[English] 日本語
Yorodumi
- EMDB-40203: CryoEM map of the locally refined interfaces-1,2,3 of soluble OPA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40203
TitleCryoEM map of the locally refined interfaces-1,2,3 of soluble OPA1 from the GDP-AlFx bound helical assembly on a lipid membrane
Map dataCryoEM map of the locally refined interfaces-1,2,3 of soluble OPA1 from the GDP-AlFx bound helical assembly on a lipid membrane
Sample
  • Complex: sOPA1 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 / 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 / neural tube closure / mitochondrion organization / 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 / cytoplasm / cytosol
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: 2.95 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

-
Structure visualization

Supplemental images

emd_40203.png

Downloads & links

-
Map

FileDownload / File: emd_40203.map.gz / Format: CCP4 / Size: 476.8 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 GDP-AlFx bound helical assembly on a lipid membrane
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 500 pix.
= 600.9 Å		1.2 Å/pix.
x 500 pix.
= 600.9 Å		1.2 Å/pix.
x 500 pix.
= 600.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2018 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.5284993 - 0.96569467
Average (Standard dev.)0.0020174116 (±0.0067456346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 600.9 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_40203_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_40203_additional_1.map
AnnotationCryoEM sharpened map 2 of the locally refined interfaces-1,2,3 of soluble OPA1 from the GDP-AlFx bound helical assembly on a lipid membrane
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_40203_additional_2.map
AnnotationCryoEM sharpened map 1 of the locally refined interfaces-1,2,3 of soluble OPA1 from the GDP-AlFx bound helical assembly on a lipid membrane
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_40203_half_map_1.map
AnnotationCryoEM half map A of the locally refined interfaces-1,2,3 of soluble OPA1 from the GDP-AlFx bound helical assembly on a lipid membrane
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_40203_half_map_2.map
AnnotationCryoEM half map B of the locally refined interfaces-1,2,3 of soluble OPA1 from the GDP-AlFx bound helical assembly on a lipid membrane
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : sOPA1 helical assembly on a lipid membrane

EntireName: sOPA1 helical assembly on a lipid membrane
Components
  • Complex: sOPA1 helical assembly on a lipid membrane
    • Protein or peptide: sOPA1 protein

-
Supramolecule #1: sOPA1 helical assembly on a lipid membrane

SupramoleculeName: sOPA1 helical assembly on a lipid membrane / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
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 GTPase OPA1, mitochondrial

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 12.933 Å
Applied symmetry - Helical parameters - Δ&Phi: 37.439 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1795507
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6jtg

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

+
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