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- PDB-2xgq: Structure of yeast DNA polymerase eta in complex with C8-N-acetyl... -

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Basic information

Entry
Database: PDB / ID: 2xgq
TitleStructure of yeast DNA polymerase eta in complex with C8-N-acetyl-2- aminoanthracene containing DNA
Components
  • 5'-D(*CP*8AG*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'
  • 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'
  • DNA POLYMERASE ETA
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / TRANSLESION DNA SYNTHESIS / DNA-BINDING / DNA DAMAGE
Function / homology
Function and homology information


Translesion Synthesis by POLH / Termination of translesion DNA synthesis / mitotic sister chromatid cohesion / error-free translesion synthesis / error-prone translesion synthesis / replication fork / chromosome segregation / response to radiation / site of double-strand break / DNA-directed DNA polymerase ...Translesion Synthesis by POLH / Termination of translesion DNA synthesis / mitotic sister chromatid cohesion / error-free translesion synthesis / error-prone translesion synthesis / replication fork / chromosome segregation / response to radiation / site of double-strand break / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA replication / mitochondrion / zinc ion binding / nucleus
Similarity search - Function
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 ...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
DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSchneider, S. / Schorr, S. / Carell, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Mechanism of Replication Blocking and Bypass of Y-Family Polymerase Eta by Bulky Acetylaminofluorene DNA Adducts.
Authors: Schorr, S. / Schneider, S. / Lammens, K. / Hopfner, K.P. / Carell, T.
History
DepositionJun 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 8, 2017Group: Advisory / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 2.0May 15, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Polymer sequence
Category: database_PDB_caveat / entity_poly ...database_PDB_caveat / entity_poly / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _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
B: DNA POLYMERASE ETA
P: 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'
Q: 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'
T: 5'-D(*CP*8AG*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'
U: 5'-D(*CP*8AG*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,34813
Polymers134,0686
Non-polymers2817
Water1,856103
1
B: DNA POLYMERASE ETA
Q: 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'
U: 5'-D(*CP*8AG*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1947
Polymers67,0343
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-65.2 kcal/mol
Surface area26640 Å2
MethodPISA
2
A: DNA POLYMERASE ETA
P: 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'
T: 5'-D(*CP*8AG*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1546
Polymers67,0343
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-56.9 kcal/mol
Surface area26380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.525, 103.525, 292.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DNA POLYMERASE ETA / RADIATION-SENSITIVE PROTEIN 30


Mass: 60708.648 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-513
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PDEST007 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q04049, DNA-directed DNA polymerase
#2: DNA chain 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'


Mass: 2835.871 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*8AG*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'


Mass: 3489.419 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-513 WITH N-TERMINAL STREP-TAG

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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: 3.04 Å3/Da / Density % sol: 57.59 % / Description: NONE
Crystal growpH: 7.6
Details: 4MG/ML,11-14% PEG3350, 0.15-0.2M CACL2, 0.1M CTP, pH 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.919
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 44732 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 52.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 23
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WTF

2wtf


Resolution: 2.7→46.3 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.871 / SU B: 29.165 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.7 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. OCCUPANCY OF DISORDERED ATOMS WAS SET TO ZERO AND DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.26366 2233 5 %RANDOM
Rwork0.21713 ---
obs0.21951 42326 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.033 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---0.46 Å20 Å2
3---0.91 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8116 826 7 103 9052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229102
X-RAY DIFFRACTIONr_bond_other_d0.0010.026023
X-RAY DIFFRACTIONr_angle_refined_deg1.4182.08512466
X-RAY DIFFRACTIONr_angle_other_deg2.169314735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.16551025
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43224.729351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.863151498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0761539
X-RAY DIFFRACTIONr_chiral_restr0.0760.21390
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029469
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021689
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8471.55081
X-RAY DIFFRACTIONr_mcbond_other0.0381.52065
X-RAY DIFFRACTIONr_mcangle_it1.52128203
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.30334021
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.264.54259
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 168 -
Rwork0.31 3059 -
obs--99.35 %
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)
10.3712-0.3283-0.37533.31322.08581.43860.0550.03560.0442-0.0562-0.15260.1690.0043-0.1680.09770.1241-0.03650.01020.1847-0.01610.1409-4.275-12.158441.8841
22.31451.0510.01862.4046-1.37391.4288-0.1405-0.27940.3020.28010.09960.1612-0.0906-0.27720.04090.12940.00790.02710.2165-0.14070.1798-8.275510.61357.2576
30.0148-0.0117-0.00572.8622.15041.61850.05710.02230.0165-0.30410.0767-0.2211-0.21410.0324-0.13380.1662-0.00770.04260.1478-0.0270.19152.5641-7.219539.7509
42.61920.1049-1.73731.33790.79651.7958-0.1177-0.2769-0.39880.08120.0018-0.28310.25740.1720.11590.1960.00150.00970.09780.00530.2065.3737-37.955734.2965
50.38840.3373-0.07991.10010.39790.3196-0.0371-0.0840.02950.1160.0350.07070.08770.01880.00210.1538-0.0131-0.00220.17140.01730.1471-8.7213-22.659343.1741
61.4161-1.8069-0.06454.0385-1.83683.90860.16560.23920.2148-0.2676-0.01780.1171-0.1216-0.1473-0.14770.1121-0.043-0.07760.1770.12960.2343-26.84-10.268525.1446
70.73920.21620.28150.1865-0.01730.2022-0.03280.06530.1663-0.0879-0.0166-0.02560.07570.01570.04930.08540.0150.00990.17420.01530.2886-3.278910.71534.1787
85.6944-0.0528-0.89134.32922.57134.9960.53570.26660.5011-0.7182-0.3501-0.8462-0.36650.4493-0.18550.18910.10530.14810.18720.19440.45443.149227.031130.0283
93.3313-3.4722-0.49746.14911.61630.62920.23220.19320.8809-0.5537-0.1094-0.5718-0.0769-0.0087-0.12280.1408-0.0338-0.08650.03130.11480.4363-3.768224.051332.2962
100.4943-1.3355-0.75064.89582.27431.18750.0339-0.06520.0485-0.10650.0229-0.055-0.04420.0706-0.05690.1130.0155-0.01020.1929-0.00180.192624.6993-20.732726.5573
114.1023-0.34521.54040.0801-0.3051.31-0.03640.18580.0891-0.0555-0.0756-0.01040.15510.12960.1120.17650.04280.02680.15-0.03010.149532.816-44.11169.8699
120.1914-0.0378-0.16893.24122.58762.4394-0.00940.0381-0.00120.0297-0.13740.18520.0966-0.05140.14680.09650.0296-0.00730.1946-0.01560.174420.4807-35.444317.4453
130.8002-0.3949-0.7361.28441.95493.00350.0215-0.56220.24750.26530.1417-0.06890.37380.3291-0.16320.1246-0.04940.02410.4388-0.12180.197521.3893-7.74645.9608
140.62130.1854-0.51541.660.46680.6718-0.0854-0.11070.00990.06760.1555-0.21150.12420.1767-0.07010.08880.0362-0.03870.2262-0.0330.213132.9976-18.463829.6172
155.5231-2.84740.4254.28161.90065.90160.20320.68060.2789-0.6653-0.0393-0.4426-0.71520.3641-0.16390.2508-0.12610.0670.23230.05570.103737.1861-4.86657.29
161.7954-0.0626-0.2951.07350.74063.43330.01970.38230.2573-0.52170.06630.0037-0.7104-0.192-0.0860.30270.0050.02830.14750.12950.140827.0298-6.84459.0816
170.35120.1714-0.36320.9820.50993.36720.01620.0198-0.0410.03010.08570.0435-0.12670.1011-0.10190.15080.00480.02410.1935-0.0140.135810.8797-37.0451.7439
181.1028-0.9726-0.84562.28891.83153.105-0.01140.0597-0.12130.0014-0.06940.1633-0.1485-0.24060.08080.14580.02090.01150.22110.01230.10297.8965-36.8561-9.0559
191.45163.4588-0.76938.3712-1.26474.694-0.0123-0.08350.184-0.1626-0.04520.5607-0.50690.5160.05750.2088-0.0512-0.07440.17910.13260.2393-15.708114.6424.0189
208.0901-2.55098.26595.7119-3.03778.48540.32710.1341-0.72590.40470.52270.70710.35630.0757-0.84980.1895-0.0222-0.04050.18080.06060.1945-13.0743.962336.2745
2111.37171.3393-3.88667.09321.35891.8494-0.7650.3684-0.5044-0.23030.6871-0.26130.11250.13730.07790.2968-0.1105-0.07370.2996-0.06480.094118.3961-22.52-9.9267
224.00722.7526-8.122.5757-5.277716.5987-0.1083-0.32420.12630.20950.06360.65760.4140.83770.04470.34490.09460.16940.52830.2440.518128.7544-23.02084.8864
234.292-0.7806-1.67261.50193.801911.76180.236-0.18910.9726-0.09610.10350.01790.1127-0.646-0.33950.1127-0.1169-0.04550.30380.14870.3703-13.934110.585241.9057
2414.9968-2.507611.74610.5908-2.681412.22310.42950.1121-0.1675-0.13750.12630.11870.6254-0.5078-0.55580.2333-0.0534-0.11060.24580.01130.1202-14.95327.661821.7862
2513.9161-7.35927.3475.1134-3.80753.88620.81481.2535-0.87710.0769-0.39280.09150.41830.6542-0.4220.2640.1128-0.17180.3578-0.06230.214524.5868-30.51171.9866
264.07071.4603-5.38624.14-9.031624.45410.578-0.16690.10.13590.06390.7706-0.40371.2679-0.64190.37-0.0083-0.0360.39940.30750.391918.1154-14.8869-7.9403
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 62
2X-RAY DIFFRACTION2A63 - 124
3X-RAY DIFFRACTION3A125 - 168
4X-RAY DIFFRACTION4A169 - 210
5X-RAY DIFFRACTION5A211 - 304
6X-RAY DIFFRACTION6A305 - 373
7X-RAY DIFFRACTION7A374 - 452
8X-RAY DIFFRACTION8A453 - 489
9X-RAY DIFFRACTION9A490 - 509
10X-RAY DIFFRACTION10B-1 - 50
11X-RAY DIFFRACTION11B51 - 101
12X-RAY DIFFRACTION12B102 - 170
13X-RAY DIFFRACTION13B171 - 209
14X-RAY DIFFRACTION14B210 - 304
15X-RAY DIFFRACTION15B305 - 353
16X-RAY DIFFRACTION16B354 - 389
17X-RAY DIFFRACTION17B390 - 441
18X-RAY DIFFRACTION18B442 - 509
19X-RAY DIFFRACTION19P5 - 9
20X-RAY DIFFRACTION20P10 - 13
21X-RAY DIFFRACTION21Q5 - 9
22X-RAY DIFFRACTION22Q10 - 13
23X-RAY DIFFRACTION23T4 - 9
24X-RAY DIFFRACTION24T10 - 14
25X-RAY DIFFRACTION25U5 - 10
26X-RAY DIFFRACTION26U11 - 14

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