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- PDB-5w2c: Structure of human DNA polymerase kappa in complex with Lucidin-d... -

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Basic information

Entry
Database: PDB / ID: 5w2c
TitleStructure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and incoming dAMPNPP
Components
  • DNA (5'-D(*CP*TP*AP*TP*(LDG)P*TP*CP*GP*AP*TP*CP*CP*G)-3')
  • DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*C)-3')
  • DNA polymerase kappaPOLK
KeywordsREPLICATION / Translesion synthesis / Lucidin-derived DNA adduct / DNA polymerase kappa / mutagenesis
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 / metal ion binding / nucleus
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 / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / DNA polymerase kappa
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsJha, V.K. / Ling, H.
CitationJournal: Chem. Res. Toxicol. / Year: 2017
Title: Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase kappa.
Authors: Yockey, O.P. / Jha, V. / Ghodke, P.P. / Xu, T. / Xu, W. / Ling, H. / Pradeepkumar, P.I. / Zhao, L.
History
DepositionJun 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
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_conn_type / 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.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 / _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*CP*GP*GP*AP*TP*CP*GP*AP*C)-3')
D: DNA (5'-D(*CP*TP*AP*TP*(LDG)P*TP*CP*GP*AP*TP*CP*CP*G)-3')
P: DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*C)-3')
T: DNA (5'-D(*CP*TP*AP*TP*(LDG)P*TP*CP*GP*AP*TP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,14820
Polymers140,5016
Non-polymers1,64714
Water3,837213
1
A: DNA polymerase kappa
C: DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*C)-3')
D: DNA (5'-D(*CP*TP*AP*TP*(LDG)P*TP*CP*GP*AP*TP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,13611
Polymers70,2513
Non-polymers8858
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA polymerase kappa
P: DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*C)-3')
T: DNA (5'-D(*CP*TP*AP*TP*(LDG)P*TP*CP*GP*AP*TP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0129
Polymers70,2513
Non-polymers7616
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.709, 128.923, 167.705
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

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPPROPRO4AA32 - 51757 - 542
21ASPASPPROPRO4BB32 - 51757 - 542
12DCDCDCDC1CC5 - 131 - 9
22DCDCDCDC1PE5 - 131 - 9
13DCDCDGDG1DD2 - 141 - 13
23DCDCDGDG1TF2 - 141 - 13

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.946093, 0.119845, 0.300906), (0.122457, -0.992421, 0.010239), (0.299853, 0.027161, -0.953599)-8.62291, -69.55007, 83.97646

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 63287.078 Da / Num. of mol.: 2 / Fragment: UNP residues 1-526
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*CP*GP*GP*AP*TP*CP*GP*AP*C)-3')


Mass: 2740.812 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: DNA chain DNA (5'-D(*CP*TP*AP*TP*(LDG)P*TP*CP*GP*AP*TP*CP*CP*G)-3')


Mass: 4222.847 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)

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Non-polymers , 6 types, 227 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: 25-30% PEG400, 0.2M ammonium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50.01 Å / Num. obs: 48405 / % possible obs: 99.5 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Net I/σ(I): 16.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 7002 / CC1/2: 0.937 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementResolution: 2.5→50.01 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 15.336 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R: 0.385 / ESU R Free: 0.263 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25325 1195 2.5 %RANDOM
Rwork0.2111 ---
obs0.21217 47145 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 80.783 Å2
Baniso -1Baniso -2Baniso -3
1-10.98 Å20 Å20 Å2
2---7.69 Å20 Å2
3----3.29 Å2
Refinement stepCycle: 1 / Resolution: 2.5→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6701 932 100 213 7946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0187960
X-RAY DIFFRACTIONr_bond_other_d0.0020.027200
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.8710933
X-RAY DIFFRACTIONr_angle_other_deg1.053316538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.475862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51723.926298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.134151245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3241552
X-RAY DIFFRACTIONr_chiral_restr0.1050.21204
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028276
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021786
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_it4.4788.1283448
X-RAY DIFFRACTIONr_mcbond_other4.4788.1273447
X-RAY DIFFRACTIONr_mcangle_it6.912.1744304
X-RAY DIFFRACTIONr_mcangle_other6.89912.1754305
X-RAY DIFFRACTIONr_scbond_it4.8628.3594512
X-RAY DIFFRACTIONr_scbond_other4.8628.364511
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.65712.3586628
X-RAY DIFFRACTIONr_long_range_B_refined10.33466.0919228
X-RAY DIFFRACTIONr_long_range_B_other10.33666.0969197
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A6522medium positional0.340.5
22A285tight thermal2.970.5
33C439tight thermal4.30.5
11D6522medium thermal6.162
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 87 -
Rwork0.4 3455 -
obs--99.41 %

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