[English] 日本語
Yorodumi
- EMDB-9902: S-OPA1 coated liposome tube at GTPgamaS bound state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9902
TitleS-OPA1 coated liposome tube at GTPgamaS bound state
Map data
Sample
  • Complex: truncated S-OPA1(253-960) coated liposomal tube at GTPgamas bound state
    • 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: 23.2 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

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.14
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.14
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9902.png

Downloads & links

-
Map

FileDownload / File: emd_9902.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.72 Å/pix.
x 128 pix.
= 348.16 Å		2.72 Å/pix.
x 128 pix.
= 348.16 Å		2.72 Å/pix.
x 128 pix.
= 348.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14 / Movie #1: 0.14
Minimum - Maximum-0.17467509 - 0.26971686
Average (Standard dev.)0.011099271 (±0.05682671)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
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
start NX/NY/NZ636181
NX/NY/NZ13113592
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.1750.2700.011

-
Supplemental data

-
Sample components

-
Entire : truncated S-OPA1(253-960) coated liposomal tube at GTPgamas bound...

EntireName: truncated S-OPA1(253-960) coated liposomal tube at GTPgamas bound state
Components
  • Complex: truncated S-OPA1(253-960) coated liposomal tube at GTPgamas bound state
    • Protein or peptide: Dynamin-like 120 kDa protein, mitochondrial, short form for isoform 1; Optic atrophy protein 1 (OPA1), short form for isoform 1

-
Supramolecule #1: truncated S-OPA1(253-960) coated liposomal tube at GTPgamas bound...

SupramoleculeName: truncated S-OPA1(253-960) coated liposomal tube at GTPgamas bound state
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. Then GTPgamaS was added to a final concentration of 1mM, and another 30 min incubation was performed.
Source (natural)Organism: Homo sapiens (human) / Organelle: Mitochondria / Location in cell: mitochondrial inner membrane
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: Rosetta (DE3)

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statehelical array

-
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 3.5s with a force 1 before plunging.
Details1mg/ml SOPA1(delta 196-252) was incubated with 1mg/ml liposome at room temperature for 30 min. Then GTPgamaS was added to a final concentration of 1mM, and another 30 min incubation was performed.

-
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: 1-20 / Average exposure time: 1.0 sec. / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 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

+
Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 23.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number subtomograms used: 2927
ExtractionNumber tomograms: 50 / Number images used: 6699 / Software: (Name: IMOD (ver. 4.9.2), RELION (ver. 1.4))
CTF correctionSoftware - Name: CTFFIND (ver. 4.0.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

3snh


Chain - Chain ID: A
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient

+
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://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