[English] 日本語
Yorodumi
- PDB-8udk: Human Mitochondrial DNA Polymerase gamma R853A Ternary Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8udk
TitleHuman Mitochondrial DNA Polymerase gamma R853A Ternary Complex
Components
  • (DNA polymerase subunit gamma- ...) x 2
  • DNA (24-MER)
  • DNA (28-MER)
  • DNA (5'-D(P*AP*AP*GP*GP*GP*CP*CP*TP*AP*TP*AP*AP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*TP*TP*AP*TP*AP*GP*GP*CP*CP*CP*TP*T)-3')
KeywordsTRANSFERASE/DNA / Mitochondrial / DNA Polymerase / 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 / Transcriptional activation of mitochondrial biogenesis / base-excision repair / 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 / Anticodon binding domain / Anticodon-binding domain superfamily / DNA-directed DNA polymerase, family A, conserved site ...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 / Anticodon binding domain / 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 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase subunit gamma-1 / DNA polymerase subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.43 Å
AuthorsPark, J. / Herrmann, G.K. / Yin, Y.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI134611 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM145925 United States
CitationJournal: Sci Adv / Year: 2024
Title: An interaction network in the polymerase active site is a prerequisite for Watson-Crick base pairing in Pol γ.
Authors: Joon Park / Geoffrey K Herrmann / Arkanil Roy / Christie K Shumate / G Andrés Cisneros / Y Whitney Yin /
Abstract: The replication accuracy of DNA polymerase gamma (Pol γ) is essential for mitochondrial genome integrity. Mutation of human Pol γ arginine-853 has been linked to neurological diseases. Although not ...The replication accuracy of DNA polymerase gamma (Pol γ) is essential for mitochondrial genome integrity. Mutation of human Pol γ arginine-853 has been linked to neurological diseases. Although not a catalytic residue, Pol γ arginine-853 mutants are void of polymerase activity. To identify the structural basis for the disease, we determined a crystal structure of the Pol γ mutant ternary complex with correct incoming nucleotide 2'-deoxycytidine 5'-triphosphate (dCTP). Opposite to the wild type that undergoes open-to-closed conformational changes when bound to a correct nucleotide that is essential for forming a catalytically competent active site, the mutant complex failed to undergo the conformational change, and the dCTP did not base pair with its Watson-Crick complementary templating residue. Our studies revealed that arginine-853 coordinates an interaction network that aligns the 3'-end of primer and dCTP with the catalytic residues. Disruption of the network precludes the formation of Watson-Crick base pairing and closing of the active site, resulting in an inactive polymerase.
History
DepositionSep 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase subunit gamma-1
B: DNA polymerase subunit gamma-2, mitochondrial
C: DNA polymerase subunit gamma-2, mitochondrial
P: DNA (24-MER)
T: DNA (28-MER)
D: DNA (5'-D(P*AP*AP*GP*GP*GP*CP*CP*TP*AP*TP*AP*AP*AP*A)-3')
E: DNA (5'-D(P*TP*TP*TP*TP*AP*TP*AP*GP*GP*CP*CP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,5378
Polymers274,0697
Non-polymers4671
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18540 Å2
ΔGint-78 kcal/mol
Surface area84800 Å2
Unit cell
Length a, b, c (Å)215.410, 215.410, 169.966
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "B" and (resid 67 through 70 or resid 72...
d_2ens_1(chain "C" and (resid 67 through 70 or resid 72...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLULEULEUBB67 - 7067 - 70
d_12ILEILEVALVALBB72 - 12072 - 120
d_13ARGARGARGARGBB122122
d_14GLNGLNHISHISBB124 - 133124 - 133
d_15LEULEULEULEUBB181 - 190181 - 190
d_16HISHISPHEPHEBB192 - 215192 - 215
d_17PROPROVALVALBB217 - 218217 - 218
d_18LYSLYSLEULEUBB229 - 260229 - 260
d_19TRPTRPASPASPBB262 - 280262 - 280
d_110GLYGLYASPASPBB283 - 308283 - 308
d_111GLUGLUGLYGLYBB310 - 317310 - 317
d_112VALVALGLYGLYBB319 - 324319 - 324
d_113ASPASPASPASPBB326326
d_114ARGARGGLNGLNBB328 - 355328 - 355
d_115LYSLYSLEULEUBB370 - 418370 - 418
d_116THRTHRTHRTHRBB420420
d_117GLNGLNSERSERBB422 - 430422 - 430
d_118TYRTYRVALVALBB432 - 485432 - 485
d_21GLUGLULEULEUCC67 - 7067 - 70
d_22ILEILEVALVALCC72 - 12072 - 120
d_23ARGARGARGARGCC122122
d_24GLNGLNHISHISCC124 - 133124 - 133
d_25LEULEULEULEUCC181 - 190181 - 190
d_26HISHISPHEPHECC192 - 215192 - 215
d_27PROPROVALVALCC217 - 218217 - 218
d_28LYSLYSLEULEUCC229 - 260229 - 260
d_29TRPTRPASPASPCC262 - 280262 - 280
d_210GLYGLYASPASPCC283 - 308283 - 308
d_211GLUGLUGLYGLYCC310 - 317310 - 317
d_212VALVALGLYGLYCC319 - 324319 - 324
d_213ASPASPASPASPCC326326
d_214ARGARGGLNGLNCC328 - 355328 - 355
d_215LYSLYSLEULEUCC370 - 418370 - 418
d_216THRTHRTHRTHRCC420420
d_217GLNGLNVALVALCC422 - 485422 - 485

NCS oper: (Code: givenMatrix: (-0.793421714272, 0.483441954073, -0.369818685795), (0.461787180143, 0.0822866707548, -0.883165615313), (-0.396528162401, -0.871500304565, -0.288535328106)Vector: 127. ...NCS oper: (Code: given
Matrix: (-0.793421714272, 0.483441954073, -0.369818685795), (0.461787180143, 0.0822866707548, -0.883165615313), (-0.396528162401, -0.871500304565, -0.288535328106)
Vector: 127.14376023, 26.8217755099, 101.364703704)

-
Components

-
DNA polymerase subunit gamma- ... , 2 types, 3 molecules ABC

#1: Protein DNA polymerase subunit gamma-1 / 3'-5' exodeoxyribonuclease / 5'-deoxyribose-phosphate lyase / Mitochondrial DNA polymerase ...3'-5' exodeoxyribonuclease / 5'-deoxyribose-phosphate lyase / Mitochondrial DNA polymerase catalytic subunit / PolG-alpha


Mass: 139542.562 Da / Num. of mol.: 1 / Mutation: D198A, E200A, R853A
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, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#2: Protein DNA polymerase subunit gamma-2, mitochondrial / DNA polymerase gamma accessory 55 kDa subunit / p55 / Mitochondrial DNA polymerase accessory ...DNA polymerase gamma accessory 55 kDa subunit / p55 / Mitochondrial DNA polymerase accessory subunit / MtPolB / PolG-beta


Mass: 54991.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLG2, MTPOLB
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9UHN1, DNA-directed DNA polymerase

-
DNA chain , 4 types, 4 molecules PTDE

#3: DNA chain DNA (24-MER)


Mass: 7341.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (28-MER)


Mass: 8644.536 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(P*AP*AP*GP*GP*GP*CP*CP*TP*AP*TP*AP*AP*AP*A)-3')


Mass: 4321.856 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (5'-D(P*TP*TP*TP*TP*AP*TP*AP*GP*GP*CP*CP*CP*TP*T)-3')


Mass: 4236.763 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES (pH 6.0), 150 mM NaCl, 10 mM CaCl2, 50 mM BME, 3% PEG 8000, 1-8% sucrose, 2% Jeffamine, 0.8 M NDSB

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.43→50 Å / Num. obs: 5106256 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 119.55 Å2 / Rpim(I) all: 0.066 / Net I/σ(I): 15.1
Reflection shellResolution: 3.43→3.48 Å / Num. unique obs: 2869 / Rpim(I) all: 0.53 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286+SVNrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.43→48.87 Å / SU ML: 0.389 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3631
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The authors state that the DCP ligand has poor density, which is likely the reason for RSR-Z outlier.
RfactorNum. reflection% reflection
Rfree0.2341 2000 3.79 %
Rwork0.1976 50824 -
obs0.199 52824 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 138.58 Å2
Refinement stepCycle: LAST / Resolution: 3.43→48.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13833 1540 28 0 15401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002615944
X-RAY DIFFRACTIONf_angle_d0.694321958
X-RAY DIFFRACTIONf_chiral_restr0.03992379
X-RAY DIFFRACTIONf_plane_restr0.00422559
X-RAY DIFFRACTIONf_dihedral_angle_d16.47445994
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.08104532628 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.43-3.520.35271330.30293383X-RAY DIFFRACTION93.07
3.52-3.620.29941390.24853527X-RAY DIFFRACTION96.68
3.62-3.720.25511380.23513513X-RAY DIFFRACTION96.74
3.72-3.840.23531390.21223545X-RAY DIFFRACTION97.1
3.84-3.980.26751420.19553572X-RAY DIFFRACTION97.84
3.98-4.140.26031400.19063587X-RAY DIFFRACTION98.49
4.14-4.330.24541440.18973637X-RAY DIFFRACTION98.85
4.33-4.550.21581410.16593612X-RAY DIFFRACTION98.87
4.55-4.840.18221440.15473661X-RAY DIFFRACTION99.35
4.84-5.210.22681440.17613668X-RAY DIFFRACTION99.45
5.21-5.740.23881470.19563693X-RAY DIFFRACTION99.46
5.74-6.560.21711460.21253711X-RAY DIFFRACTION99.54
6.57-8.260.25521480.20923775X-RAY DIFFRACTION99.72
8.27-48.870.21471550.1963940X-RAY DIFFRACTION99.81
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)
1-0.1457695369110.1392892968960.1373995528791.408867148070.2356101559910.0606007504247-0.000393405018489-0.05692700293880.02539426165-0.259900038663-0.05025272218720.03119511730770.04680022808780.0492072495921-0.05190979034260.617850586153-0.06285584665230.01625731980140.4955220652930.1668174613530.59826656367753.526-21.37619.054
20.4165727629560.203311150898-0.3266911467081.27202804294-0.163074315970.889819882260.1122044590140.07291655717120.0634343776115-0.133474408669-0.07961186507240.169395656907-0.154278813695-0.00941454391630.6752390150280.05161305933870.06764490868370.5869881481280.09153482978160.55403665239961.77822.72532.039
30.738869681987-0.4527246332540.5200091032021.18686876209-0.3784742520860.880788829017-0.0164311191768-0.2413733283940.1675799632360.4123012811520.0057206435167-0.411011180441-0.3400341623280.07037623776610.05835569043450.84938739926-0.0497366607577-0.06475707478260.6480745512960.0698901377710.78433035495177.17528.96347.434
40.2015017599930.0639426775852-0.0900183278090.187082106333-0.2142149751640.221261302926-0.3759855303170.155277870567-0.587545097545-0.204554685585-0.08355586991440.1187733676950.2980111943520.0503649853407-9.9188974735E-51.83711128969-0.2293807346780.06494042328881.224812545970.1767027870021.4236686183538.612-12.93144.475
50.165260794296-0.277265575321-0.1694591726250.3131816574280.3302884242620.468032063283-0.138634697777-0.39803262976-0.0822992647452-0.3545486437960.8135634702750.287762159891-0.0429818997852-0.01017544831360.03998994321871.544521080730.04704556771890.08349801432041.614665032720.2062867279961.6169980025938.083-15.3440.349
60.147511986657-0.07269999460540.05540381234380.0251742215461-0.02370191777460.0178194675096-0.6737691297180.301871553245-0.837363435242-0.0619050688549-0.1017538534040.0896406225817-0.00735700332950.224229494857-0.000148512882482.269180413080.2640932688950.27779572252.225765242810.353291605782.02673920467104.584-1.78919.793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 68:1238 )A68 - 1238
2X-RAY DIFFRACTION2( CHAIN B AND RESID 64:485 )B64 - 485
3X-RAY DIFFRACTION3( CHAIN C AND RESID 67:485 )C67 - 485
4X-RAY DIFFRACTION4( CHAIN P AND ( RESID 3:23 OR RESID 24:24 ) )P3 - 23
5X-RAY DIFFRACTION4( CHAIN P AND ( RESID 3:23 OR RESID 24:24 ) )P24
6X-RAY DIFFRACTION5( CHAIN T AND RESID 2:26 )T2 - 26
7X-RAY DIFFRACTION6( CHAIN D AND RESID 20:33 ) OR ( CHAIN E AND RESID 95:108 )D20 - 33
8X-RAY DIFFRACTION6( CHAIN D AND RESID 20:33 ) OR ( CHAIN E AND RESID 95:108 )E95 - 108

+
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