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- EMDB-25743: Octameric Human Twinkle Helicase Clinical Variant W315L -

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Basic information

Entry
Database: EMDB / ID: EMD-25743
TitleOctameric Human Twinkle Helicase Clinical Variant W315L
Map data
Sample
  • Complex: Heptameric Human Twinkle Clinical Variant W315L
    • Protein or peptide: Twinkle mtDNA helicase
KeywordsHelicase / walker A / walker B / DNA binding / DNA BINDING PROTEIN
Function / homology
Function and homology information


mitochondrial DNA replication / mitochondrial transcription / DNA 5'-3' helicase / protein hexamerization / DNA unwinding involved in DNA replication / mitochondrial nucleoid / Mitochondrial protein degradation / DNA helicase activity / isomerase activity / cellular response to glucose stimulus ...mitochondrial DNA replication / mitochondrial transcription / DNA 5'-3' helicase / protein hexamerization / DNA unwinding involved in DNA replication / mitochondrial nucleoid / Mitochondrial protein degradation / DNA helicase activity / isomerase activity / cellular response to glucose stimulus / Transcriptional activation of mitochondrial biogenesis / single-stranded DNA binding / 5'-3' DNA helicase activity / protease binding / mitochondrial inner membrane / mitochondrial matrix / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding
Similarity search - Function
AAA domain / Twinkle-like protein / Archaeal primase DnaG/twinkle-like, TOPRIM domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Twinkle mtDNA helicase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsRiccio AA / Bouvette J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01 ES065078 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01 ES065080 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structural insight and characterization of human Twinkle helicase in mitochondrial disease.
Authors: Amanda A Riccio / Jonathan Bouvette / Lalith Perera / Matthew J Longley / Juno M Krahn / Jason G Williams / Robert Dutcher / Mario J Borgnia / William C Copeland /
Abstract: Twinkle is the mammalian helicase vital for replication and integrity of mitochondrial DNA. Over 90 Twinkle helicase disease variants have been linked to progressive external ophthalmoplegia and ...Twinkle is the mammalian helicase vital for replication and integrity of mitochondrial DNA. Over 90 Twinkle helicase disease variants have been linked to progressive external ophthalmoplegia and ataxia neuropathies among other mitochondrial diseases. Despite the biological and clinical importance, Twinkle represents the only remaining component of the human minimal mitochondrial replisome that has yet to be structurally characterized. Here, we present 3-dimensional structures of human Twinkle W315L. Employing cryo-electron microscopy (cryo-EM), we characterize the oligomeric assemblies of human full-length Twinkle W315L, define its multimeric interface, and map clinical variants associated with Twinkle in inherited mitochondrial disease. Cryo-EM, crosslinking-mass spectrometry, and molecular dynamics simulations provide insight into the dynamic movement and molecular consequences of the W315L clinical variant. Collectively, this ensemble of structures outlines a framework for studying Twinkle function in mitochondrial DNA replication and associated disease states.
History
DepositionDec 16, 2021-
Header (metadata) releaseJul 27, 2022-
Map releaseJul 27, 2022-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25743.png

Downloads & links

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Map

FileDownload / File: emd_25743.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 423.2 Å		1.06 Å/pix.
x 400 pix.
= 423.2 Å		1.06 Å/pix.
x 400 pix.
= 423.2 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.233
Minimum - Maximum-0.0018800781 - 2.191262
Average (Standard dev.)0.0011483012 (±0.024932457)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25743_msk_1.map
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Half map: #2

Fileemd_25743_half_map_1.map
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Half map: #1

Fileemd_25743_half_map_2.map
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Sample components

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Entire : Heptameric Human Twinkle Clinical Variant W315L

EntireName: Heptameric Human Twinkle Clinical Variant W315L
Components
  • Complex: Heptameric Human Twinkle Clinical Variant W315L
    • Protein or peptide: Twinkle mtDNA helicase

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Supramolecule #1: Heptameric Human Twinkle Clinical Variant W315L

SupramoleculeName: Heptameric Human Twinkle Clinical Variant W315L / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 504 KDa

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Macromolecule #1: Twinkle mtDNA helicase

MacromoleculeName: Twinkle mtDNA helicase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 78.469422 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MWVLLRSGYP LRILLPLRGE WMGRRGLPRN LAPGPPRRRY RKETLQALDM PVLPVTATEI RQYLRGHGIP FQDGHSCLRA LSPFAESSQ LKGQTGVTTS FSLFIDKTTG HFLCMTSLAE GSWEDFQASV EGRGDGAREG FLLSKAPEFE DSEEVRRIWN R AIPLWELP ...String:
MWVLLRSGYP LRILLPLRGE WMGRRGLPRN LAPGPPRRRY RKETLQALDM PVLPVTATEI RQYLRGHGIP FQDGHSCLRA LSPFAESSQ LKGQTGVTTS FSLFIDKTTG HFLCMTSLAE GSWEDFQASV EGRGDGAREG FLLSKAPEFE DSEEVRRIWN R AIPLWELP DQEEVQLADT MFGLTKVTDD TLKRFSVRYL RPARSLVFPW FSPGGSGLRG LKLLEAKCQG DGVSYEETTI PR PSAYHNL FGLPLISRRD AEVVLTSREL DSLALNQSTG LPTLTLPRGT TCLPPALLPY LEQFRRIVFW LGDDLRSLEA AKL FARKLN PKRCFLVRPG DQQPRPLEAL NGGFNLSRIL RTALPAWHKS IVSFRQLREE VLGELSNVEQ AAGLRWSRFP DLNR ILKGH RKGELTVFTG PTGSGKTTFI SEYALDLCSQ GVNTLWGSFE ISNVRLARVM LTQFAEGRLE DQLDKYDHWA DRFED LPLY FMTFHGQQSI RTVIDTMQHA VYVYDICHVI IDNLQFMMGH EQLSTDRIAA QDYIIGVFRK FATDNNCHVT LVIHPR KED DDKELQTASI FGSAKASQEA DNVLILQDRK LVTGPGKRYL QVSKNRFDGD VGVFPLEFNK NSLTFSIPPK NKARLKK IK DDTGPVAKKP SSGKKGATTQ NSEICSGQAP TPDQPDTSKR SKAAALEHHH HHH

UniProtKB: Twinkle mtDNA helicase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.2 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55198
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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