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- PDB-4ycx: Binary complex of human DNA Polymerase Mu with 2-nt gapped DNA su... -

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Basic information

Entry
Database: PDB / ID: 4ycx
TitleBinary complex of human DNA Polymerase Mu with 2-nt gapped DNA substrate
Components
  • DNA (5'-D(*CP*GP*GP*CP*AP*AP*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/DNA / polymerase / DNA repair / NHEJ / 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 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
IMIDAZOLE / DNA / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMoon, A.F. / Gosavi, R.A. / Kunkel, T.A. / Pedersen, L.C. / Bebenek, K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1AIZ ES102645-03 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01 ES065070 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Creative template-dependent synthesis by human polymerase mu.
Authors: Moon, A.F. / Gosavi, R.A. / Kunkel, T.A. / Pedersen, L.C. / Bebenek, K.
History
DepositionFeb 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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*AP*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)45,67310
Polymers45,2814
Non-polymers3936
Water5,242291
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.043, 68.683, 116.830
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 / Fragment: unp residues 134-494
Mutation: deletion of P398-P410, with insertion of a singly glycine residue (labelled G410)
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

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DNA chain , 3 types, 3 molecules TPD

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


Mass: 3054.019 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 , 5 types, 297 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris, 20% PEG 8K, 0.2M MgCl2

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Sep 1, 2012
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 28624 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rsym value: 0.138 / Net I/σ(I): 9.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.94 / Rsym value: 0.494 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LZD

4lzd


Resolution: 2.1→22.47 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1435 5.01 %Random selection
Rwork0.201 ---
obs0.203 27189 99.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→22.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2585 365 25 291 3266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023120
X-RAY DIFFRACTIONf_angle_d0.5654304
X-RAY DIFFRACTIONf_dihedral_angle_d11.876996
X-RAY DIFFRACTIONf_chiral_restr0.023472
X-RAY DIFFRACTIONf_plane_restr0.003503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1023-2.17740.29871400.2522680X-RAY DIFFRACTION99
2.1774-2.26450.29161430.24442685X-RAY DIFFRACTION100
2.2645-2.36750.26381410.23762684X-RAY DIFFRACTION100
2.3675-2.49210.26031410.23812686X-RAY DIFFRACTION100
2.4921-2.6480.31791440.24062702X-RAY DIFFRACTION99
2.648-2.85210.29361420.252708X-RAY DIFFRACTION99
2.8521-3.13850.2711400.23612685X-RAY DIFFRACTION99
3.1385-3.5910.19361450.18442725X-RAY DIFFRACTION100
3.591-4.51820.20121470.16112754X-RAY DIFFRACTION99
4.5182-22.46960.19331520.17042880X-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)
12.5488-0.561-0.15951.914-1.07453.08860.10580.1937-0.1347-0.1492-0.1022-0.16480.20680.33860.00470.23350.0454-0.00390.2026-0.04020.249711.8035-18.8455-14.2578
22.0479-0.4322-1.54762.48541.05673.55320.1979-0.00730.2411-0.27840.0043-0.3551-0.42180.3426-0.17960.282-0.0510.06250.27990.06290.290215.76758.4475-17.2643
35.63470.834-0.24333.901-0.22020.41920.143-0.07760.58330.0495-0.1131-0.0952-0.0994-0.054-0.02530.21950.00870.02260.1991-0.02180.1859-3.96958.6723-1.1224
42.8397-1.16220.18623.0540.98384.04340.06790.193-0.0458-0.1325-0.10890.09-0.0234-0.23570.02460.1551-0.0257-0.00450.16770.0030.1791-11.8176-10.6699-11.3139
51.42690.5097-0.52294.3092-0.31931.21710.08220.30520.1037-0.38530.00670.2991-0.0671-0.1688-0.05320.26130.0211-0.04380.33180.0320.2225-1.3315-6.0461-23.9365
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 137:231 )A137 - 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 1:10 ) OR ( CHAIN D AND RESID 1:4 )P1 - 4
6X-RAY DIFFRACTION5( CHAIN P AND RESID 1:4 ) OR ( CHAIN T AND RESID 1:10 ) OR ( CHAIN D AND RESID 1:4 )T1 - 10
7X-RAY DIFFRACTION5( CHAIN P AND RESID 1:4 ) OR ( CHAIN T AND RESID 1:10 ) OR ( CHAIN D AND RESID 1:4 )D1 - 4

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