[English] 日本語
Yorodumi
- PDB-5c53: Probing the Structural and Molecular Basis of Nucleotide Selectiv... -

+
Open data


ID or keywords:

Loading...

-
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 DNA replication / positive regulation of DNA-directed DNA polymerase activity / single-stranded DNA 3'-5' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA replication proofreading / DNA metabolic process / DNA polymerase processivity factor activity / mitochondrial nucleoid / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases ...gamma DNA polymerase complex / mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / single-stranded DNA 3'-5' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA replication proofreading / DNA metabolic process / DNA polymerase processivity factor activity / mitochondrial nucleoid / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / DNA polymerase binding / 3'-5' exonuclease activity / base-excision repair, gap-filling / base-excision repair / Transcriptional activation of mitochondrial biogenesis / DNA-templated DNA replication / double-stranded DNA binding / protease 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 / : / DNA mitochondrial polymerase exonuclease domain / POLG2, C-terminal / 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 / : / DNA mitochondrial polymerase exonuclease domain / POLG2, C-terminal / 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, conserved site / DNA polymerase family A signature. / Anticodon-binding domain superfamily / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • 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

-
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

Read more