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- EMDB-0722: Full length S-OPA1 coated liposome tube at nucleotide-free state -

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Basic information

Entry
Database: EMDB / ID: EMD-0722
TitleFull length S-OPA1 coated liposome tube at nucleotide-free state
Map data
Sample
  • Complex: full length S-OPA1 coated liposome tube
    • Protein or peptide: Dynamin-like 120 kDa protein, mitochondrial, short form for isoform 1, Optic atrophy protein 1 (OPA1), short form for isoform 1
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 31.7 Å
AuthorsZhang D / Niu T / Zhang Y / Sun F
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China31770794 China
Ministry of Science and Technology (China) China
Chinese Academy of SciencesXDB08030202 China
CitationJournal: Elife / Year: 2020
Title: Cryo-EM structures of S-OPA1 reveal its interactions with membrane and changes upon nucleotide binding.
Authors: Danyang Zhang / Yan Zhang / Jun Ma / Chunmei Zhu / Tongxin Niu / Wenbo Chen / Xiaoyun Pang / Yujia Zhai / Fei Sun /
Abstract: Mammalian mitochondrial inner membrane fusion is mediated by optic atrophy 1 (OPA1). Under physiological conditions, OPA1 undergoes proteolytic processing to form a membrane-anchored long isoform (L- ...Mammalian mitochondrial inner membrane fusion is mediated by optic atrophy 1 (OPA1). Under physiological conditions, OPA1 undergoes proteolytic processing to form a membrane-anchored long isoform (L-OPA1) and a soluble short isoform (S-OPA1). A combination of L-OPA1 and S-OPA1 is essential for efficient membrane fusion; however, the relevant mechanism is not well understood. In this study, we investigate the cryo-electron microscopic structures of S-OPA1-coated liposomes in nucleotide-free and GTPγS-bound states. S-OPA1 exhibits a general dynamin-like structure and can assemble onto membranes in a helical array with a dimer building block. We reveal that hydrophobic residues in its extended membrane-binding domain are critical for its tubulation activity. The binding of GTPγS triggers a conformational change and results in a rearrangement of the helical lattice and tube expansion similar to that of S-Mgm1. These observations indicate that S-OPA1 adopts a dynamin-like power stroke membrane remodeling mechanism during mitochondrial inner membrane fusion.
History
DepositionJul 30, 2019-
Header (metadata) releaseApr 15, 2020-
Map releaseApr 15, 2020-
UpdateApr 15, 2020-
Current statusApr 15, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0722.png

Downloads & links

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Map

FileDownload / File: emd_0722.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 2.72 Å
Density
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.23188168 - 0.29639256
Average (Standard dev.)0.008297293 (±0.05131582)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 348.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.722.722.72
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z348.160348.160348.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-0.2320.2960.008

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Supplemental data

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Sample components

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Entire : full length S-OPA1 coated liposome tube

EntireName: full length S-OPA1 coated liposome tube
Components
  • Complex: full length S-OPA1 coated liposome tube
    • Protein or peptide: Dynamin-like 120 kDa protein, mitochondrial, short form for isoform 1, Optic atrophy protein 1 (OPA1), short form for isoform 1

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Supramolecule #1: full length S-OPA1 coated liposome tube

SupramoleculeName: full length S-OPA1 coated liposome tube / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: 1mg/ml full length S-OPA1 was incubated with 1mg/ml liposome at room temperature for 30 min.
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Dynamin-like 120 kDa protein, mitochondrial, short form for isofo...

MacromoleculeName: Dynamin-like 120 kDa protein, mitochondrial, short form for isoform 1, Optic atrophy protein 1 (OPA1), short form for isoform 1
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPGSTDRGSE SDKHFRKVSD KEKIDQLQEE LLHTQLKYQR ILERLEKEN KELRKLVLQK DDKGIHHRKL KKSLIDMYSE VLDVLSDYDA SYNTQDHLPR VVVVGDQSAG KTSVLEMIA QARIFPRGSG EMMTRSPVKV TLSEGPHHVA LFKDSSREFD LTKEEDLAAL R ...String:
GPGSTDRGSE SDKHFRKVSD KEKIDQLQEE LLHTQLKYQR ILERLEKEN KELRKLVLQK DDKGIHHRKL KKSLIDMYSE VLDVLSDYDA SYNTQDHLPR VVVVGDQSAG KTSVLEMIA QARIFPRGSG EMMTRSPVKV TLSEGPHHVA LFKDSSREFD LTKEEDLAAL R HEIELRMR KNVKEGCTVS PETISLNVKG PGLQRMVLVD LPGVINTVTS GMAPDTKETI FS ISKAYMQ NPNAIILCIQ DGSVDAERSI VTDLVSQMDP HGRRTIFVLT KVDLAEKNVA SPS RIQQII EGKLFPMKAL GYFAVVTGKG NSSESIEAIR EYEEEFFQNS KLLKTSMLKA HQVT TRNLS LAVSDCFWKM VRESVEQQAD SFKATRFNLE TEWKNNYPRL RELDRNELFE KAKNE ILDE VISLSQVTPK HWEEILQQSL WERVSTHVIE NIYLPAAQTM NSGTFNTTVD IKLKQW TDK QLPNKAVEVA WETLQEEFSR FMTEPKGKEH DDIFDKLKEA VKEESIKRHK WNDFAED SL RVIQHNALED RSISDKQQWD AAIYFMEEAL QARLKDTENA IENMVGPDWK KRWLYWKN R TQEQCVHNET KNELEKMLKC NEEHPAYLAS DEITTVRKNL ESRGVEVDPS LIKDTWHQV YRRHFLKTAL NHCNLCRRGF YYYQRHFVDS ELECNDVVLF WRIQRMLAIT ANTLRQQLTN TEVRRLEKN VKEVLEDFAE DGEKKIKLLT GKRVQLAEDL KKVREIQEKL DAFIEALHQE K

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statehelical array

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Sample preparation

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormula
20.0 mMTris
1.0 mMMgCl2
1.0 mMEGTA
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV
Details: The grid was blotted for 3.5s with force 1 before plunging..
Details1mg/ml full length S-OPA1 was incubated with 1mg/ml liposome at room temperature for 30 min.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-12 / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 4.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 31.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number subtomograms used: 436
ExtractionNumber tomograms: 9 / Number images used: 773 / Software: (Name: IMOD (ver. 4.2.9), RELION (ver. 1.4))
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3snh


Chain - Chain ID: A
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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