dependent Long Patch Base Excision Repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / spindle microtubule / response to gamma radiation / base-excision repair / double-strand break repair via nonhomologous end joining / DNA-templated DNA replication / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / response to ethanol / in utero embryonic development / microtubule / 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
Beta Polymerase; domain 3 / DNA polymerase, thumb domain / 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 ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / 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, thumb domain superfamily / DNA polymerase beta thumb / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase, domain 2 / 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'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 3 Å
AuthorsPelletier, H. / Sawaya, M.R.
Citation
Journal: Biochemistry / Year: 1996
Title: Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis.
Authors: Pelletier, H. / Sawaya, M.R.
#1: Journal: To be Published
Title: Crystal Structures of Human DNA Polymerase Beta Complexed with Nicked and Gapped DNA Substrates
Authors: Sawaya, M.R. / Rawson, T. / Wilson, S.H. / Kraut, J. / Pelletier, H.
#2: Journal: To be Published
Title: The Role of Thumb Movement and Template Bending in Polymerase Fidelity
Authors: Pelletier, H.
#3: Journal: Biochemistry / Year: 1996
Title: Crystal Structures of Human DNA Polymerase Beta Complexed with DNA; Implications for Catalytic Mechanism, Processivity, and Fidelity
Authors: Pelletier, H. / Sawaya, M.R. / Wolfle, W. / Wilson, S.H. / Kraut, J.
#4: Journal: Biochemistry / Year: 1996
Title: A Structural Basis for Metal Ion Mutagenicity and Nucleotide Selectivity in Human DNA Polymerase Beta
Authors: Pelletier, H. / Sawaya, M.R. / Wolfle, W. / Wilson, S.H. / Kraut, J.
#5: Journal: Science / Year: 1994
Title: Polymerase Structures and Mechanism
Authors: Pelletier, H.
#6: Journal: Science / Year: 1994
Title: Structures of Ternary Complexes of Rat DNA Polymerase Beta, a DNA Template- Primer, and ddCTP
Authors: Pelletier, H. / Sawaya, M.R. / Kumar, A. / Wilson, S.H. / Kraut, J.
#7: Journal: Science / Year: 1994
Title: Crystal Structure of Rat DNA Polymerase Beta: Evidence for a Common Polymerase Mechanism
Authors: Sawaya, M.R. / Pelletier, H. / Kumar, A. / Wilson, S.H. / Kraut, J.
History
DepositionDec 15, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Nov 15, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
T: DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3')
P: DNA (5'-D(*TP*CP*TP*AP*AP*TP*G)-3')
A: PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4989
Polymers42,7893
Non-polymers7096
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.890, 57.600, 48.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
DNA chain , 2 types, 2 molecules TP

#1: DNA chain DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3')


Mass: 2434.643 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*CP*TP*AP*AP*TP*G)-3')


Mass: 2112.422 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Protein , 1 types, 1 molecules A

#3: Protein PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7))


Mass: 38241.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P06746

-
Non-polymers , 4 types, 140 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsA POSSIBLE PHYSIOLOGICAL SUBSTRATE FOR POL BETA IS A DNA GAP, WHERE THE LENGTH OF THE GAP CAN RANGE ...A POSSIBLE PHYSIOLOGICAL SUBSTRATE FOR POL BETA IS A DNA GAP, WHERE THE LENGTH OF THE GAP CAN RANGE FROM ONE TO SIX NUCLEOTIDES, AND THE DOWNSTREAM END OF THE DNA GAP IS 5'-PHOSPHORYLATED. IN ORDER TO CREATE VARIOUS GAPPED-DNA SUBSTRATES FOR USE IN POL BETA-DNA CO-CRYSTALLIZATION ATTEMPTS, THE AUTHORS HAD TO ANNEAL THREE DIFFERENT OLIGONUCLEOTIDES TOGETHER PRIOR TO CRYSTALLIZATION: (1) A RELATIVELY LONG (14 TO 20 MER) OLIGONUCLEOTIDE THAT WAS TO SERVE AS THE TEMPLATE, (2) ONE SHORTER (5 OR 6 MER) OLIGONUCLEOTIDE THAT WAS TO SERVE AS THE PRIMER, AND (3) ANOTHER SHORTER (4 TO 10 MER) OLIGONUCLEOTIDE THAT WAS 5'-PHOSPHORYLATED AND WAS TO SERVE AS THE DOWNSTREAM OLIGONUCLEOTIDE. DNA SEQUENCES CORRESPONDING TO THE TEMPLATE, THE PRIMER, AND THE DOWNSTREAM OLIGONUCLEOTIDE FOR THE CRYSTAL STRUCTURE PRESENTED HERE ARE: 5'-CATTAGAAAGGGAAGCGCCG-3' (20-MER), 5'-CGGCGC-3' (6-MER), AND 5'-PO4-TCTAATG-3' (7-MER), RESPECTIVELY, WHERE "5'-PO4" INDICATES THAT THE 5' TERMINUS OF THIS OLIGONUCLEOTIDE IS 5'-PHOSPHORYLATED. HOWEVER, AN UNEXPECTED POL BETA-DNA COMPLEX RESULTED FROM THE CO-CRYSTALLIZATION ATTEMPTS SO THAT WHAT WAS ORIGINALLY INTENDED TO BE THE 5'-PHOSPHORYLATED DOWNSTREAM OLIGONUCLEOTIDE IS BOUND WHERE THE PRIMER STRAND WAS EXPECTED TO BIND (SEE REFERENCE 1). IN ADDITION, A MAJORITY OF THE GAPPED-DNA SUBSTRATE (THAT IS, SIX BASE PAIRS OF TEMPLATE-PRIMER TETHERED TO A FLEXIBLE, SINGLE-STRANDED DNA GAP) IS TOO DISORDERED TO BE OBSERVABLE IN THE CRYSTAL STRUCTURE, ALTHOUGH IT IS NEVERTHELESS THOUGHT TO BE PRESENT IN THE CRYSTAL LATTICE (SEE REFERENCE 1). THE END RESULT IS THAT, ALTHOUGH THE AFOREMENTIONED TEMPLATE IS STILL REFERRED TO AS THE TEMPLATE IN THE STRUCTURES PRESENTED HERE, THE AFOREMENTIONED "DOWNSTREAM OLIGONUCLEOTIDE" IS NOW CALLED THE "PRIMER" -- BY ANALOGY WITH PREVIOUSLY REPORTED POL BETA-DNA-DDCTP TERNARY COMPLEX STRUCTURES (SEE ENTRIES 2BPF AND 2BPG AND REFERENCE 8). ONLY THE DNA NUCLEOTIDES THAT WERE VISIBLE IN THE STRUCTURE ARE INCLUDED IN THE SEQRES SECTION BELOW.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.4 %
Crystal growpH: 6.5
Details: THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE ...Details: THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DCTP, 1 MILLIMOLAR ZNCL2, 1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Mar 10, 1995
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 9273 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rsym value: 5.8
Reflection shellResolution: 3→3.1 Å / Redundancy: 1.6 % / Rsym value: 16.6 / % possible all: 77

-
Processing

Software
NameVersionClassification
TNT5-Drefinement
SDMSdata reduction
SDMSdata scaling
TNTV. 5-Dphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 8ICB

8icb


Resolution: 3→20 Å / σ(F): 0 / Stereochemistry target values: STANDARD TNT /
RfactorNum. reflection% reflection
obs0.161 9273 87 %
Solvent computationSolvent model: MOEWS / Bsol: 830.7 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2623 289 25 134 3071
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01930170.02
X-RAY DIFFRACTIONt_angle_deg340793
X-RAY DIFFRACTIONt_dihedral_angle_d19.41805
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.016730.02
X-RAY DIFFRACTIONt_gen_planes0.0063950.02
X-RAY DIFFRACTIONt_it530176
X-RAY DIFFRACTIONt_nbd0.0191880.02

+
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