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- PDB-5c53: Probing the Structural and Molecular Basis of Nucleotide Selectiv... -

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Basic information

Entry
Database: PDB / ID: 5c53
TitleProbing the Structural and Molecular Basis of Nucleotide Selectivity by Human Mitochondrial DNA Polymerase gamma
Components
  • DNA (26-MER)
  • DNA (5'-D(*AP*AP*AP*AP*CP*GP*AP*GP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*GP*TP*AP*C)-3')
  • DNA polymerase subunit gamma-1
  • Pol gamma B
Keywordstransferase/dna / Nucleoside reverse transcriptase inhibitors (NRTIs) / HIV reverse transcriptase (RT) / human mitochondrial DNA polymerase / mitochondrial toxicity / drug efficacy and toxicity / TRANSFERASE / transferase-dna complex
Function / homology
Function and homology information


gamma DNA polymerase complex / mitochondrial chromosome / Strand-asynchronous mitochondrial DNA replication / mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / DNA polymerase processivity factor activity ...gamma DNA polymerase complex / mitochondrial chromosome / Strand-asynchronous mitochondrial DNA replication / mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / DNA polymerase processivity factor activity / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / mitochondrial nucleoid / 5'-deoxyribose-5-phosphate lyase activity / base-excision repair, gap-filling / DNA polymerase binding / 3'-5' exonuclease activity / Transcriptional activation of mitochondrial biogenesis / base-excision repair / DNA-templated DNA replication / protease binding / double-stranded DNA binding / in utero embryonic development / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mitochondrial matrix / intracellular membrane-bounded organelle / chromatin binding / protein-containing complex / mitochondrion / DNA binding / identical protein binding / cytoplasm
Similarity search - Function
DNA-directed DNA-polymerase, family A, mitochondria / DNA mitochondrial polymerase, exonuclease domain / POLG2, C-terminal / : / DNA mitochondrial polymerase exonuclease domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Anticodon-binding domain / Anticodon-binding / Anticodon binding domain / DNA polymerase family A ...DNA-directed DNA-polymerase, family A, mitochondria / DNA mitochondrial polymerase, exonuclease domain / POLG2, C-terminal / : / DNA mitochondrial polymerase exonuclease domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Anticodon-binding domain / Anticodon-binding / Anticodon binding domain / DNA polymerase family A / Anticodon-binding domain superfamily / 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 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4Y3 / 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE / DNA / DNA (> 10) / DNA polymerase subunit gamma-1 / DNA polymerase subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human)
DNA launch vector pDE-GFP2 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.567 Å
AuthorsSohl, C.D. / Szymanski, M.R. / Mislak, A.C. / Shumate, C.K. / Amiralaei, S. / Schinazi, R.F. / Anderson, K.S. / Yin, Y.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma.
Authors: Sohl, C.D. / Szymanski, M.R. / Mislak, A.C. / Shumate, C.K. / Amiralaei, S. / Schinazi, R.F. / Anderson, K.S. / Yin, Y.W.
History
DepositionJun 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 2.0Mar 6, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _atom_site.type_symbol / _chem_comp.formula ..._atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase subunit gamma-1
B: Pol gamma B
C: Pol gamma B
T: DNA (26-MER)
P: DNA (5'-D(*AP*AP*AP*AP*CP*GP*AP*GP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*GP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)356,4869
Polymers355,6575
Non-polymers8294
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16300 Å2
ΔGint-71 kcal/mol
Surface area85460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.447, 217.447, 163.593
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein DNA polymerase subunit gamma-1 / Mitochondrial DNA polymerase catalytic subunit / PolG-alpha


Mass: 135989.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLG, MDP1, POLG1, POLGA
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: P54098, DNA-directed DNA polymerase
#2: Protein Pol gamma B


Mass: 102458.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9UHN1*PLUS

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DNA chain , 2 types, 2 molecules TP

#3: DNA chain DNA (26-MER)


Mass: 7955.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA launch vector pDE-GFP2 (others)
#4: DNA chain DNA (5'-D(*AP*AP*AP*AP*CP*GP*AP*GP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*GP*TP*AP*C)-3')


Mass: 6795.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA launch vector pDE-GFP2 (others)

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Non-polymers , 3 types, 4 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-4Y3 / [[(2~{S},5~{R})-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3$l^{4}-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 489.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15FN3O12P3S
#7: Chemical ChemComp-DOC / 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 291.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O6P

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG4000, KCl, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.62→50 Å / Num. obs: 47258 / % possible obs: 100 % / Redundancy: 7.7 % / Net I/σ(I): 2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 3.567→48.909 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3382 1983 4.24 %
Rwork0.2998 --
obs0.3014 46718 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.567→48.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13627 962 48 0 14637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315104
X-RAY DIFFRACTIONf_angle_d0.75120668
X-RAY DIFFRACTIONf_dihedral_angle_d15.1445683
X-RAY DIFFRACTIONf_chiral_restr0.0282225
X-RAY DIFFRACTIONf_plane_restr0.0042474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5665-3.65570.48161390.43393125X-RAY DIFFRACTION99
3.6557-3.75450.44171420.4273191X-RAY DIFFRACTION100
3.7545-3.86490.44631400.41873162X-RAY DIFFRACTION100
3.8649-3.98960.38311410.37793182X-RAY DIFFRACTION100
3.9896-4.13220.39931400.36923162X-RAY DIFFRACTION99
4.1322-4.29750.39851400.36133121X-RAY DIFFRACTION98
4.2975-4.4930.40281340.35283121X-RAY DIFFRACTION98
4.493-4.72970.36071410.32963156X-RAY DIFFRACTION98
4.7297-5.02570.3711430.32393164X-RAY DIFFRACTION99
5.0257-5.41330.30591390.31463187X-RAY DIFFRACTION99
5.4133-5.95720.35871420.32393222X-RAY DIFFRACTION100
5.9572-6.81730.36191450.32343270X-RAY DIFFRACTION100
6.8173-8.58150.33361450.27263282X-RAY DIFFRACTION100
8.5815-48.91320.26941520.22383390X-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)
11.3302-0.08880.39081.0807-0.51463.6638-0.2945-0.04560.43190.48260.1864-0.11780.02580.6276-0.00031.0276-0.0533-0.21811.2862-0.00411.385536.425365.0055-16.8479
20.78860.9169-0.60681.0498-1.45250.4005-0.35710.1438-0.412-0.0312-0.0685-2.1049-0.4329-0.33460.13891.59140.0891-0.54131.5120.09321.3864-9.419144.70153.5709
36.3201-1.00330.81931.2518-0.62710.1703-0.18330.8593-2.4011-0.26060.8018-0.76391.3202-0.39910.09691.7432-0.14580.09761.2134-0.29411.9786-0.457524.4363-22.2998
40.7717-0.3878-0.42381.7511.1355-0.53550.05390.67520.0268-0.1287-0.05710.5012-0.1502-0.22060.02941.30060.026-0.33031.6752-0.04161.353223.964756.0074-35.0487
51.58692.1892-3.35523.1808-4.99288.2030.4042-1.738-0.10721.08730.45481.0406-1.5759-1.85510.67050.71380.045-0.04941.9860.55060.6497-36.952749.0984-11.6339
62.8374-0.24531.59152.6963-0.44981.28080.15750.58110.84560.0215-0.0798-0.6236-0.03030.26830.00281.4782-0.18640.01851.51890.26780.5583-25.431774.6659-10.821
72.3199-0.28220.64133.46650.60770.1292-0.52290.870.3257-0.44260.3289-0.9264-0.34940.44110.00081.46870.04-0.20331.39990.25751.3771-20.296969.7678-18.8522
81.9363-1.0619-1.27750.59640.84311.6774-0.83892.12041.3171-1.35490.41431.3928-0.0932-0.0016-0.00231.5129-0.2438-0.38971.60710.17110.9497-21.712866.9498-26.5255
91.99470.49826.49721.51770.96834.43190.6583-1.82744.15062.4387-1.2428-0.29670.7167-0.37670.00851.9625-0.739-0.66931.47150.48232.7919-16.669193.0248-20.3587
107.4449-0.40161.9821.81170.28456.13050.5862-0.5605-1.21650.4964-0.0661-0.15441.28630.09850.01080.939-0.0209-0.24011.08160.0740.885-22.566952.5143-12.8618
113.3898-1.21870.64652.2512-1.46131.0933-0.25610.2925-2.1386-0.69220.2805-0.60071.0416-0.34880.0071.45410.0682-0.23491.45970.36581.571-24.751643.56699.9878
120.19340.0003-0.6870.2089-0.15982.5566-0.1625-1.64120.98741.0855-0.62840.6462-0.62722.8251-0.05671.3885-0.16670.06251.70520.53182.1671-11.818150.30556.8652
138.51471.25515.84436.0526-4.87999.57580.41670.8739-1.7602-0.9275-0.6687-3.29641.18822.0156-1.06521.6843-0.276-0.8430.87250.50451.9359-27.034494.11921.2087
145.48260.0201-1.37957.13-1.81773.012-1.15641.07752.4748-1.49360.9986-0.3163-0.2895-0.88170.02561.09980.0692-0.41751.2165-0.35381.6769-30.918279.55153.2673
152.6841-0.249-0.43092.2767-0.04131.4473-1.18-1.2033-2.42341.09291.77011.77041.0572-0.17170.15351.50790.2110.48421.82940.02552.695-41.376465.2545-1.1367
164.0418-4.9696-2.34982.00380.58882.97270.9099-0.3634-3.2528-0.6402-1.8207-1.05791.0999-1.928-1.06861.244-0.5182-0.17562.54320.59751.7691-44.192554.2191.762
171.07730.6829-0.74110.9820.11551.0542-0.55720.27141.1754-0.68230.48641.1944-0.6811-0.966-0.00041.72570.2458-0.44591.9537-0.17511.5864-43.836571.60952.5179
183.42240.30672.12893.21993.14653.7827-0.2287-1.80790.03280.1545-0.45981.62350.6611-0.70540.0011.54390.11360.00062.4894-0.36991.5454-44.205370.555512.4297
190.61280.30430.65812.35470.59371.8098-1.0379-0.2937-0.513-0.95680.94240.78020.65240.2958-0.01231.43740.0466-0.18441.7764-0.45341.4809-8.580782.48846.2318
203.0442-2.5866-1.60363.60350.29011.30090.0866-0.41491.5066-0.44010.1274-2.0096-0.6891.08590.05251.3466-0.0467-0.27161.4535-0.24830.9765-6.624683.187910.9174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 78:434 )A78 - 434
2X-RAY DIFFRACTION2( CHAIN A AND RESID 435:590 )A435 - 590
3X-RAY DIFFRACTION3( CHAIN A AND RESID 591:756 )A591 - 756
4X-RAY DIFFRACTION4( CHAIN A AND RESID 757:1228 )A757 - 1228
5X-RAY DIFFRACTION5( CHAIN B AND RESID 68:87 )B68 - 87
6X-RAY DIFFRACTION6( CHAIN B AND RESID 88:205 )B88 - 205
7X-RAY DIFFRACTION7( CHAIN B AND RESID 206:279 )B206 - 279
8X-RAY DIFFRACTION8( CHAIN B AND RESID 280:306 )B280 - 306
9X-RAY DIFFRACTION9( CHAIN B AND RESID 307:333 )B307 - 333
10X-RAY DIFFRACTION10( CHAIN B AND RESID 334:382 )B334 - 382
11X-RAY DIFFRACTION11( CHAIN B AND RESID 383:462 )B383 - 462
12X-RAY DIFFRACTION12( CHAIN B AND RESID 463:485 )B463 - 485
13X-RAY DIFFRACTION13( CHAIN C AND RESID 67:86 )C67 - 86
14X-RAY DIFFRACTION14( CHAIN C AND RESID 87:119 )C87 - 119
15X-RAY DIFFRACTION15( CHAIN C AND RESID 120:186 )C120 - 186
16X-RAY DIFFRACTION16( CHAIN C AND RESID 187:205 )C187 - 205
17X-RAY DIFFRACTION17( CHAIN C AND RESID 206:248 )C206 - 248
18X-RAY DIFFRACTION18( CHAIN C AND RESID 249:353 )C249 - 353
19X-RAY DIFFRACTION19( CHAIN C AND RESID 354:409 )C354 - 409
20X-RAY DIFFRACTION20( CHAIN C AND RESID 410:485 )C410 - 485

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