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- EMDB-40204: CryoEM map of the locally refined interfaces-1,2,3 of soluble OPA... -

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Basic information

Entry
Database: EMDB / ID: EMD-40204
TitleCryoEM map of the locally refined interfaces-1,2,3 of soluble OPA1 from the apo bound helical assembly on a lipid membrane
Map dataCryoEM map of the locally refined interfaces-1,2,3 of soluble OPA1 from the apo bound helical assembly on a lipid membrane
Sample
  • Complex: CryoEM map of the locally refined soluble OPA1 Z-clip from the apo helical assembly on a lipid membrane
    • Protein or peptide: sOPA1 protein
KeywordsGTPase / Dynamin-family protein / mitochondrial fusion protein / mitochondria / Optic Atrophy / LIPID BINDING PROTEIN
Function / homology
Function and homology information


Regulation of Apoptosis / membrane tubulation / inner mitochondrial membrane organization / dynamin GTPase / cardiolipin binding / mitochondrial genome maintenance / phosphatidic acid binding / mitochondrial fission / GTP metabolic process / mitochondrial fusion ...Regulation of Apoptosis / membrane tubulation / inner mitochondrial membrane organization / dynamin GTPase / cardiolipin binding / mitochondrial genome maintenance / phosphatidic acid binding / mitochondrial fission / GTP metabolic process / mitochondrial fusion / axonal transport of mitochondrion / negative regulation of release of cytochrome c from mitochondria / mitochondrial crista / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / axon cytoplasm / visual perception / mitochondrion organization / neural tube closure / mitochondrial membrane / mitochondrial intermembrane space / cellular senescence / protein complex oligomerization / microtubule binding / mitochondrial inner membrane / microtubule / mitochondrial outer membrane / GTPase activity / dendrite / apoptotic process / GTP binding / negative regulation of apoptotic process / magnesium ion binding / mitochondrion / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
Dynamin-like GTPase OPA1, C-terminal / Dynamin-like GTPase OPA1 C-terminal / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dynamin-like 120 kDa protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 5.51 Å
AuthorsNyenhuis SB / Wu X / Strub MP / Yim YI / Stanton AE / Baena V / Syed ZA / Canagarajah B / Hammer JA / Hinshaw JE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Nature / Year: 2023
Title: OPA1 helical structures give perspective to mitochondrial dysfunction.
Authors: Sarah B Nyenhuis / Xufeng Wu / Marie-Paule Strub / Yang-In Yim / Abigail E Stanton / Valentina Baena / Zulfeqhar A Syed / Bertram Canagarajah / John A Hammer / Jenny E Hinshaw /
Abstract: Dominant optic atrophy is one of the leading causes of childhood blindness. Around 60-80% of cases are caused by mutations of the gene that encodes optic atrophy protein 1 (OPA1), a protein that has ...Dominant optic atrophy is one of the leading causes of childhood blindness. Around 60-80% of cases are caused by mutations of the gene that encodes optic atrophy protein 1 (OPA1), a protein that has a key role in inner mitochondrial membrane fusion and remodelling of cristae and is crucial for the dynamic organization and regulation of mitochondria. Mutations in OPA1 result in the dysregulation of the GTPase-mediated fusion process of the mitochondrial inner and outer membranes. Here we used cryo-electron microscopy methods to solve helical structures of OPA1 assembled on lipid membrane tubes, in the presence and absence of nucleotide. These helical assemblies organize into densely packed protein rungs with minimal inter-rung connectivity, and exhibit nucleotide-dependent dimerization of the GTPase domains-a hallmark of the dynamin superfamily of proteins. OPA1 also contains several unique secondary structures in the paddle domain that strengthen its membrane association, including membrane-inserting helices. The structural features identified in this study shed light on the effects of pathogenic point mutations on protein folding, inter-protein assembly and membrane interactions. Furthermore, mutations that disrupt the assembly interfaces and membrane binding of OPA1 cause mitochondrial fragmentation in cell-based assays, providing evidence of the biological relevance of these interactions.
History
DepositionMar 22, 2023-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateSep 13, 2023-
Current statusSep 13, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40204.png

Downloads & links

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Map

FileDownload / File: emd_40204.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of the locally refined interfaces-1,2,3 of soluble OPA1 from the apo bound helical assembly on a lipid membrane
Voxel sizeX=Y=Z: 1.2518 Å
Density
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.34740275 - 0.75966763
Average (Standard dev.)-0.0007175304 (±0.0067008017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 600.86395 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40204_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: CryoEM sharpened map 1 of the locally refined...

Fileemd_40204_additional_1.map
AnnotationCryoEM sharpened map 1 of the locally refined interfaces-1,2,3 of soluble OPA1 from the apo bound helical assembly on a lipid membrane
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: CryoEM sharpened map 2 of the locally refined...

Fileemd_40204_additional_2.map
AnnotationCryoEM sharpened map 2 of the locally refined interfaces-1,2,3 of soluble OPA1 from the apo bound helical assembly on a lipid membrane
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM half map A of the locally refined...

Fileemd_40204_half_map_1.map
AnnotationCryoEM half map A of the locally refined interfaces-1,2,3 of soluble OPA1 from the apo bound helical assembly on a lipid membrane
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM half map B of the locally refined...

Fileemd_40204_half_map_2.map
AnnotationCryoEM half map B of the locally refined interfaces-1,2,3 of soluble OPA1 from the apo bound helical assembly on a lipid membrane
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CryoEM map of the locally refined soluble OPA1 Z-clip from the ap...

EntireName: CryoEM map of the locally refined soluble OPA1 Z-clip from the apo helical assembly on a lipid membrane
Components
  • Complex: CryoEM map of the locally refined soluble OPA1 Z-clip from the apo helical assembly on a lipid membrane
    • Protein or peptide: sOPA1 protein

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Supramolecule #1: CryoEM map of the locally refined soluble OPA1 Z-clip from the ap...

SupramoleculeName: CryoEM map of the locally refined soluble OPA1 Z-clip from the apo helical assembly on a lipid membrane
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: sOPA1 protein

MacromoleculeName: sOPA1 protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: ATDRGSESDK HFRKVSDKEK IDQLQEELLH TQLKYQRILE RLEKENKELR KLVLQKDDKG IHHRKLKKSL IDMYSEVLD VLSDYDASYN TQDHLPRVVV VGDQSAGKTS VLEMIAQARI FPRGSGEMMT RSPVKVTLSE G PHHVALFK DSSREFDLTK EEDLAALRHE ...String:
ATDRGSESDK HFRKVSDKEK IDQLQEELLH TQLKYQRILE RLEKENKELR KLVLQKDDKG IHHRKLKKSL IDMYSEVLD VLSDYDASYN TQDHLPRVVV VGDQSAGKTS VLEMIAQARI FPRGSGEMMT RSPVKVTLSE G PHHVALFK DSSREFDLTK EEDLAALRHE IELRMRKNVK EGCTVSPETI SLNVKGPGLQ RMVLVDLPGV IN TVTSGMA PDTKETIFSI SKAYMQNPNA IILCIQDGSV DAERSIVTDL VSQMDPHGRR TIFVLTKVDL AEK NVASPS RIQQIIEGKL FPMKALGYFA VVTGKGNSSE SIEAIREYEE EFFQNSKLLK TSMLKAHQVT TRNL SLAVS DCFWKMVRES VEQQADSFKA TRFNLETEWK NNYPRLRELD RNELFEKAKN EILDEVISLS QVTPK HWEE ILQQSLWERV STHVIENIYL PAAQTMNSGT FNTTVDIKLK QWTDKQLPNK AVEVAWETLQ EEFSRF MTE PKGKEHDDIF DKLKEAVKEE SIKRHKWNDF AEDSLRVIQH NALEDRSISD KQQWDAAIYF MEEALQA RL KDTENAIENM VGPDWKKRWL YWKNRTQEQC VHNETKNELE KMLKCNEEHP AYLASDEITT VRKNLESR G VEVDPSLIKD TWHQVYRRHF LKTALNHCNL CRRGFYYYQR HFVDSELECN DVVLFWRIQR MLAITANTL RQQLTNTEVR RLEKNVKEVL EDFAEDGEKK IKLLTGKRVQ LAEDLKKVRE IQEKLDAFIE ALHQEK

UniProtKB: Dynamin-like 120 kDa protein, mitochondrial

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 24.86 e/Å2

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6jtg

Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 14.07 Å
Applied symmetry - Helical parameters - Δ&Phi: 37.25 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 5.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 352618
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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