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- PDB-4ecq: Human DNA polymerase eta- DNA ternary complex: AT crystal at pH6.... -

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Basic information

Entry
Database: PDB / ID: 4ecq
TitleHuman DNA polymerase eta- DNA ternary complex: AT crystal at pH6.8(K+ MES) with 1 Ca2+ ion
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*A)-3')
  • DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')
  • DNA polymerase eta
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


response to UV-C / error-free translesion synthesis / DNA synthesis involved in DNA repair / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH ...response to UV-C / error-free translesion synthesis / DNA synthesis involved in DNA repair / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / response to radiation / HDR through Homologous Recombination (HRR) / site of double-strand break / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA replication / DNA repair / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Ubiquitin-Binding Zinc Finger / DNApol eta/Rev1, HhH motif / DNA polymerase eta, ubiquitin-binding zinc finger / : / Zinc finger UBZ3-type profile. / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain ...Ubiquitin-Binding Zinc Finger / DNApol eta/Rev1, HhH motif / DNA polymerase eta, ubiquitin-binding zinc finger / : / Zinc finger UBZ3-type profile. / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsNakamura, T. / Zhao, Y. / Yang, W.
CitationJournal: Nature / Year: 2012
Title: Watching DNA polymerase eta make a phosphodiester bond
Authors: Nakamura, T. / Zhao, Y. / Yamagata, Y. / Hua, Y.J. / Yang, W.
History
DepositionMar 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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.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.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,8028
Polymers54,9953
Non-polymers8085
Water7,999444
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-45 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.786, 98.786, 82.431
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase eta / RAD30 homolog A / Xeroderma pigmentosum variant type protein


Mass: 48617.707 Da / Num. of mol.: 1 / Fragment: Catalytic core (UNP RESIDUES 1-432)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLH, RAD30, RAD30A, XPV / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q9Y253, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

#2: DNA chain DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')


Mass: 3637.391 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*A)-3')


Mass: 2739.824 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 449 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES, 6-17%(W/V) PEG 2K-MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 72821 / % possible obs: 99.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 15.98 Å2 / Rsym value: 0.058 / Net I/σ(I): 17.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.618 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→24.012 Å / Occupancy max: 1.2 / Occupancy min: 0.1 / FOM work R set: 0.8811 / SU ML: 0.18 / σ(F): 0.05 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2005 5626 7.74 %
Rwork0.1725 --
obs0.1747 72699 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.637 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 153.67 Å2 / Biso mean: 27.27 Å2 / Biso min: 4.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.0362 Å20 Å20 Å2
2---0.0362 Å20 Å2
3---0.0724 Å2
Refinement stepCycle: LAST / Resolution: 1.5→24.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 387 49 444 4246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064116
X-RAY DIFFRACTIONf_angle_d1.1265664
X-RAY DIFFRACTIONf_chiral_restr0.066631
X-RAY DIFFRACTIONf_plane_restr0.005656
X-RAY DIFFRACTIONf_dihedral_angle_d18.1751633
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.51710.28761860.27082202238898
1.5171-1.53490.30581860.259322182404100
1.5349-1.55360.24741670.239822622429100
1.5536-1.57330.26181750.231422552430100
1.5733-1.5940.2881900.223522512441100
1.594-1.61580.23921870.219822012388100
1.6158-1.63890.23232120.208721972409100
1.6389-1.66330.23781870.203422522439100
1.6633-1.68930.23811930.205722472440100
1.6893-1.7170.22771940.189222192413100
1.717-1.74660.19591830.182322482431100
1.7466-1.77840.22332050.180222002405100
1.7784-1.81260.22881890.185122622451100
1.8126-1.84960.21191910.172321962387100
1.8496-1.88980.20672110.167822302441100
1.8898-1.93370.22241760.166422522428100
1.9337-1.9820.1911770.164922692446100
1.982-2.03560.18411860.161522232409100
2.0356-2.09550.17611900.162822472437100
2.0955-2.16310.20461710.155522552426100
2.1631-2.24030.181950.156422412436100
2.2403-2.32990.22051710.163822492420100
2.3299-2.43590.20721910.167822462437100
2.4359-2.56420.2152200.182622192439100
2.5642-2.72460.22141930.18532230242399
2.7246-2.93460.1961670.17812237240499
2.9346-3.22930.1931810.17092262244399
3.2293-3.69520.16871890.146422432432100
3.6952-4.650.15851680.13562272244099
4.65-24.01480.17161950.16492188238395
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)
10.7177-0.376-0.04191.0194-0.19640.58160.02870.0290.0187-0.0649-0.0764-0.22320.04590.04920.00560.0550.0140.01140.0260.01970.077567.7151-5.3069-1.8122
20.12840.06150.04620.290.07810.33090.0312-0.0872-0.01350.0208-0.07990.0207-0.0772-0.00730.00460.09050.00910.00550.06730.00220.054448.363813.493211.0606
30.17370.0364-0.06140.4065-0.11480.5793-0.0429-0.01720.0197-0.06210.00140.07280.1146-0.1154-0.02510.1062-0.0064-0.01530.09630.00030.104251.6681-22.31226.0808
40.4379-0.06290.26461.07370.64590.83390.06570.06450.1233-0.1123-0.24830.22140.0258-0.34770.11010.11050.02010.00840.2128-0.04970.125630.80425.7119-7.7659
50.09310.1043-0.04360.0966-0.0301-0.02290.2838-0.206-0.0574-0.0038-0.319-0.01670.002-0.5012-0.00090.2629-0.053-0.03010.23780.00010.215838.0992-3.0091-0.3953
60.0374-0.04480.05070.0435-0.04040.0236-0.0974-0.2607-0.0994-0.3452-0.0104-0.2118-0.2635-0.191-0.00060.23420.0188-0.05060.1855-0.00720.193735.8892-8.1571-2.8204
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and (resid -2:15 or resid 88:239))A-2 - 15
2X-RAY DIFFRACTION1(chain A and (resid -2:15 or resid 88:239))A88 - 239
3X-RAY DIFFRACTION2(chain A and resid 16:87)A16 - 87
4X-RAY DIFFRACTION3(chain A and resid 240:306)A240 - 306
5X-RAY DIFFRACTION4(chain A and resid 307:432)A307 - 432
6X-RAY DIFFRACTION5(chain T and resid 1:12)T1 - 12
7X-RAY DIFFRACTION6(chain P and resid 1:8)P1 - 8

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