[English] 日本語
Yorodumi
- PDB-4rpz: Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rpz
TitleHuman DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MgCl2 for 60 s
Components
  • DNA (5'-D(*CP*CP*GP*AP*CP*(8OG)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3')
  • DNA (5'-D(P*GP*TP*CP*GP*G)-3')
  • DNA polymerase beta
KeywordsTRANSFERASE/DNA / X-family / pol beta / 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 / somatic hypermutation of immunoglobulin genes / response to hyperoxia / 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 / PYROPHOSPHATE / DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsVyas, R. / Reed, A.J. / Suo, Z.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography.
Authors: Vyas, R. / Reed, A.J. / Tokarsky, E.J. / Suo, Z.
History
DepositionOct 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_alt_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.ptnr2_auth_asym_id / _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_alt_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_ref_seq_dif.details / _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
A: DNA polymerase beta
D: DNA (5'-D(P*GP*TP*CP*GP*G)-3')
P: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3')
T: DNA (5'-D(*CP*CP*GP*AP*CP*(8OG)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,41417
Polymers49,0304
Non-polymers1,38413
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-145 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.410, 79.320, 55.410
Angle α, β, γ (deg.)90.00, 106.20, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase beta


Mass: 39258.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POL B, POLB / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

-
DNA chain , 3 types, 3 molecules DPT

#2: DNA chain DNA (5'-D(P*GP*TP*CP*GP*G)-3') / 5-mer phosphorylated Downstream Primer


Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3') / 10-mer Primer


Mass: 3350.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*CP*CP*GP*AP*CP*(8OG)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') / 16-mer Template


Mass: 4885.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 6 types, 171 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2
#9: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.19→44.19 Å / Num. obs: 20173 / % possible obs: 97.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 6.4
Reflection shellResolution: 2.19→2.26 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5585 / % possible all: 96.6

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→44.19 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.896 / SU B: 8.412 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 974 4.7 %RANDOM
Rwork0.19545 ---
obs0.19813 19738 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.937 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å20.01 Å2
2--0.09 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.19→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2613 652 75 158 3498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0183534
X-RAY DIFFRACTIONr_bond_other_d0.0010.023008
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.8174859
X-RAY DIFFRACTIONr_angle_other_deg0.84836973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88724.127126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51615516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8011519
X-RAY DIFFRACTIONr_chiral_restr0.0640.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023413
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02788
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_it1.362.6971307
X-RAY DIFFRACTIONr_mcbond_other1.362.6961306
X-RAY DIFFRACTIONr_mcangle_it2.3924.0411633
X-RAY DIFFRACTIONr_mcangle_other2.3914.0431634
X-RAY DIFFRACTIONr_scbond_it1.362.8872227
X-RAY DIFFRACTIONr_scbond_other1.3592.8872226
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2474.3043224
X-RAY DIFFRACTIONr_long_range_B_refined4.02523.3694297
X-RAY DIFFRACTIONr_long_range_B_other3.97423.3584267
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 76 -
Rwork0.288 1441 -
obs--96.56 %

+
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