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

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Basic information

Entry
Database: PDB / ID: 4xvm
TitleBinary complex of human polymerase nu and DNA with the finger domain closed and thumb domain rotated out
Components
  • DNA (5'-D(*CP*TP*AP*GP*CP*GP*TP*CP*A)-3')
  • DNA (5'-D(*GP*AP*TP*CP*TP*GP*AP*CP*GP*CP*TP*AP*G)-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: 3.2 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 ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
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_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
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
T: DNA (5'-D(*CP*TP*AP*GP*CP*GP*TP*CP*A)-3')
P: DNA (5'-D(*GP*AP*TP*CP*TP*GP*AP*CP*GP*CP*TP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)81,4833
Polymers81,4833
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-7 kcal/mol
Surface area32270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.995, 110.924, 277.418
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 2715.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*AP*TP*CP*TP*GP*AP*CP*GP*CP*TP*AP*G)-3')


Mass: 4006.621 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: 4.63 Å3/Da / Density % sol: 73.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1.5 M Ammonium Sulfate, 100 mM MES

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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: Feb 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 25080 / % possible obs: 98.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 78.78 Å2 / Rmerge(I) obs: 0.098 / Χ2: 1.053 / Net I/av σ(I): 12.966 / Net I/σ(I): 9 / Num. measured all: 131464
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.2-3.265.10.61912121.02998.6
3.26-3.315.30.58612411.03799.2
3.31-3.385.20.44712641.04599.5
3.38-3.455.30.39812291.08100
3.45-3.525.30.34712551.05999.4
3.52-3.65.30.28912451.08199.7
3.6-3.695.30.23112551.08599.6
3.69-3.795.30.212351.06199.4
3.79-3.95.30.16612501.08699.6
3.9-4.035.30.14212711.09499.6
4.03-4.175.30.12212191.05799.3
4.17-4.345.30.112671.04599.2
4.34-4.545.30.09212421.06299.2
4.54-4.785.20.07912741.07499.1
4.78-5.075.30.08212530.98898.8
5.07-5.465.20.09512481.04198.4
5.46-6.015.30.09112631.0698.7
6.01-6.875.20.07412681.09397.8
6.87-8.625.20.04812680.99697.4
8.62-3050.03813210.98395.7

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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

4xvi


Resolution: 3.2→29.699 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2812 1282 5.12 %
Rwork0.2424 23781 -
obs0.2445 25063 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.75 Å2 / Biso mean: 80.5699 Å2 / Biso min: 29.71 Å2
Refinement stepCycle: final / Resolution: 3.2→29.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4952 449 0 0 5401
Num. residues----649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135547
X-RAY DIFFRACTIONf_angle_d1.6837595
X-RAY DIFFRACTIONf_chiral_restr0.108879
X-RAY DIFFRACTIONf_plane_restr0.008889
X-RAY DIFFRACTIONf_dihedral_angle_d18.5182090
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1974-3.32530.3321300.29712526265695
3.3253-3.47640.30851170.27722659277699
3.4764-3.65940.31421330.259726412774100
3.6594-3.88820.3261470.245526392786100
3.8882-4.18760.27081440.23282642278699
4.1876-4.60770.24141580.21772652281099
4.6077-5.27120.26431460.22262648279499
5.2712-6.62890.33171620.29372633279598
6.6289-29.70010.2521450.22092741288697

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