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- PDB-6cst: Structure of human DNA polymerase kappa with DNA -

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Basic information

Entry
Database: PDB / ID: 6cst
TitleStructure of human DNA polymerase kappa with DNA
Components
  • DNA (5'-D(P*AP*TP*AP*CP*AP*TP*AP*CP*C)-3')
  • DNA (5'-D(P*TP*AP*CP*TP*GP*GP*TP*AP*TP*GP*TP*AP*T)-3')
  • DNA polymerase kappa
KeywordsREPLICATION / TRANSFERASE/DNA / DNA polymerase kappa / translesion synthesis / DNA replication / TRANSFERASE-DNA complex
Function / homology
Function and homology information


nucleotide-excision repair, DNA gap filling / error-prone translesion synthesis / Translesion synthesis by POLK / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV ...nucleotide-excision repair, DNA gap filling / error-prone translesion synthesis / Translesion synthesis by POLK / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear body / DNA repair / DNA damage response / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
DNA polymerase; domain 1 - #810 / Rad18-like CCHC zinc finger / DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / MutS, DNA mismatch repair protein, domain I ...DNA polymerase; domain 1 - #810 / Rad18-like CCHC zinc finger / DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-DZ4 / IODIDE ION / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / DNA / DNA (> 10) / DNA polymerase kappa
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsJha, V. / Ling, H.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-94590 Canada
CitationJournal: Sci Rep / Year: 2018
Title: 2.0 angstrom resolution crystal structure of human pol kappa reveals a new catalytic function of N-clasp in DNA replication.
Authors: Jha, V. / Ling, H.
History
DepositionMar 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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.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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)143,55147
Polymers139,9356
Non-polymers3,61641
Water8,701483
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.579, 124.630, 165.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22P
13D
23T

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA20 - 51745 - 542
21GLYGLYPROPROBB20 - 51745 - 542
12DADADCDCCC5 - 131 - 9
22DADADCDCPE5 - 131 - 9
13DTDTDTDTDD2 - 141 - 13
23DTDTDTDTTF2 - 141 - 13

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.817381, 0.005808, 0.576068), (0.006596, -0.999978, 0.000723), (0.57606, 0.003209, -0.817401)-112.851097, 57.06332, 355.734009

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase kappa / DINB protein / DINP


Mass: 63287.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLK, DINB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBT6, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules CPDT

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


Mass: 2683.801 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*AP*CP*TP*GP*GP*TP*AP*TP*GP*TP*AP*T)-3')


Mass: 3996.618 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 9 types, 524 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-DZ4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine


Mass: 490.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O11P3
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#11: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 400 and 0.2M ammonium iodide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→44.14 Å / Num. obs: 93082 / % possible obs: 98.3 % / Redundancy: 4.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.079 / Net I/σ(I): 12
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 13313 / CC1/2: 0.88 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2→44.14 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.796 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23416 2327 2.5 %RANDOM
Rwork0.19833 ---
obs0.19923 90700 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.577 Å2
Baniso -1Baniso -2Baniso -3
1-4.99 Å20 Å20 Å2
2---1.65 Å20 Å2
3----3.34 Å2
Refinement stepCycle: 1 / Resolution: 2→44.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6979 898 168 483 8528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0188231
X-RAY DIFFRACTIONr_bond_other_d0.0030.027608
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.86611238
X-RAY DIFFRACTIONr_angle_other_deg1.072317513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7295886
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5424.114316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.035151352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3451555
X-RAY DIFFRACTIONr_chiral_restr0.0950.21227
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028492
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021807
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_it2.6953.9553550
X-RAY DIFFRACTIONr_mcbond_other2.6943.9533549
X-RAY DIFFRACTIONr_mcangle_it4.0365.914431
X-RAY DIFFRACTIONr_mcangle_other4.0365.9124432
X-RAY DIFFRACTIONr_scbond_it3.6144.3454681
X-RAY DIFFRACTIONr_scbond_other3.6144.3454680
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5726.3576807
X-RAY DIFFRACTIONr_long_range_B_refined7.58432.7029703
X-RAY DIFFRACTIONr_long_range_B_other7.54932.5679514
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A6826MEDIUM POSITIONAL0.420.5
1A6826MEDIUM THERMAL6.612
2C282MEDIUM POSITIONAL0.110.5
2C282MEDIUM THERMAL2.362
3D417MEDIUM POSITIONAL0.210.5
3D417MEDIUM THERMAL3.152
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 175 -
Rwork0.301 6498 -
obs--96.15 %

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