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- PDB-5vzh: Post-catalytic complex of human Polymerase Mu (W434H) mutant with... -

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Basic information

Entry
Database: PDB / ID: 5vzh
TitlePost-catalytic complex of human Polymerase Mu (W434H) mutant with incoming UTP
Components
  • DNA (5'-D(*CP*GP*GP*CP*AP*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*U)-3')
KeywordsTRANSFERASE/DNA / Family X DNA polymerase / nonhomologous end-joining / DNA double strand break repair / ribonucleotide incorporation / 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 / nucleus / metal ion binding
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
GLYCOLIC ACID / URIDINE 5'-TRIPHOSPHATE / DNA / DNA/RNA hybrid / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMoon, A.F. / Pryor, J.M. / Ramsden, D.A. / Kunkel, T.A. / Bebenek, K. / Pedersen, L.C.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIA ES 102645 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01 ES065070 United States
American Cancer SocietyPF-14-0438-01-DMC United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA097096 United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu.
Authors: Moon, A.F. / Pryor, J.M. / Ramsden, D.A. / Kunkel, T.A. / Bebenek, K. / Pedersen, L.C.
History
DepositionMay 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
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_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_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_conn.ptnr2_label_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_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*AP*TP*AP*CP*G)-3')
P: DNA/RNA (5'-D(*CP*GP*TP*A)-R(P*U)-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,99012
Polymers45,2264
Non-polymers7658
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-66 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.637, 68.722, 109.404
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*AP*TP*AP*CP*G)-3')


Mass: 2740.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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.) synthetic construct (others)

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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: 39796.094 Da / Num. of mol.: 1 / Fragment: UNP residues 134-494 / Mutation: W434H
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) / References: UniProt: Q9NP87, DNA-directed DNA polymerase
#3: DNA/RNA hybrid DNA/RNA (5'-D(*CP*GP*TP*A)-R(P*U)-3')


Mass: 1496.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 7 types, 266 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#9: Chemical ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID


Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O3
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsAnomalous signal is observed at one position in this structure--at the metal occupying the HhH2 ...Anomalous signal is observed at one position in this structure--at the metal occupying the HhH2 site (peak greater than 6.5 sigma). No known anomalous scatterers were added, so this position has been putatively modeled as sodium (in the HhH2 site), which is consistent with its identity in other reported structures

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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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 90mM HEPES pH 7.5, 18% PEG4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 7, 2017 / Details: VariMax HF
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 33554 / % possible obs: 100 % / Redundancy: 7 % / Rpim(I) all: 0.023 / Rsym value: 0.065 / Χ2: 0.974 / Net I/σ(I): 22.7
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.01 / Num. unique obs: 1620 / CC1/2: 0.771 / Rpim(I) all: 0.332 / Rsym value: 0.613 / Χ2: 0.736 / % possible all: 99.9

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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: 1.95→45.042 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 20.14
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 1649 5 %random
Rwork0.1789 ---
obs0.1805 32953 98.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→45.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 350 43 258 3153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073190
X-RAY DIFFRACTIONf_angle_d0.8194436
X-RAY DIFFRACTIONf_dihedral_angle_d12.4081005
X-RAY DIFFRACTIONf_chiral_restr0.043488
X-RAY DIFFRACTIONf_plane_restr0.005518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9497-2.0070.26091140.22782175X-RAY DIFFRACTION84
2.007-2.07180.27051360.20862527X-RAY DIFFRACTION96
2.0718-2.14590.23721340.19962611X-RAY DIFFRACTION99
2.1459-2.23180.22621380.17822607X-RAY DIFFRACTION100
2.2318-2.33330.21531390.1812627X-RAY DIFFRACTION100
2.3333-2.45630.22471380.18542635X-RAY DIFFRACTION100
2.4563-2.61020.22041380.1922611X-RAY DIFFRACTION100
2.6102-2.81170.24571410.19482647X-RAY DIFFRACTION100
2.8117-3.09460.21921370.1922667X-RAY DIFFRACTION100
3.0946-3.54230.20011430.16632665X-RAY DIFFRACTION100
3.5423-4.46230.15521410.14712701X-RAY DIFFRACTION100
4.4623-45.05370.20581500.1782831X-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)
11.3652-0.43530.24951.378-0.12941.77380.08220.2364-0.1757-0.1148-0.1229-0.12280.19050.30770.00350.15380.0505-0.00330.1456-0.04220.121312.9077-18.7988-14.526
20.3683-0.1555-0.25190.79040.55690.70650.24010.29050.45-0.367-0.0146-0.4848-0.38990.13150.08110.23190.00130.12760.24790.10730.342917.06597.9652-17.126
31.8307-0.1001-0.3991.7290.34580.49690.1437-0.17520.54470.1271-0.0937-0.199-0.134-0.0518-0.02420.1393-0.01380.0340.1048-0.04190.1755-2.18058.7186-0.5538
40.93930.0709-0.66871.40230.34121.07590.06850.3498-0.1841-0.1099-0.08090.2168-0.0046-0.2369-0.02070.09550.0077-0.01350.128-0.02330.0853-11.0254-10.3923-11.1875
50.48540.1568-0.0970.4560.11240.39620.03580.3818-0.015-0.3393-0.01290.0702-0.041-0.03160.03020.21860.039-0.02240.2655-0.0440.09480.6007-8.8663-23.2273
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 138:231
2X-RAY DIFFRACTION2chain A and resid 232:289
3X-RAY DIFFRACTION3chain A and resid 290:423
4X-RAY DIFFRACTION4chain A and resid 424:494
5X-RAY DIFFRACTION5chain T or chain P or chain D

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