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- PDB-6p1m: Binary complex of human DNA Polymerase Mu with 1-nt gapped substr... -

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Basic information

Entry
Database: PDB / ID: 6p1m
TitleBinary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG
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 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
BROMIDE ION / CARBON DIOXIDE / : / DNA / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 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.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)45,68616
Polymers45,0004
Non-polymers68612
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, tetramer is one protein molecule (chain A) binding one DNA duplex comprised of DNA strands T, P, and D
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-16 kcal/mol
Surface area15840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.929, 68.263, 110.413
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 , 6 types, 402 molecules

#5: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.835 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 92mM Bis-Tris pH 6.5, 0.276M KBr, 20.7% w/v PolyPure PEGs 0.3-8KDa

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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 92 / Detector: CCD / Date: Mar 23, 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: 1.65→50 Å / Num. obs: 55216 / % possible obs: 99.7 % / Redundancy: 9 % / Rsym value: 0.053 / Χ2: 1.075 / Net I/σ(I): 34.6
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.13 / Num. unique obs: 5329 / Rsym value: 0.38 / Χ2: 1.241 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M04

4m04


Resolution: 1.65→26.127 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.43
RfactorNum. reflection% reflectionSelection details
Rfree0.1898 2755 5 %random
Rwork0.1657 ---
obs0.1669 55124 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→26.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 346 32 390 3292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093112
X-RAY DIFFRACTIONf_angle_d1.0644298
X-RAY DIFFRACTIONf_dihedral_angle_d12.0331018
X-RAY DIFFRACTIONf_chiral_restr0.057470
X-RAY DIFFRACTIONf_plane_restr0.008510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6493-1.67770.24891290.22472455X-RAY DIFFRACTION95
1.6777-1.70820.22561350.1992602X-RAY DIFFRACTION100
1.7082-1.74110.21521360.17732564X-RAY DIFFRACTION100
1.7411-1.77660.22351360.17252604X-RAY DIFFRACTION100
1.7766-1.81520.16261380.16472623X-RAY DIFFRACTION100
1.8152-1.85740.20051350.16832563X-RAY DIFFRACTION100
1.8574-1.90390.19311420.1712604X-RAY DIFFRACTION100
1.9039-1.95530.23061300.17052601X-RAY DIFFRACTION100
1.9553-2.01280.21171400.16692614X-RAY DIFFRACTION100
2.0128-2.07780.18411370.16082603X-RAY DIFFRACTION100
2.0778-2.1520.15621400.15652603X-RAY DIFFRACTION100
2.152-2.23810.19251380.15952615X-RAY DIFFRACTION100
2.2381-2.33990.20611320.16592608X-RAY DIFFRACTION100
2.3399-2.46320.20151430.16722629X-RAY DIFFRACTION100
2.4632-2.61740.19721350.17092631X-RAY DIFFRACTION100
2.6174-2.81930.19361390.17982640X-RAY DIFFRACTION100
2.8193-3.10260.18631430.18592649X-RAY DIFFRACTION100
3.1026-3.55060.17291370.16282658X-RAY DIFFRACTION100
3.5506-4.46970.151440.13932685X-RAY DIFFRACTION100
4.4697-26.13020.21681460.16652818X-RAY DIFFRACTION99
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)
11.0893-0.24050.06870.6142-0.19820.62440.00250.0654-0.1147-0.027-0.0468-0.07930.12380.1496-00.16550.0281-0.00590.1593-0.02660.166912.9143-18.302-14.447
20.09610.00220.07140.58270.08560.38390.01580.04270.0839-0.0926-0.0485-0.1512-0.11550.0512-00.187-0.01870.02580.19830.01770.221616.90988.2525-16.9509
30.82410.0773-0.40430.8058-0.06950.27820.0484-0.10490.12870.1422-0.036-0.063-0.04810.02740.00030.1440.0031-0.00250.1329-0.02190.1581-2.24128.4087-0.113
40.5096-0.0727-0.47620.74780.06570.9401-0.00410.1005-0.0688-0.004-0.02930.09990.0131-0.1458-0.00030.1302-0.0085-0.00970.149-0.01850.1369-10.7852-10.0891-11.1568
50.11540.14870.04920.3868-0.18070.32150.02350.15510.0195-0.1514-0.01420.03870.0019-0.04590.00780.19810.0053-0.02270.2161-0.01780.14050.2444-7.1213-23.161
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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