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- PDB-6p1s: Post-catalytic nicked complex of human DNA Polymerase Mu with 1-n... -

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Basic information

Entry
Database: PDB / ID: 6p1s
TitlePost-catalytic nicked complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and newly incorporated AMP
Components
  • DNA (5'-D(*CP*GP*GP*CP*(8OG)P*TP*AP*CP*G)-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA-directed DNA/RNA polymerase mu
  • DNA/RNA (5'-D(*CP*GP*TP*A)-R(P*A)-3')
KeywordsTRANSFERASE/DNA / Family X polymerase / NHEJ / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
DNA-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / 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-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / 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 lambda lyase domain superfamily / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / 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
ADENOSINE-5'-TRIPHOSPHATE / : / DNA / DNA/RNA hybrid / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKaminski, A.M. / Pedersen, L.C. / Bebenek, K. / Chiruvella, K.K. / Ramsden, D.A. / Kunkel, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIA ES 102645 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine.
Authors: Kaminski, A.M. / Chiruvella, K.K. / Ramsden, D.A. / Kunkel, T.A. / Bebenek, K. / Pedersen, L.C.
History
DepositionMay 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 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 / 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_alt_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_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_alt_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.pdbx_ptnr1_label_alt_id / _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-directed DNA/RNA polymerase mu
T: DNA (5'-D(*CP*GP*GP*CP*(8OG)P*TP*AP*CP*G)-3')
P: DNA/RNA (5'-D(*CP*GP*TP*A)-R(P*A)-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,30812
Polymers45,3294
Non-polymers9798
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, tetramer consists of one protein molecule (chain A) bound to one DNA duplex comprised of three annealed DNA strands (chains T, P, and D)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-67 kcal/mol
Surface area15620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.880, 68.838, 110.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules TD

#2: DNA chain DNA (5'-D(*CP*GP*GP*CP*(8OG)P*TP*AP*CP*G)-3')


Mass: 2772.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(P*GP*CP*CP*G)-3')


Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein / DNA/RNA hybrid , 2 types, 2 molecules AP

#1: Protein DNA-directed DNA/RNA polymerase mu / Pol Mu / Terminal transferase


Mass: 39844.160 Da / Num. of mol.: 1 / Fragment: residues 134-494
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLM, polmu / Plasmid: pGEXM / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta2 (DE3) / References: UniProt: Q9NP87, DNA-directed DNA polymerase
#3: DNA/RNA hybrid DNA/RNA (5'-D(*CP*GP*TP*A)-R(P*A)-3')


Mass: 1520.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 7 types, 343 molecules

#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsThe authors state that anomalous signal is observed for the metal A site (peak greater than 10 ...The authors state that anomalous signal is observed for the metal A site (peak greater than 10 sigma), though no anomalous scatterers were added to the crystallization or soaking solutions. Therefore, this metal has been modeled as manganese, based on the coordination geometry and interatomic distances.

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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: 2.861 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100mM HEPES pH 7.5, 100mM NaCl, 10% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 27, 2015 / Details: VARIMAX HF
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 46614 / % possible obs: 99.3 % / Redundancy: 12 % / Rpim(I) all: 0.015 / Rrim(I) all: 0.06 / Rsym value: 0.06 / Χ2: 1.025 / Net I/σ(I): 42.2
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 3.26 / Num. unique obs: 2182 / Rpim(I) all: 0.194 / Rrim(I) all: 0.568 / Rsym value: 0.452 / Χ2: 0.68 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M04

4m04


Resolution: 1.75→31.386 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.38
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 2320 4.98 %random
Rwork0.172 ---
obs0.1731 46541 99.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→31.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 368 28 335 3256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093188
X-RAY DIFFRACTIONf_angle_d1.0874415
X-RAY DIFFRACTIONf_dihedral_angle_d9.711661
X-RAY DIFFRACTIONf_chiral_restr0.058478
X-RAY DIFFRACTIONf_plane_restr0.007517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7493-1.7850.25471240.22892455X-RAY DIFFRACTION96
1.785-1.82380.22741330.19892515X-RAY DIFFRACTION97
1.8238-1.86620.22281320.18612530X-RAY DIFFRACTION97
1.8662-1.91280.20451320.17372528X-RAY DIFFRACTION98
1.9128-1.96460.22811370.18222584X-RAY DIFFRACTION100
1.9646-2.02240.2261310.1722581X-RAY DIFFRACTION100
2.0224-2.08760.20371390.17132592X-RAY DIFFRACTION100
2.0876-2.16220.19591370.17052580X-RAY DIFFRACTION100
2.1622-2.24880.21731340.17192612X-RAY DIFFRACTION100
2.2488-2.35110.21511400.17342604X-RAY DIFFRACTION100
2.3511-2.4750.20111390.17582617X-RAY DIFFRACTION100
2.475-2.630.21491380.18512614X-RAY DIFFRACTION100
2.63-2.83290.22031340.19192627X-RAY DIFFRACTION100
2.8329-3.11780.20281400.19262628X-RAY DIFFRACTION100
3.1178-3.56840.18061400.16642660X-RAY DIFFRACTION100
3.5684-4.49370.15331410.14292683X-RAY DIFFRACTION100
4.4937-31.39090.19291490.17162811X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 2.9262 Å / Origin y: -4.3784 Å / Origin z: -11.4618 Å
111213212223313233
T0.1678 Å20.0043 Å20.0041 Å2-0.1696 Å20.0123 Å2--0.1461 Å2
L0.9894 °2-0.2336 °2-0.1327 °2-0.6454 °20.0998 °2--0.516 °2
S0.0543 Å °0.1004 Å °0.0678 Å °-0.0357 Å °-0.0386 Å °-0.0297 Å °0.0164 Å °0.003 Å °0 Å °
Refinement TLS groupSelection details: all

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