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- PDB-6p1p: Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-n... -

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Basic information

Entry
Database: PDB / ID: 6p1p
TitlePre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and bound incoming dCMPNPP
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


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
Chem-0KX / DNA / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 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)46,05914
Polymers45,0004
Non-polymers1,06010
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, tetramer is comprised of one protein molecule (chain A) bound to one DNA duplex comprised of three DNA strands (chains T, P, and D)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-40 kcal/mol
Surface area15980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.940, 68.608, 110.282
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, 379 molecules

#5: Chemical ChemComp-0KX / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine


Mass: 466.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17N4O12P3 / 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.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / 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.: 369 / 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: 2.847 Å3/Da / Density % sol: 56.8 %
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 3, 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: 1.75→50 Å / Num. obs: 46401 / % possible obs: 99.1 % / Redundancy: 12.8 % / Rpim(I) all: 0.012 / Rrim(I) all: 0.053 / Rsym value: 0.051 / Χ2: 1.153 / Net I/σ(I): 49.2
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.34 / Num. unique obs: 2044 / Rpim(I) all: 0.171 / Rrim(I) all: 0.308 / Rsym value: 0.254 / Χ2: 0.751 / % possible all: 89.1

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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: 1.75→25.08 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.44
RfactorNum. reflection% reflectionSelection details
Rfree0.184 2310 4.99 %random
Rwork0.1645 ---
obs0.1655 46304 98.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→25.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2554 346 53 369 3322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093198
X-RAY DIFFRACTIONf_angle_d1.0864433
X-RAY DIFFRACTIONf_dihedral_angle_d9.7891677
X-RAY DIFFRACTIONf_chiral_restr0.059483
X-RAY DIFFRACTIONf_plane_restr0.007521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7466-1.78220.26291110.23362206X-RAY DIFFRACTION86
1.7822-1.8210.20921280.20062470X-RAY DIFFRACTION95
1.821-1.86330.20361370.18392577X-RAY DIFFRACTION100
1.8633-1.90990.18081360.17222573X-RAY DIFFRACTION100
1.9099-1.96150.21361340.17072594X-RAY DIFFRACTION100
1.9615-2.01920.21051380.16782596X-RAY DIFFRACTION100
2.0192-2.08440.1971360.16842571X-RAY DIFFRACTION100
2.0844-2.15880.17351380.16812605X-RAY DIFFRACTION100
2.1588-2.24520.16291340.16352581X-RAY DIFFRACTION100
2.2452-2.34730.20641390.16732617X-RAY DIFFRACTION100
2.3473-2.4710.17811390.16442607X-RAY DIFFRACTION100
2.471-2.62560.20031360.17762613X-RAY DIFFRACTION100
2.6256-2.82810.20181340.18412616X-RAY DIFFRACTION100
2.8281-3.11220.1891430.18192627X-RAY DIFFRACTION100
3.1122-3.56150.16311380.15922658X-RAY DIFFRACTION100
3.5615-4.48290.14581420.13642676X-RAY DIFFRACTION100
4.4829-25.08270.2021470.15742807X-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)
11.0023-0.2999-0.01731.099-0.35891.21280.00490.11-0.1709-0.0669-0.0786-0.1030.16340.19180.06940.2060.02730.00130.2031-0.02620.208412.6227-18.6391-14.532
21.0004-0.3765-0.45170.75580.87181.33890.0910.08460.1805-0.2276-0.0003-0.2701-0.21390.1313-0.06750.2413-0.01620.04760.23450.02880.296317.08338.075-16.7087
31.5986-0.024-0.28731.19830.27640.36510.0425-0.090.2550.1124-0.0282-0.0482-0.0968-0.0009-0.00530.192-0.00040.00160.1832-0.01370.1921-1.86329.0071-0.4977
41.19110.1717-0.19011.16760.37451.1944-0.00240.2077-0.1061-0.0899-0.04210.19810.0455-0.18120.03940.1839-0.0089-0.01110.201-0.01420.1913-10.9216-10.2628-11.0675
50.3576-0.20970.03710.92780.09050.78330.07120.265-0.0552-0.2022-0.07870.05850.0749-0.0798-0.00040.24140.0012-0.01290.2792-0.01160.1810.2535-7.0616-23.0726
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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