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- PDB-4xvk: Binary complex of human polymerase nu and DNA with the finger dom... -

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Basic information

Entry
Database: PDB / ID: 4xvk
TitleBinary complex of human polymerase nu and DNA with the finger domain closed
Components
  • DNA (5'-D(*GP*AP*TP*CP*TP*GP*AP*CP*GP*CP*TP*AP*CP*GP*G)-3')
  • DNA (5'-D(*TP*CP*CP*GP*TP*AP*GP*CP*GP*TP*CP*A)-3')
  • DNA polymerase nu
KeywordsTRANSFERASE/DNA / Pol Nu / Polymerase / error-prone DNA synthesis / TRANSFERASE-DNA complex
Function / homology
Function and homology information


translesion synthesis / interstrand cross-link repair / cyclin binding / Fanconi Anemia Pathway / double-strand break repair via homologous recombination / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding ...translesion synthesis / interstrand cross-link repair / cyclin binding / Fanconi Anemia Pathway / double-strand break repair via homologous recombination / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / nucleus
Similarity search - Function
DNA polymerase nu, pseudo-exo domain / DNA polymerase nu pseudo-exo / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / Ribonuclease H superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase nu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsLee, Y.-S. / Yang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK036146-08 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: How a homolog of high-fidelity replicases conducts mutagenic DNA synthesis.
Authors: Lee, Y.S. / Gao, Y. / Yang, W.
History
DepositionJan 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase nu
P: DNA (5'-D(*GP*AP*TP*CP*TP*GP*AP*CP*GP*CP*TP*AP*CP*GP*G)-3')
T: DNA (5'-D(*TP*CP*CP*GP*TP*AP*GP*CP*GP*TP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2275
Polymers83,0093
Non-polymers2182
Water43224
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-14 kcal/mol
Surface area32050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)290.876, 290.876, 110.161
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-902-

NA

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase nu /


Mass: 74760.141 Da / Num. of mol.: 1 / Fragment: catalytic core (UNP residues 194-859)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLN / Plasmid: pLEXm / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q7Z5Q5, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules PT

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


Mass: 4609.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*CP*CP*GP*TP*AP*GP*CP*GP*TP*CP*A)-3')


Mass: 3638.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 26 molecules

#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 24 / 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: 5.66 Å3/Da / Density % sol: 78.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1.5 M Ammonium Sulfate, 100 mM MES / PH range: 5.9-6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2012
RadiationMonochromator: double crystal-liqued nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. obs: 37343 / % possible obs: 99.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 65.28 Å2 / Rmerge(I) obs: 0.079 / Χ2: 1.008 / Net I/av σ(I): 16.737 / Net I/σ(I): 11.6 / Num. measured all: 175163
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.95-34.30.63718780.98100
3-3.064.30.55418600.97100
3.06-3.114.40.47818821.00299.9
3.11-3.184.50.39518521.01699.9
3.18-3.254.60.29318851.02499.9
3.25-3.324.60.2618691.04100
3.32-3.44.70.20718541.02499.9
3.4-3.54.70.17718861.01999.8
3.5-3.64.80.14418671.00499.7
3.6-3.724.80.12618551.03399.7
3.72-3.854.80.10918880.97999.6
3.85-44.80.0918660.95799.5
4-4.184.80.07718601.01499.4
4.18-4.44.80.06418750.98399
4.4-4.684.80.0618561.08699
4.68-5.044.80.05818641.0698.7
5.04-5.544.80.06218650.99598.4
5.54-6.344.80.05518551.00298.1
6.34-7.964.80.04618660.97497.2
7.96-304.80.02718600.9995.5

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XVI
Resolution: 2.95→29.64 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2411 1889 5.06 %
Rwork0.2221 35444 -
obs0.2231 37333 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.51 Å2 / Biso mean: 75.1607 Å2 / Biso min: 23.48 Å2
Refinement stepCycle: final / Resolution: 2.95→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4971 550 13 24 5558
Biso mean--67.95 52.3 -
Num. residues----657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075692
X-RAY DIFFRACTIONf_angle_d1.0617815
X-RAY DIFFRACTIONf_chiral_restr0.066904
X-RAY DIFFRACTIONf_plane_restr0.007898
X-RAY DIFFRACTIONf_dihedral_angle_d16.9162155
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9421-3.02160.35921560.31642686284298
3.0216-3.11040.31721400.303927352875100
3.1104-3.21070.33441090.283327682877100
3.2107-3.32530.28021510.271927242875100
3.3253-3.45820.27311490.252927392888100
3.4582-3.61530.25871330.240627442877100
3.6153-3.80560.25871690.22827072876100
3.8056-4.04350.27171410.2227442885100
4.0435-4.35480.20011560.18922707286399
4.3548-4.79130.21781610.18642721288299
4.7913-5.48090.23571290.21162728285799
5.4809-6.8910.22931620.23642708287098
6.891-29.64180.19141330.18532733286696

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