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- EMDB-9901: Helical Reconstruction of S-OPA1 At Nucleotide-free State -

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Basic information

Entry
Database: EMDB / ID: EMD-9901
TitleHelical Reconstruction of S-OPA1 At Nucleotide-free State
Map dataThis is the map by helical reconstruction using IHRSR for SOPA-1 of the nucleotide free state. The resolution is about 15 angstrom by FSC 0.143 criterion.
Sample
  • Complex: truncated S-OPA1(253-960) coated liposomal 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)
Methodhelical reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsZhang D / Zhang Y / Sun F
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China31770794 China
Ministry of Science and Technology (China)2017YFA0504700 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
DepositionMay 6, 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: 0.027
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9901.png

Downloads & links

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Map

FileDownload / File: emd_9901.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the map by helical reconstruction using IHRSR for SOPA-1 of the nucleotide free state. The resolution is about 15 angstrom by FSC 0.143 criterion.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.42 Å/pix.
x 384 pix.
= 545.28 Å		1.42 Å/pix.
x 384 pix.
= 545.28 Å		1.42 Å/pix.
x 384 pix.
= 545.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.027 / Movie #1: 0.027
Minimum - Maximum-0.02275986 - 0.04268268
Average (Standard dev.)0.008421425 (±0.010727704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 545.27997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.421.421.42
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z545.280545.280545.280
α/β/γ90.00090.00090.000
start NX/NY/NZ636181
NX/NY/NZ13113592
MAP C/R/S123
start NC/NR/NS-192-192-192
NC/NR/NS384384384
D min/max/mean-0.0230.0430.008

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Supplemental data

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Sample components

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Entire : truncated S-OPA1(253-960) coated liposomal tube

EntireName: truncated S-OPA1(253-960) coated liposomal tube
Components
  • Complex: truncated S-OPA1(253-960) coated liposomal 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: truncated S-OPA1(253-960) coated liposomal tube

SupramoleculeName: truncated S-OPA1(253-960) coated liposomal tube / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: 1mg/ml S-OPA1(253-960) was incubated with 1mg/ml liposome at room temperature for 30 min.
Source (natural)Organism: Homo sapiens (human) / Organelle: Mitochondrion / Location in cell: Mitochondrion inner membrane
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: Rosetta (DE3) / Recombinant plasmid: pET32M-3C

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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: GPGSDKGIHH RKLKKSLIDM YSEVLDVLSD YDASYNTQDH LPRVVVVGDQ SAGKTSVLEM IAQARIFPRG SGEMMTRSPV KVTLSEGPHH VALFKDSSRE FDLTKEEDLA ALRHEIELRM RKNVKEGCTV SPETISLNVK GPGLQRMVLV DLPGVINTVT SGMAPDTKET ...String:
GPGSDKGIHH RKLKKSLIDM YSEVLDVLSD YDASYNTQDH LPRVVVVGDQ SAGKTSVLEM IAQARIFPRG SGEMMTRSPV KVTLSEGPHH VALFKDSSRE FDLTKEEDLA ALRHEIELRM RKNVKEGCTV SPETISLNVK GPGLQRMVLV DLPGVINTVT SGMAPDTKET IFSISKAYMQ NPNAIILCIQ DGSVDAERSI VTDLVSQMDP HGRRTIFVLT KVDLAEKNVA SPSRIQQIIE GKLFPMKALG YFAVVTGKGN SSESIEAIRE YEEEFFQNSK LLKTSMLKAH QVTTRNLSLA VSDCFWKMVR ESVEQQADSF KATRFNLETE WKNNYPRLRE LDRNELFEKA KNEILDEVIS LSQVTPKHWE EILQQSLWER VSTHVIENIY LPAAQTMNSG TFNTTVDIKL KQWTDKQLPN KAVEVAWETL QEEFSRFMTE PKGKEHDDIF DKLKEAVKEE SIKRHKWNDF AEDSLRVIQH NALEDRSISD KQQWDAAIYF MEEALQARLK DTENAIENMV GPDWKKRWLY WKNRTQEQCV HNETKNELEK MLKCNEEHPA YLASDEITTV RKNLESRGVE VDPSLIKDTW HQVYRRHFLK TALNHCNLCR RGFYYYQRHF VDSELECNDV VLFWRIQRML AITANTLRQQ LTNTEVRRLE KNVKEVLEDF AEDGEKKIKL LTGKRVQLAE DLKKVREIQE KLDAFIEALH QEK

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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

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTrisTris(hydroxymethyl)aminomethane
1.0 mMMgCl2magnesium chloride
1.0 mMEGTAEGTA
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / 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 3s with a force 1 before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 77.0 K / Max: 82.0 K
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number real images: 2112 / Average exposure time: 2.0 sec. / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 98591 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 59000
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 reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 27.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 20.87 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPIDER (ver. spiderweb.24.08) / Number images used: 5437
CTF correctionSoftware - Name: Gctf (ver. 1.18)
Segment selectionNumber selected: 6644 / Software - Name: SPIDER (ver. spiderweb.24.08)
Software - details: a spider script with operation command wi was used to cut the tubes into segments
Details: Tubes were boxed out using the tool e2helixboxer.py of EMAN2. Diameter classification were performed for all the boxed tubes. Then 6644 segments of particles were cutting out with an overlap ...Details: Tubes were boxed out using the tool e2helixboxer.py of EMAN2. Diameter classification were performed for all the boxed tubes. Then 6644 segments of particles were cutting out with an overlap of 94% for the main diameter class 53nm.
Startup modelType of model: OTHER
Details: A cylinder was generated by SPIDER with diameter same as the main diameter class 53nm of S-OPA1 and used as starting model to avoid model bias.
Final angle assignmentType: NOT APPLICABLE / Software - Name: SPIDER (ver. spiderweb.24.08)
Details: Final angles were determined by projection matching calculation.
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 / Overall B value: 1000 / Target criteria: Cross correlation

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