[English] 日本語
Yorodumi
- EMDB-0935: Cryo-EM structure of the TIM22 complex from yeast -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0935
TitleCryo-EM structure of the TIM22 complex from yeast
Map data
Sample
  • Complex: TIM22 complex
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM22
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM54
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM18
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM9
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM12
  • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM10
Keywordsmitochondrial import / Tim22 / protein translocation / membrane protein insertion / PROTEIN TRANSPORT
Function / homology
Function and homology information


Glycerophospholipid biosynthesis / Citric acid cycle (TCA cycle) / mitochondrial intermembrane space protein transporter complex / Sphingolipid de novo biosynthesis / TIM22 mitochondrial import inner membrane insertion complex / Mitochondrial protein import / mitochondrion targeting sequence binding / : / mitochondrial electron transport, succinate to ubiquinone / protein transporter activity ...Glycerophospholipid biosynthesis / Citric acid cycle (TCA cycle) / mitochondrial intermembrane space protein transporter complex / Sphingolipid de novo biosynthesis / TIM22 mitochondrial import inner membrane insertion complex / Mitochondrial protein import / mitochondrion targeting sequence binding / : / mitochondrial electron transport, succinate to ubiquinone / protein transporter activity / protein transmembrane transport / protein insertion into mitochondrial inner membrane / response to arsenic-containing substance / cellular respiration / response to osmotic stress / protein transmembrane transporter activity / quinone binding / tricarboxylic acid cycle / phospholipid binding / mitochondrial intermembrane space / unfolded protein binding / cellular response to oxidative stress / mitochondrial inner membrane / electron transfer activity / intracellular membrane-bounded organelle / apoptotic process / structural molecule activity / mitochondrion / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Mitochondrial import inner membrane translocase subunit Tim54 / Inner membrane protein import complex subunit Tim54 / : / Mitochondrial import inner membrane translocase subunit TIM22 / Tim10-like / Tim10-like domain superfamily / Tim10/DDP family zinc finger / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site ...Mitochondrial import inner membrane translocase subunit Tim54 / Inner membrane protein import complex subunit Tim54 / : / Mitochondrial import inner membrane translocase subunit TIM22 / Tim10-like / Tim10-like domain superfamily / Tim10/DDP family zinc finger / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Tim17/Tim22/Tim23/Pmp24 family
Similarity search - Domain/homology
Mitochondrial import inner membrane translocase subunit TIM9 / Mitochondrial import inner membrane translocase subunit TIM12 / Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial / Mitochondrial import inner membrane translocase subunit TIM54 / Mitochondrial import inner membrane translocase subunit TIM10 / Mitochondrial import inner membrane translocase subunit TIM18 / Mitochondrial import inner membrane translocase subunit TIM22
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsZhang Y / Zhou X
CitationJournal: Cell Res / Year: 2021
Title: Structure of the mitochondrial TIM22 complex from yeast.
Authors: Yutong Zhang / Xiaomin Ou / Xuezheng Wang / Dongjie Sun / Xueyin Zhou / Xiaofei Wu / Qing Li / Long Li /
History
DepositionJan 4, 2020-
Header (metadata) releaseSep 30, 2020-
Map releaseSep 30, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6lo8
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0935.png

Downloads & links

-
Map

FileDownload / File: emd_0935.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 337.6 Å		1.06 Å/pix.
x 320 pix.
= 337.6 Å		1.06 Å/pix.
x 320 pix.
= 337.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.041294344 - 0.09148557
Average (Standard dev.)0.00018763824 (±0.0018313394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 337.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0551.0551.055
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z337.600337.600337.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0410.0910.000

-
Supplemental data

-
Sample components

-
Entire : TIM22 complex

EntireName: TIM22 complex
Components
  • Complex: TIM22 complex
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM22
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM54
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM18
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM9
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM12
  • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM10

-
Supramolecule #1: TIM22 complex

SupramoleculeName: TIM22 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
Macromolecule #1: Mitochondrial import inner membrane translocase subunit TIM22

MacromoleculeName: Mitochondrial import inner membrane translocase subunit TIM22
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 21.75174 KDa
SequenceString: MVYTGFGLEQ ISPAQKKPYN ELTPEEQGER GAEMIMNFMT SCPGKSVVSG VTGFALGGVL GLFMASMAYD TPLHTPTPAN TAATATAGN IGVGGISRTV QQISDLPFRQ QMKLQFTDMG KKSYSSAKNF GYIGMIYAGV ECVIESLRAK NDIYNGVTAG F FTGAGLAY ...String:
MVYTGFGLEQ ISPAQKKPYN ELTPEEQGER GAEMIMNFMT SCPGKSVVSG VTGFALGGVL GLFMASMAYD TPLHTPTPAN TAATATAGN IGVGGISRTV QQISDLPFRQ QMKLQFTDMG KKSYSSAKNF GYIGMIYAGV ECVIESLRAK NDIYNGVTAG F FTGAGLAY KAGPQAALMG GAGFAAFSAA IDLYMKSEDG RPPQNDFK

UniProtKB: Mitochondrial import inner membrane translocase subunit TIM22

-
Macromolecule #2: Mitochondrial import inner membrane translocase subunit TIM54

MacromoleculeName: Mitochondrial import inner membrane translocase subunit TIM54
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 54.252637 KDa
SequenceString: MSSESGKPIA KPIRKPGYTN PALKALGIPA LRLPSRNWMI FWSVLTVSIG GIAYDKYKQR QILSHATDLV KPLAEESMEV DKVPRKITV FIAPPPNDYL ESSLKVWRRY VKPVLYYAGL DYELVQEDRQ GIIRTNVANR IRELRKEILA STDGQPVKEP N QTVAKPSG ...String:
MSSESGKPIA KPIRKPGYTN PALKALGIPA LRLPSRNWMI FWSVLTVSIG GIAYDKYKQR QILSHATDLV KPLAEESMEV DKVPRKITV FIAPPPNDYL ESSLKVWRRY VKPVLYYAGL DYELVQEDRQ GIIRTNVANR IRELRKEILA STDGQPVKEP N QTVAKPSG SSTSKISSLL PFNKIIQDPA EEDDSFDPEI GKKFKENFDW RNVIGIFYTM PKPKHIISED ALTKDPILSG GV ICLGRGA YKEYIAGIHE GLLGPIEKTE KTGSTEPKMT GVVEANQIES KVSESGATEL VDAEKETALE EAKVQDDLKV DEE NSSEDS QKFLKPFISS DQYPDLQIAS ELQTPNGEFI RNPNTNIPLL INQPLLVIPI PNLIGFTTIP RRIHRFYQKR FYVE DVCSS VVNCVRQTRI RPFDIAKDID LAKDEEKDWP QNWVKQGKEK NSEWTQELVC DPRITKHMFV YEKPPKEEPE SDI

UniProtKB: Mitochondrial import inner membrane translocase subunit TIM54

-
Macromolecule #3: Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitoch...

MacromoleculeName: Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 22.094963 KDa
SequenceString: MSAMMVKLGL NKSALLLKPS AFSRAAALSS SRRLLFNTAR TNFLSTSPLK NVASEMNTKA AIAEEQILNK QRAKRPISPH LTIYQPQLT WYLSSLHRIS LVLMGLGFYL FTILFGVSGL LGLGLTTEKV SNWYHQKFSK ITEWSIKGSF AYLFAIHYGG A IRHLIWDT ...String:
MSAMMVKLGL NKSALLLKPS AFSRAAALSS SRRLLFNTAR TNFLSTSPLK NVASEMNTKA AIAEEQILNK QRAKRPISPH LTIYQPQLT WYLSSLHRIS LVLMGLGFYL FTILFGVSGL LGLGLTTEKV SNWYHQKFSK ITEWSIKGSF AYLFAIHYGG A IRHLIWDT AKELTLKGVY RTGYALIGFT AVLGTYLLTL

UniProtKB: Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial

-
Macromolecule #4: Mitochondrial import inner membrane translocase subunit TIM18

MacromoleculeName: Mitochondrial import inner membrane translocase subunit TIM18
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 21.994391 KDa
SequenceString: MLLFPGLKPV LNASTVIVNP VRAVFPGLVL STKRSFYSIN RLNAENKIND IANTSKEASS SVQMFKPPEF SQFKDSYQKD YERIAKYTL IPLTMVPFYA SFTGGVINPL LDASLSSIFL IYLQYGFTSC IIDYIPKEKY PRWHKLALYC LYGGSMLSLY G IYELETKN ...String:
MLLFPGLKPV LNASTVIVNP VRAVFPGLVL STKRSFYSIN RLNAENKIND IANTSKEASS SVQMFKPPEF SQFKDSYQKD YERIAKYTL IPLTMVPFYA SFTGGVINPL LDASLSSIFL IYLQYGFTSC IIDYIPKEKY PRWHKLALYC LYGGSMLSLY G IYELETKN NGFVDLVKKL WNENDDHLYI FGRN

UniProtKB: Mitochondrial import inner membrane translocase subunit TIM18

-
Macromolecule #5: Mitochondrial import inner membrane translocase subunit TIM9

MacromoleculeName: Mitochondrial import inner membrane translocase subunit TIM9
type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 10.216649 KDa
SequenceString:
MDALNSKEQQ EFQKVVEQKQ MKDFMRLYSN LVERCFTDCV NDFTTSKLTN KEQTCIMKCS EKFLKHSERV GQRFQEQNAA LGQGLGR

UniProtKB: Mitochondrial import inner membrane translocase subunit TIM9

-
Macromolecule #6: Mitochondrial import inner membrane translocase subunit TIM12

MacromoleculeName: Mitochondrial import inner membrane translocase subunit TIM12
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 12.299962 KDa
SequenceString:
MSFFLNSLRG NQEVSQEKLD VAGVQFDAMC STFNNILSTC LEKCIPHEGF GEPDLTKGEQ CCIDRCVAKM HYSNRLIGGF VQTRGFGPE NQLRHYSRFV AKEIADDSKK

UniProtKB: Mitochondrial import inner membrane translocase subunit TIM12

-
Macromolecule #7: Mitochondrial import inner membrane translocase subunit TIM10

MacromoleculeName: Mitochondrial import inner membrane translocase subunit TIM10
type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 10.313589 KDa
SequenceString:
MSFLGFGGGQ PQLSSQQKIQ AAEAELDLVT DMFNKLVNNC YKKCINTSYS EGELNKNESS CLDRCVAKYF ETNVQVGENM QKMGQSFNA AGKF

UniProtKB: Mitochondrial import inner membrane translocase subunit TIM10

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3663107
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 251984
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 8 / Software - Name: RELION

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6lo8:
Cryo-EM structure of the TIM22 complex from yeast

+
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