[English] 日本語
Yorodumi
- EMDB-43349: CryoEM structure of human S-OPA1 assembled on lipid membrane cont... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43349
TitleCryoEM structure of human S-OPA1 assembled on lipid membrane containing brominated cardiolipin in membrane-adjacent state
Map data
Sample
  • Complex: OPA1
    • Protein or peptide: Dynamin-like 120 kDa protein, mitochondrial
KeywordsGTPase / polymer / filament / membrane / remodeling / fusion / mitochondria / MEMBRANE PROTEIN
Function / homology
Function and homology information


Regulation of Apoptosis / mitochondrial inner membrane fusion / membrane tubulation / membrane bending activity / inner mitochondrial membrane organization / GTPase-dependent fusogenic activity / dynamin GTPase / cristae formation / peroxisome fission / : ...Regulation of Apoptosis / mitochondrial inner membrane fusion / membrane tubulation / membrane bending activity / inner mitochondrial membrane organization / GTPase-dependent fusogenic activity / dynamin GTPase / cristae formation / peroxisome fission / : / phosphatidic acid binding / cardiolipin binding / mitochondrial fission / GTP metabolic process / mitochondrial fusion / axonal transport of mitochondrion / negative regulation of release of cytochrome c from mitochondria / mitochondrial crista / intracellular distribution of mitochondria / positive regulation of interleukin-17 production / protein complex oligomerization / positive regulation of T-helper 17 cell lineage commitment / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / visual perception / axon cytoplasm / Mitochondrial protein degradation / mitochondrion organization / neural tube closure / mitochondrial membrane / mitochondrial intermembrane space / endocytosis / cellular senescence / microtubule binding / microtubule / mitochondrial outer membrane / mitochondrial inner membrane / GTPase activity / apoptotic process / dendrite / negative regulation of apoptotic process / GTP binding / 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 GTPase OPA1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsZuccaro KE / Aydin H
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM150942 United States
American Heart Association23POST1020756 United States
CitationJournal: Nat Commun / Year: 2025
Title: Cardiolipin dynamics promote membrane remodeling by mitochondrial OPA1.
Authors: Sirikrishna Thatavarthy / Luciano A Abriata / Fernando Teixeira Pinto Meireles / Kelly E Zuccaro / Akhil Gargey Iragavarapu / Gabriela May Sullivan / Frank R Moss / Adam Frost / Matteo Dal ...Authors: Sirikrishna Thatavarthy / Luciano A Abriata / Fernando Teixeira Pinto Meireles / Kelly E Zuccaro / Akhil Gargey Iragavarapu / Gabriela May Sullivan / Frank R Moss / Adam Frost / Matteo Dal Peraro / Halil Aydin /
Abstract: Cardiolipin is a mitochondria-specific phospholipid that forms heterotypic interactions with membrane-shaping proteins and regulates the dynamic remodeling and function of mitochondria. However, the ...Cardiolipin is a mitochondria-specific phospholipid that forms heterotypic interactions with membrane-shaping proteins and regulates the dynamic remodeling and function of mitochondria. However, the precise mechanisms through which cardiolipin influences mitochondrial morphology are not well understood. In this study, employing molecular dynamics simulations, we determined that cardiolipin molecules extensively engage with the paddle domain of mitochondrial fusion protein OPA1, which controls membrane-shaping mechanisms. Structure-function analysis confirmed the interactions between cardiolipin and two conserved motifs of OPA1 at the membrane-binding sites. We further developed a bromine-labeled cardiolipin probe to enhance cryoEM contrast and characterized the structure of OPA1 assemblies bound to the cardiolipin brominated lipid bilayers. Our images provide direct evidence of cardiolipin enrichment within the OPA1-binding leaflet. Last, we observed a decrease in membrane remodeling activity for OPA1 in lipid compositions with increasing concentrations of monolyso-cardiolipin. This suggests that the partial replacement of cardiolipin by monolyso-cardiolipin, as observed in Barth syndrome, alters the malleability of the membrane and compromises proper remodeling. Together, these data provide insights into how biological membranes regulate the mechanisms governing mitochondrial homeostasis.
History
DepositionJan 12, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43349.png

Downloads & links

-
Map

FileDownload / File: emd_43349.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 420 pix.
= 700.56 Å		1.67 Å/pix.
x 420 pix.
= 700.56 Å		1.67 Å/pix.
x 420 pix.
= 700.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.668 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.042212784 - 0.0813403
Average (Standard dev.)0.000007755032 (±0.0050123804)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 700.56 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_43349_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_43349_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_43349_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_43349_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : OPA1

EntireName: OPA1
Components
  • Complex: OPA1
    • Protein or peptide: Dynamin-like 120 kDa protein, mitochondrial

-
Supramolecule #1: OPA1

SupramoleculeName: OPA1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Uniprot ID: O60313 - HUMAN OPA1, Dynamin-like 120 kDa protein, mitochondrial
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 820 KDa

-
Macromolecule #1: Dynamin-like 120 kDa protein, mitochondrial

MacromoleculeName: Dynamin-like 120 kDa protein, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: dynamin GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 111.804789 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MWRLRRAAVA CEVCQSLVKH SSGIKGSLPL QKLHLVSRSI YHSHHPTLKL QRPQLRTSFQ QFSSLTNLPL RKLKFSPIKY GYQPRRNFW PARLATRLLK LRYLILGSAV GGGYTAKKTF DQWKDMIPDL SEYKWIVPDI VWEIDEYIDF EKIRKALPSS E DLVKLAPD ...String:
MWRLRRAAVA CEVCQSLVKH SSGIKGSLPL QKLHLVSRSI YHSHHPTLKL QRPQLRTSFQ QFSSLTNLPL RKLKFSPIKY GYQPRRNFW PARLATRLLK LRYLILGSAV GGGYTAKKTF DQWKDMIPDL SEYKWIVPDI VWEIDEYIDF EKIRKALPSS E DLVKLAPD FDKIVESLSL LKDFFTSGSP EETAFRATDR GSESDKHFRK VSDKEKIDQL QEELLHTQLK YQRILERLEK EN KELRKLV LQKDDKGIHH RKLKKSLIDM YSEVLDVLSD YDASYNTQDH LPRVVVVGDQ SAGKTSVLEM IAQARIFPRG SGE MMTRSP VKVTLSEGPH HVALFKDSSR EFDLTKEEDL AALRHEIELR MRKNVKEGCT VSPETISLNV KGPGLQRMVL VDLP GVINT VTSGMAPDTK ETIFSISKAY MQNPNAIILC IQDGSVDAER SIVTDLVSQM DPHGRRTIFV LTKVDLAEKN VASPS RIQQ IIEGKLFPMK ALGYFAVVTG KGNSSESIEA IREYEEEFFQ NSKLLKTSML KAHQVTTRNL SLAVSDCFWK MVRESV EQQ ADSFKATRFN LETEWKNNYP RLRELDRNEL FEKAKNEILD EVISLSQVTP KHWEEILQQS LWERVSTHVI ENIYLPA AQ TMNSGTFNTT VDIKLKQWTD KQLPNKAVEV AWETLQEEFS RFMTEPKGKE HDDIFDKLKE AVKEESIKRH KWNDFAED S LRVIQHNALE DRSISDKQQW DAAIYFMEEA LQARLKDTEN AIENMVGPDW KKRWLYWKNR TQEQCVHNET KNELEKMLK CNEEHPAYLA SDEITTVRKN LESRGVEVDP SLIKDTWHQV YRRHFLKTAL NHCNLCRRGF YYYQRHFVDS ELECNDVVLF WRIQRMLAI TANTLRQQLT NTEVRRLEKN VKEVLEDFAE DGEKKIKLLT GKRVQLAEDL KKVREIQEKL DAFIEALHQE K

UniProtKB: Dynamin-like GTPase OPA1, mitochondrial

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration1.0 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 82.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 7.69 Å
Applied symmetry - Helical parameters - Δ&Phi: 128.642 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 11469
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
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