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- PDB-6p1n: Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-n... -

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Basic information

Entry
Database: PDB / ID: 6p1n
TitlePre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and bound incoming dAMPNPP
Components
  • DNA (5'-D(*CP*GP*GP*CP*(8OG)P*TP*AP*CP*G)-3')
  • DNA (5'-D(*CP*GP*TP*A)-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA-directed DNA/RNA polymerase mu
KeywordsTRANSFERASE / Family X polymerase / NHEJ
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 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 / 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
Chem-DZ4 / DNA / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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-directed DNA/RNA polymerase mu
T: DNA (5'-D(*CP*GP*GP*CP*(8OG)P*TP*AP*CP*G)-3')
P: DNA (5'-D(*CP*GP*TP*A)-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,99513
Polymers45,0004
Non-polymers9959
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, tetramer is comprised of one protein molecule (chain) bound to a duplex DNA substrate comprised of three DNA strands (chains T, P, and D)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-60 kcal/mol
Surface area15900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.926, 68.772, 110.609
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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Protein , 1 types, 1 molecules A

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


Mass: 39844.160 Da / Num. of mol.: 1
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

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DNA chain , 3 types, 3 molecules TPD

#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)
#3: DNA chain DNA (5'-D(*CP*GP*TP*A)-3')


Mass: 1190.830 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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Non-polymers , 7 types, 392 molecules

#5: Chemical ChemComp-DZ4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine


Mass: 490.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O11P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.862 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% w/v 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 6, 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: 1.6→50 Å / Num. obs: 60668 / % possible obs: 99.6 % / Redundancy: 3.1 % / Rpim(I) all: 0.015 / Rrim(I) all: 0.059 / Rsym value: 0.057 / Χ2: 1.117 / Net I/σ(I): 96.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.1 % / Num. unique obs: 2842 / Rpim(I) all: 0.212 / Rrim(I) all: 0.403 / Rsym value: 0.339 / Χ2: 0.712 / % possible all: 94

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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: 1.6→26.659 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.45
RfactorNum. reflection% reflectionSelection details
Rfree0.1866 3027 5 %random
Rwork0.165 ---
obs0.1661 60585 99.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→26.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2549 346 49 383 3327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123184
X-RAY DIFFRACTIONf_angle_d1.2384416
X-RAY DIFFRACTIONf_dihedral_angle_d9.5541675
X-RAY DIFFRACTIONf_chiral_restr0.075483
X-RAY DIFFRACTIONf_plane_restr0.009517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6250.24511160.20562227X-RAY DIFFRACTION86
1.625-1.65170.19291350.18512551X-RAY DIFFRACTION99
1.6517-1.68010.20391360.17062623X-RAY DIFFRACTION100
1.6801-1.71070.18871370.17042595X-RAY DIFFRACTION100
1.7107-1.74360.22691350.17452569X-RAY DIFFRACTION100
1.7436-1.77920.19741380.18022613X-RAY DIFFRACTION100
1.7792-1.81790.20561380.17362632X-RAY DIFFRACTION100
1.8179-1.86010.20181380.1692609X-RAY DIFFRACTION100
1.8601-1.90660.20671380.16432612X-RAY DIFFRACTION100
1.9066-1.95820.19731360.17192592X-RAY DIFFRACTION100
1.9582-2.01580.20481340.16932629X-RAY DIFFRACTION100
2.0158-2.08080.19181420.16432629X-RAY DIFFRACTION100
2.0808-2.15510.16751400.1642616X-RAY DIFFRACTION100
2.1551-2.24140.19841350.16422617X-RAY DIFFRACTION100
2.2414-2.34330.19271410.16682633X-RAY DIFFRACTION100
2.3433-2.46680.19071380.16592644X-RAY DIFFRACTION100
2.4668-2.62120.1951400.1782622X-RAY DIFFRACTION100
2.6212-2.82340.20581360.18062660X-RAY DIFFRACTION100
2.8234-3.10720.18861410.18082660X-RAY DIFFRACTION100
3.1072-3.55590.17431420.15652676X-RAY DIFFRACTION100
3.5559-4.47660.14711420.14052710X-RAY DIFFRACTION100
4.4766-26.6630.19861490.16682839X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7141-0.29720.36550.7161-0.26240.66520.0330.1275-0.1295-0.0278-0.078-0.08920.12580.1688-00.21280.0340.00140.2219-0.02630.213612.8393-18.653-14.579
20.2190.02530.02390.30660.07140.19660.0790.09720.1847-0.0897-0.0285-0.236-0.16870.052700.2374-0.00010.06540.25070.05110.315117.03788.1993-16.9609
30.8576-0.0858-0.08070.5254-0.16170.16270.0991-0.09850.260.1181-0.0602-0.0551-0.0424-0.02660.00050.2022-0.00250.01540.1831-0.02180.2323-2.11638.9875-0.594
40.5246-0.0813-0.28190.760.28480.81750.01480.1586-0.06280.0157-0.05150.13440.009-0.131400.1763-0.0056-0.00910.2044-0.01080.1862-11.0572-10.3689-11.3049
50.21020.01290.09250.3443-0.25450.22890.06250.240.0502-0.1587-0.01630.0158-0.0234-0.08540.00840.26780.0112-0.00160.3128-0.01580.18140.2683-7.1731-23.1572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 138:231 )A138 - 231
2X-RAY DIFFRACTION2( CHAIN A AND RESID 232:289 )A232 - 289
3X-RAY DIFFRACTION3( CHAIN A AND RESID 290:423 )A290 - 423
4X-RAY DIFFRACTION4( CHAIN A AND RESID 424:494 )A424 - 494
5X-RAY DIFFRACTION5( CHAIN P AND RESID 1:4 ) OR ( CHAIN T AND RESID 1:9 ) OR ( CHAIN D AND RESID 1:4 )P1 - 4
6X-RAY DIFFRACTION5( CHAIN P AND RESID 1:4 ) OR ( CHAIN T AND RESID 1:9 ) OR ( CHAIN D AND RESID 1:4 )T1 - 9
7X-RAY DIFFRACTION5( CHAIN P AND RESID 1:4 ) OR ( CHAIN T AND RESID 1:9 ) OR ( CHAIN D AND RESID 1:4 )D1 - 4

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