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- PDB-4yd1: Ternary complex of human DNA Polymerase Mu with 2-nt gapped DNA s... -

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Basic information

Entry
Database: PDB / ID: 4yd1
TitleTernary complex of human DNA Polymerase Mu with 2-nt gapped DNA substrate and an incoming nonhydrolyzable dUMPNPP
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


somatic hypermutation of immunoglobulin genes / B cell differentiation / 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
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / DNA / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 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 Environmental Health Sciences (NIH/NIEHS)1ZIA 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 18, 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _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 / _struct_conn.ptnr2_symmetry

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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)46,29417
Polymers45,2814
Non-polymers1,01313
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-85 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.259, 69.042, 116.988
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
Mutation: deletion of residues P398-P410, replaced by a single glycine (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 , 7 types, 481 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#9: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris, 20% PEG8K, 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 8, 2012
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 49927 / % possible obs: 99.9 % / Redundancy: 9.2 % / Rsym value: 0.077 / Net I/σ(I): 26.11
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.58 / % possible all: 99.1

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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: 4YCX

4ycx


Resolution: 1.75→24.97 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2497 5 %same as for 4YCX
Rwork0.163 ---
obs0.164 49927 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→24.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2612 365 56 468 3501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093218
X-RAY DIFFRACTIONf_angle_d1.2384449
X-RAY DIFFRACTIONf_dihedral_angle_d14.0161034
X-RAY DIFFRACTIONf_chiral_restr0.059486
X-RAY DIFFRACTIONf_plane_restr0.007519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7489-1.78250.26921330.23362543X-RAY DIFFRACTION98
1.7825-1.81890.26551370.22042608X-RAY DIFFRACTION100
1.8189-1.85840.27291370.22092598X-RAY DIFFRACTION100
1.8584-1.90170.23331370.19992606X-RAY DIFFRACTION100
1.9017-1.94920.21731370.17592626X-RAY DIFFRACTION100
1.9492-2.00190.19831370.1692600X-RAY DIFFRACTION100
2.0019-2.06080.20481430.1672593X-RAY DIFFRACTION100
2.0608-2.12720.18151340.1652637X-RAY DIFFRACTION100
2.1272-2.20320.20581380.15552609X-RAY DIFFRACTION100
2.2032-2.29140.20161370.14972633X-RAY DIFFRACTION100
2.2914-2.39560.1521390.15312636X-RAY DIFFRACTION100
2.3956-2.52180.20541380.16762619X-RAY DIFFRACTION100
2.5218-2.67960.24171390.17712616X-RAY DIFFRACTION99
2.6796-2.88620.21411400.18292659X-RAY DIFFRACTION99
2.8862-3.17610.20341410.17182651X-RAY DIFFRACTION100
3.1761-3.63450.16411390.14352670X-RAY DIFFRACTION100
3.6345-4.57450.13641430.12982697X-RAY DIFFRACTION100
4.5745-24.97420.18771480.1652829X-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)
11.4922-0.1749-0.02481.4161-0.38941.43920.05090.1966-0.1788-0.1315-0.1089-0.13540.18650.30130.05940.1420.0596-0.00130.1627-0.01880.140512.3796-18.7138-14.158
21.8487-0.3844-1.26271.58670.97362.57110.08690.16690.2279-0.3253-0.006-0.3902-0.28340.2652-0.03970.187-0.02470.05070.21510.05430.21615.63968.1073-17.2829
33.08380.0399-0.07332.4783-0.23350.65090.0534-0.04090.24540.0777-0.03160.1203-0.1132-0.055-0.00410.12780.00290.01170.0907-0.01640.0926-3.92088.354-1.8139
42.3395-0.11640.17051.81320.35552.10630.04690.1911-0.0932-0.1047-0.06080.20730.0773-0.16710.00490.0862-0.007-0.0060.0784-0.01030.1013-11.5573-11.0299-11.1775
51.931-0.3591-0.32421.01340.32022.33050.09950.32170.0071-0.296-0.09120.0154-0.0707-0.0518-0.00530.17540.0094-0.010.22770.0110.1017-1.2484-6.5604-23.8428

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