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- PDB-6dia: DNA polymerase beta substrate complex with templating cytosine an... -

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Basic information

Entry
Database: PDB / ID: 6dia
TitleDNA polymerase beta substrate complex with templating cytosine and incoming Fapy-dGTP analog
Components
  • DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
  • DNA (5'-D(P*GP*TP*CP*GP*G)-3')
  • DNA polymerase beta
KeywordsDNA BINDING PROTEIN/DNA / Transferase Activity / DNA BINDING PROTEIN / DNA BINDING PROTEIN-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 / homeostasis of number of cells / pyrimidine dimer 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 / POLB-Dependent Long Patch Base Excision Repair / homeostasis of number of cells / pyrimidine dimer repair / 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 / damaged DNA binding / in utero embryonic development / microtubule / DNA-directed DNA polymerase / 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-GKS / DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.969 Å
AuthorsFreudenthal, B.D. / Smith, M.R. / Wilson, S.H. / Beard, W.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES027558 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition.
Authors: Smith, M.R. / Shock, D.D. / Beard, W.A. / Greenberg, M.M. / Freudenthal, B.D. / Wilson, S.H.
History
DepositionMay 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,35810
Polymers47,6684
Non-polymers6906
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-80 kcal/mol
Surface area20630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.947, 80.584, 55.314
Angle α, β, γ (deg.)90.000, 109.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase beta


Mass: 38241.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Production host: Escherichia coli (E. coli)
References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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DNA chain , 3 types, 3 molecules TPD

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


Mass: 4829.133 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*C)-3')


Mass: 3061.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: 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.) synthetic construct (others)

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Non-polymers , 4 types, 381 molecules

#5: Chemical ChemComp-GKS / 1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol


Mass: 524.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N4O14P3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 mM imidazole, 350 mM sodium chloride, 15% PEG3350, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.97→25 Å / Num. obs: 32111 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.03 / Rrim(I) all: 0.075 / Χ2: 1.743 / Net I/σ(I): 13 / Num. measured all: 188198
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.97-23.30.68615920.6210.4510.8241.391100
2-2.043.50.55216110.6380.3450.6531.564100
2.04-2.083.80.43615710.6980.2590.5091.582100
2.08-2.124.10.40216180.7910.2270.4631.67100
2.12-2.174.50.35615910.8470.1910.4051.669100
2.17-2.224.80.36416130.8790.1880.411.718100
2.22-2.2750.30915910.9240.1540.3461.666100
2.27-2.345.20.30815960.9480.150.3431.63100
2.34-2.45.40.25415980.9650.1210.2821.642100
2.4-2.485.70.23516020.9730.1090.261.565100
2.48-2.576.10.20116030.9810.0890.2211.612100
2.57-2.676.80.17315940.9880.0710.1871.667100
2.67-2.797.30.13516120.9940.0540.1451.689100
2.79-2.947.30.11616050.9960.0460.1251.668100
2.94-3.137.40.08315990.9970.0330.0891.648100
3.13-3.377.50.05816200.9980.0230.0621.847100
3.37-3.77.40.04816110.9990.0190.0522.341100
3.7-4.247.40.03916350.9990.0160.0421.89599.8
4.24-5.337.40.03816080.9990.0150.0411.91799.7
5.33-257.30.03416410.9990.0130.0361.77299.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ISB

3isb


Resolution: 1.969→22.571 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2462 3799 6.2 %
Rwork0.1964 57440 -
obs0.1995 61239 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.52 Å2 / Biso mean: 32.6009 Å2 / Biso min: 12.56 Å2
Refinement stepCycle: final / Resolution: 1.969→22.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2549 629 37 375 3590
Biso mean--37.37 35.98 -
Num. residues----355
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9692-1.99420.37751290.33131809193885
1.9942-2.02040.38481140.30011958207288
2.0204-2.0480.31871410.30452024216590
2.048-2.07730.33461250.27551971209692
2.0773-2.10830.35841440.27522074221894
2.1083-2.14120.34721340.26612047218194
2.1412-2.17630.3241400.24242127226796
2.1763-2.21370.26041440.25182090223497
2.2137-2.2540.28841400.21582108224897
2.254-2.29730.2351360.22782131226797
2.2973-2.34410.26261410.23642136227798
2.3441-2.3950.29991510.22132205235699
2.395-2.45070.31161380.23942157229599
2.4507-2.51190.28041400.22282231237199
2.5119-2.57970.26391410.206821632304100
2.5797-2.65550.24281410.208521722313100
2.6555-2.74110.26051440.20422112355100
2.7411-2.83890.33881400.22942161230199
2.8389-2.95230.33931500.23492179232999
2.9523-3.08640.26031470.232821972344100
3.0864-3.24860.27491490.208622012350100
3.2486-3.45150.19921470.178621602307100
3.4515-3.71690.21141450.164622022347100
3.7169-4.0890.2171460.160821792325100
4.089-4.67610.17481420.1462172231499
4.6761-5.87410.19681490.152321702319100
5.8741-22.5730.18881410.14862205234699

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