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- PDB-6nkr: Ternary complex crystal structure of K289M variant of DNA polymer... -

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Basic information

Entry
Database: PDB / ID: 6nkr
TitleTernary complex crystal structure of K289M variant of DNA polymerase Beta with dGTP
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*(DOC))-3')
  • DNA (5'-D(P*GP*TP*CP*GP*G)-3')
  • DNA polymerase beta
Keywordstranscription/dna / DNA Polymerase Beta / Conformational Change / enzyme mechanism / K289M / LFER / TRANSCRIPTION / 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 / 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 / in utero embryonic development / DNA-directed DNA polymerase / microtubule / damaged DNA binding / 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
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsBatra, V.K. / Wilson, S.H.
CitationJournal: Biochemistry / Year: 2020
Title: Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography.
Authors: Batra, V.K. / Alnajjar, K.S. / Sweasy, J.B. / McKenna, C.E. / Goodman, M.F. / Wilson, S.H.
History
DepositionJan 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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 / 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_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.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
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*(DOC))-3')
T: DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,32511
Polymers47,6544
Non-polymers6717
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-93 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.531, 80.125, 55.267
Angle α, β, γ (deg.)90.000, 108.140, 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: 38243.688 Da / Num. of mol.: 1 / Mutation: K289M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Plasmid: pGEx4T3 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
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 DPT

#2: 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)
#3: 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)
#4: 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.) Homo sapiens (human)

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Non-polymers , 5 types, 74 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.28 Å3/Da / Density % sol: 46.08 % / Mosaicity: 2.227 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 13, 2017 / Details: Viramax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 15467 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Χ2: 1.393 / Net I/σ(I): 11.1 / Num. measured all: 55431
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.45-2.492.80.7287500.818194.5
2.49-2.543.10.6097640.786198.8
2.54-2.593.30.617450.813199.3
2.59-2.643.50.5687800.894199.9
2.64-2.73.60.5037550.8611100
2.7-2.763.60.4327850.8731100
2.76-2.833.60.4317710.9651100
2.83-2.93.70.3497781.0791100
2.9-2.993.70.2717650.9911100
2.99-3.093.70.27731.0651100
3.09-3.23.70.1247711.0571100
3.2-3.323.70.0787731.21100
3.32-3.483.70.0637841.3721100
3.48-3.663.70.0587841.4821100
3.66-3.893.70.0637742.4641100
3.89-4.193.70.0497651.643199.4
4.19-4.613.70.0527903.008199.6
4.61-5.283.70.0447571.568199.5
5.28-6.653.70.0447931.7481100
6.65-503.60.0368102.608199.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2fms

2fms


Resolution: 2.45→31.853 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.09
RfactorNum. reflection% reflection
Rfree0.2897 1529 10.02 %
Rwork0.2074 --
obs0.2155 15262 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.21 Å2 / Biso mean: 50.7388 Å2 / Biso min: 28.38 Å2
Refinement stepCycle: final / Resolution: 2.45→31.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2603 628 37 67 3335
Biso mean--40.41 45.99 -
Num. residues----357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093387
X-RAY DIFFRACTIONf_angle_d1.0454697
X-RAY DIFFRACTIONf_chiral_restr0.052513
X-RAY DIFFRACTIONf_plane_restr0.006495
X-RAY DIFFRACTIONf_dihedral_angle_d19.4951931
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.446-2.52490.39131330.28641187132093
2.5249-2.61510.36161370.27271239137699
2.6151-2.71970.3851400.30221254139499
2.7197-2.84340.50721360.36951229136597
2.8434-2.99320.48951370.34771220135796
2.9932-3.18060.36141400.28231252139299
3.1806-3.42590.28271400.222912641404100
3.4259-3.77020.28081410.182712701411100
3.7702-4.31460.26381380.18161254139298
4.3146-5.43160.25881410.16611251139298
5.4316-31.85610.18351460.140513131459100

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