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- PDB-4x0q: Ternary complex of human DNA polymerase theta C-terminal domain b... -

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Basic information

Entry
Database: PDB / ID: 4x0q
TitleTernary complex of human DNA polymerase theta C-terminal domain binding ddGTP opposite dCMP
Components
  • DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*G)-3')
  • DNA (5'-D(P*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
  • DNA polymerase theta
KeywordsTransferase/DNA / DNA polymerase / Transferase-DNA complex
Function / homology
Function and homology information


single-stranded DNA endodeoxyribonuclease activity / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / double-strand break repair via alternative nonhomologous end joining / replication fork processing / site of DNA damage / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / negative regulation of double-strand break repair via homologous recombination / error-prone translesion synthesis ...single-stranded DNA endodeoxyribonuclease activity / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / double-strand break repair via alternative nonhomologous end joining / replication fork processing / site of DNA damage / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / negative regulation of double-strand break repair via homologous recombination / error-prone translesion synthesis / DNA helicase activity / base-excision repair / protein homooligomerization / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / double-strand break repair / site of double-strand break / DNA helicase / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA damage response / chromatin binding / Golgi apparatus / magnesium ion binding / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / cytosol
Similarity search - Function
DNA polymerase theta-like, helix-turn-helix domain / : / Helix-turn-helix domain / DNA_pol_Q helicase like region helical domain / Alpha-Beta Plaits - #370 / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain ...DNA polymerase theta-like, helix-turn-helix domain / : / Helix-turn-helix domain / DNA_pol_Q helicase like region helical domain / Alpha-Beta Plaits - #370 / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 5' to 3' exonuclease, C-terminal subdomain / Helicase conserved C-terminal domain / DNA polymerase; domain 1 / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase theta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsZahn, K.E. / Doublie, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA052040 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Human DNA polymerase theta grasps the primer terminus to mediate DNA repair.
Authors: Zahn, K.E. / Averill, A.M. / Aller, P. / Wood, R.D. / Doublie, S.
History
DepositionNov 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Sep 13, 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 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase theta
B: DNA polymerase theta
E: DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*G)-3')
F: DNA (5'-D(P*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
G: DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*G)-3')
H: DNA (5'-D(P*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,18214
Polymers191,7836
Non-polymers1,3998
Water00
1
A: DNA polymerase theta
E: DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*G)-3')
F: DNA (5'-D(P*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5917
Polymers95,8913
Non-polymers7004
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-27 kcal/mol
Surface area33740 Å2
MethodPISA
2
B: DNA polymerase theta
G: DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*G)-3')
H: DNA (5'-D(P*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5917
Polymers95,8913
Non-polymers7004
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-26 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.704, 135.392, 159.819
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase theta / DNA polymerase eta


Mass: 86735.461 Da / Num. of mol.: 2 / Fragment: UNP residues 1815-2590
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLQ, POLH / Plasmid: pSUMO3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: O75417, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules EGFH

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


Mass: 5157.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')


Mass: 3998.595 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 8 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-DG3 / 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3

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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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 2000mme, MPD, potassium chloride, TRIS buffer, glycerol
PH range: 8-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.9→40 Å / Num. obs: 31372 / % possible obs: 85.6 % / Redundancy: 22.6 % / Net I/σ(I): 12.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
DENZOdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XOP

4xop


Resolution: 3.9→29.927 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 40.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3163 1581 5.04 %Random selection
Rwork0.2575 ---
obs0.2605 31372 82.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.9→29.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9926 890 86 0 10902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01411202
X-RAY DIFFRACTIONf_angle_d1.16915284
X-RAY DIFFRACTIONf_dihedral_angle_d18.5154250
X-RAY DIFFRACTIONf_chiral_restr0.0461706
X-RAY DIFFRACTIONf_plane_restr0.0051794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-4.02560.45351070.34991987X-RAY DIFFRACTION60
4.0256-4.16910.37151160.3352109X-RAY DIFFRACTION65
4.1691-4.33560.37151160.28692226X-RAY DIFFRACTION67
4.3356-4.53220.34541270.2912386X-RAY DIFFRACTION72
4.5322-4.77030.33741260.26822466X-RAY DIFFRACTION76
4.7703-5.06780.3861470.27012674X-RAY DIFFRACTION81
5.0678-5.45690.3341580.27692947X-RAY DIFFRACTION90
5.4569-6.00210.36121700.30533225X-RAY DIFFRACTION98
6.0021-6.86150.38391720.28033254X-RAY DIFFRACTION99
6.8615-8.61050.34011710.23513277X-RAY DIFFRACTION99
8.6105-29.92830.19591710.19063240X-RAY DIFFRACTION98
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)
10.53990.7131-0.9031.3621-1.81242.0652-0.09460.3922-0.6336-1.4068-0.037-0.12170.42060.32790.01281.78780.1578-0.07421.0867-0.66991.069121.0249147.42949.8917
20.3677-0.5881-0.36481.06980.01553.43360.00550.0888-0.02-0.0832-0.1950.14331.2828-0.24180.44871.15380.19390.44040.6246-0.92881.3259112.7352143.994225.5981
38.1172.8210.44292.91590.48882.8298-0.5874-2.3994-2.31461.29470.1973-1.4370.11171.29750.0891.18340.37520.03191.94560.17811.5914137.5036132.156652.8357
40.74490.1806-1.25251.92440.02232.2007-0.2338-0.0632-1.2053-0.6406-2.3176-0.7711.22161.80522.18692.530.44960.61851.89190.54613.1575135.9555113.335153.8259
53.910.8906-0.79462.6907-1.24992.26060.4321-0.6164-0.01460.0848-0.16180.0928-0.49610.5156-0.3060.6478-0.1039-0.02091.1013-0.52971.0451125.9817141.85243.1798
62.84571.295-1.33553.7203-0.70273.03450.7398-0.1225-0.17390.4378-0.38430.80990.4695-0.0682-0.34540.76520.08430.06540.7126-0.18051.7788106.0261120.411543.8894
73.23330.18581.02613.3865-0.61980.87480.69850.5927-1.2035-0.36920.3743-0.7793-0.35560.21190.81820.77550.59280.5411-0.0744-1.3151.4807108.2147133.990132.5505
83.7925-0.2873-0.76510.54570.56981.85560.83470.99550.0362-0.9705-0.6813-0.7868-0.9149-0.7897-0.12961.62890.3938-0.23730.848-0.29292.287120.9606161.737131.5176
91.6240.79121.28982.9021-0.55091.5020.2197-1.33690.26381.29830.3650.9725-0.53960.0419-0.43150.70750.03310.14210.9468-0.71731.9779109.2709146.634544.4681
100.67830.602-0.36452.29051.69462.45740.31470.40440.2713-1.525-0.6457-0.65820.4195-0.11390.28711.85250.15620.1541.1065-0.05010.4231117.32655.664110.0144
111.21830.6056-0.09850.93180.50263.42680.39180.2346-0.0138-0.9848-0.3499-0.3101-0.89830.3779-0.67540.73180.60340.34171.0931-0.42750.8919125.718159.042525.7985
120.1672-0.150.64141.1329-1.53583.17460.0217-0.87480.9770.7488-0.38421.1866-1.082-1.44120.40791.3035-0.22230.36631.7083-1.6491.8443100.646571.136452.5013
130.04080.0384-0.05980.8306-0.79860.7569-0.4033-1.27071.19431.2378-1.96441.1728-0.4339-1.51391.7661.7138-0.1317-0.51041.9517-1.00763.1079101.794189.85453.8116
142.76150.00730.90633.5241-1.2471.1618-0.8478-0.5626-0.00730.5502-0.61220.2288-0.1753-0.4148-0.09080.41190.14660.04711.1395-1.21261.0049112.165961.282343.2006
150.86160.0920.67973.74960.19232.1726-0.0213-0.32240.38110.786-0.65020.1871-0.17610.2120.37250.9582-0.06980.0651.0431-0.75092.3412132.102582.736344.1009
164.1140.6162-0.26052.74-0.11072.4960.3053-0.12091.72350.09090.5406-0.26630.43190.3282-0.37741.00390.10450.35740.7557-0.42621.121130.061469.069832.7952
173.9479-0.29410.5113.0786-0.13751.98020.82510.8846-0.7519-1.2097-0.5246-0.38211.70410.3989-0.25681.1434-0.1687-0.22210.8095-0.78071.9651117.376141.306831.6883
181.75460.5361-1.83832.3423-1.15622.28840.0618-1.2440.29290.8209-0.6315-0.63770.61530.05410.03591.19510.0448-0.70790.9693-0.47880.7535128.918256.536344.6419
190.12470.38170.1131.6604-1.21553.79430.6263-0.2352-1.193-0.0802-0.1923-1.19150.75361.4603-0.3591.09470.2095-0.23381.1395-0.55962.889126.2396119.759335.1935
200.66570.8446-0.92725.24754.17779.86180.75810.7068-0.3735-1.67571.2412-0.75761.49270.4119-2.06781.9601-0.2597-0.41261.2714-0.06541.5647127.7813122.804136.8922
210.49210.8559-1.26182.8499-1.65743.40180.80180.27072.18780.0518-0.131.2857-0.1739-0.8405-0.10060.92520.3216-0.17521.1916-0.82132.2272112.047583.371235.0476
222.83721.5644-2.15844.5155-2.2353.15280.3990.2227-0.4238-1.88540.7171.22970.04750.1357-0.37861.46340.0784-0.28580.7159-0.86471.9099110.39880.394236.7368
230.0881-0.22410.17942.32671.3092.1425-0.6007-0.986-0.0528-0.01140.11720.23261.0441-0.00080.61070.80380.35020.19690.7130.11952.235112.3228130.756246.1083
240.39240.0964-0.20111.01670.18140.75560.2297-0.1667-0.01470.2589-0.29550.0375-0.5903-0.0560.18750.96620.0384-0.73420.8876-0.74360.7984126.193372.578245.895
25-0.0258-0.00480.0446-0.0079-0.0021-0.06790.16160.24590.44280.30990.3604-0.020.23930.2956-0.20630.77840.12280.31970.8739-0.47040.792119.721101.832931.5301
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1824:2068 )A1824 - 2068
2X-RAY DIFFRACTION2( CHAIN A AND RESID 2069:2092 )A2069 - 2092
3X-RAY DIFFRACTION3( CHAIN A AND ( RESID 2093:2124 OR RESID 2192:2217 ) )A2093 - 2124
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 2093:2124 OR RESID 2192:2217 ) )A2192 - 2217
5X-RAY DIFFRACTION4( CHAIN A AND RESID 2125:2191 )A2125 - 2191
6X-RAY DIFFRACTION5( CHAIN A AND RESID 2218:2323 )A2218 - 2323
7X-RAY DIFFRACTION6( CHAIN A AND RESID 2332:2459 )A2332 - 2459
8X-RAY DIFFRACTION7( CHAIN A AND RESID 2460:2495 )A2460 - 2495
9X-RAY DIFFRACTION8( CHAIN A AND RESID 2496:2532 )A2496 - 2532
10X-RAY DIFFRACTION9( CHAIN A AND ( RESID 2324:2331 OR RESID 2533:2590 ) )A2324 - 2331
11X-RAY DIFFRACTION9( CHAIN A AND ( RESID 2324:2331 OR RESID 2533:2590 ) )A2533 - 2590
12X-RAY DIFFRACTION10( CHAIN B AND RESID 1824:2068 )B1824 - 2068
13X-RAY DIFFRACTION11( CHAIN B AND RESID 2069:2092 )B2069 - 2092
14X-RAY DIFFRACTION12( CHAIN B AND ( RESID 2093:2124 OR RESID 2192:2217 ) )B2093 - 2124
15X-RAY DIFFRACTION12( CHAIN B AND ( RESID 2093:2124 OR RESID 2192:2217 ) )B2192 - 2217
16X-RAY DIFFRACTION13( CHAIN B AND RESID 2125:2191 )B2125 - 2191
17X-RAY DIFFRACTION14( CHAIN B AND RESID 2218:2323 )B2218 - 2323
18X-RAY DIFFRACTION15( CHAIN B AND RESID 2332:2459 )B2332 - 2459
19X-RAY DIFFRACTION16( CHAIN B AND RESID 2460:2495 )B2460 - 2495
20X-RAY DIFFRACTION17( CHAIN B AND RESID 2496:2532 )B2496 - 2532
21X-RAY DIFFRACTION18( CHAIN B AND ( RESID 2324:2331 OR RESID 2533:2590 ) )B2324 - 2331
22X-RAY DIFFRACTION18( CHAIN B AND ( RESID 2324:2331 OR RESID 2533:2590 ) )B2533 - 2590
23X-RAY DIFFRACTION19( CHAIN E AND RESID 1:13 )E1 - 13
24X-RAY DIFFRACTION20( CHAIN F AND RESID 5:13 )F5 - 13
25X-RAY DIFFRACTION21( CHAIN G AND RESID 1:13 )G1 - 13
26X-RAY DIFFRACTION22( CHAIN H AND RESID 5:13 )H5 - 13
27X-RAY DIFFRACTION23( CHAIN A AND ( RESID 2604:2604 OR RESID 2603:2603 ) )A2604
28X-RAY DIFFRACTION23( CHAIN A AND ( RESID 2604:2604 OR RESID 2603:2603 ) )A2603
29X-RAY DIFFRACTION24( CHAIN B AND ( RESID 2604:2604 OR RESID 2603:2603 ) )B2604
30X-RAY DIFFRACTION24( CHAIN B AND ( RESID 2604:2604 OR RESID 2603:2603 ) )B2603
31X-RAY DIFFRACTION25( CHAIN A AND RESID 2601:2602 ) OR ( CHAIN B AND RESID 2601:2602 )A2601 - 2602
32X-RAY DIFFRACTION25( CHAIN A AND RESID 2601:2602 ) OR ( CHAIN B AND RESID 2601:2602 )B2601 - 2602

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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