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- PDB-6cto: Ternary complex crystal structure of DNA polymerase Beta with a d... -

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Basic information

Entry
Database: PDB / ID: 6cto
TitleTernary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dTTP analogue
Components
  • DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3')
  • DNA (5'-D(P*GP*TP*CP*GP*G)-3')
  • DNA polymerase beta
Keywordstranscription/dna / DNA Polymerase Beta / Conformational Change / enzyme mechanism / LFER / transcription-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 / POLB-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / homeostasis of number of cells / 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 / POLB-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / response to hyperoxia / lymph node development / salivary gland morphogenesis / somatic hypermutation of immunoglobulin genes / 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 / response to gamma radiation / spindle microtubule / base-excision repair / double-strand break repair via nonhomologous end joining / DNA-templated DNA replication / intrinsic apoptotic signaling pathway in response to DNA damage / neuron apoptotic process / response to ethanol / microtubule binding / in utero embryonic development / DNA-directed DNA polymerase / damaged DNA binding / microtubule / DNA-directed DNA polymerase activity / Ub-specific processing proteases / lyase activity / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / metal ion binding / nucleus / 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, 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
Chem-VT7 / DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsBatra, V.K. / Wilson, S.H.
CitationJournal: Biochemistry / Year: 2018
Title: Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.
Authors: Batra, V.K. / Oertell, K. / Beard, W.A. / Kashemirov, B.A. / McKenna, C.E. / Goodman, M.F. / Wilson, S.H.
History
DepositionMar 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 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 / struct_conn_type
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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
P: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3')
D: DNA (5'-D(P*GP*TP*CP*GP*G)-3')
A: DNA polymerase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,39811
Polymers47,7184
Non-polymers6807
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-91 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.784, 79.168, 55.494
Angle α, β, γ (deg.)90.000, 107.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 3 types, 3 molecules TPD

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


Mass: 4853.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3')


Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*GP*TP*CP*GP*G)-3')


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

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Protein , 1 types, 1 molecules A

#4: Protein DNA polymerase beta


Mass: 38283.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Plasmid: pwl-11 / Production host: Escherichia coli (E. coli) / Strain (production host): tap56
References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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Non-polymers , 5 types, 300 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-VT7 / 5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine


Mass: 516.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17F2N2O13P3 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.22 % / Mosaicity: 1.586 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 16-18% PEG 3350 / PH range: 7.5, 50 mM Imidazole, 350 mM Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.04→20 Å / Num. obs: 23574 / % possible obs: 87.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.068 / Χ2: 1.14 / Net I/σ(I): 9.4 / Num. measured all: 81118
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.04-2.082.40.4385800.835144.7
2.08-2.112.50.3397301.011153.6
2.11-2.152.60.3377961.013160.3
2.15-2.22.70.2949330.894168.5
2.2-2.252.80.2949901.005175.2
2.25-2.32.90.28211231.026183.9
2.3-2.353.10.26411671.031188.5
2.35-2.423.20.2412761.022194.1
2.42-2.493.40.23312631.094196.6
2.49-2.573.50.213131.053197.9
2.57-2.663.70.17913271.058198.7
2.66-2.773.70.14213431.083199
2.77-2.893.80.12113131.103199.2
2.89-3.043.80.09813341.186198.8
3.04-3.233.80.07213321.137199.6
3.23-3.483.80.05513471.302199.3
3.48-3.833.80.04613101.413199.5
3.83-4.383.80.03913521.274199.8
4.38-5.53.80.03813581.17199.7
5.5-203.70.03613871.328199.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FMS

2fms


Resolution: 2.04→19.792 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.14
RfactorNum. reflection% reflection
Rfree0.2319 1999 8.49 %
Rwork0.1788 --
obs0.1832 23556 87.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.66 Å2 / Biso mean: 31.775 Å2 / Biso min: 12.94 Å2
Refinement stepCycle: final / Resolution: 2.04→19.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2612 630 37 293 3572
Biso mean--24.84 35.5 -
Num. residues----357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083407
X-RAY DIFFRACTIONf_angle_d0.9184726
X-RAY DIFFRACTIONf_chiral_restr0.048514
X-RAY DIFFRACTIONf_plane_restr0.005498
X-RAY DIFFRACTIONf_dihedral_angle_d18.9711946
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0358-2.08660.3288680.225373179942
2.0866-2.1430.2738940.24031022111658
2.143-2.2060.34811110.23531197130868
2.206-2.27710.2531270.22641364149179
2.2771-2.35830.28791440.21771553169788
2.3583-2.45260.28571530.2271657181095
2.4526-2.5640.27931590.21751716187598
2.564-2.69880.30151610.21121736189799
2.6988-2.86750.26031630.20641741190499
2.8675-3.08810.24541610.19551741190299
3.0881-3.39740.22341630.17781762192599
3.3974-3.88580.20871640.158817651929100
3.8858-4.88360.18641640.137517701934100
4.8836-19.79290.18931670.148718021969100

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