[English] 日本語
Yorodumi
- EMDB-66279: Human TIM22 complex wtih substrate GGC1-sfGFP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-66279
TitleHuman TIM22 complex wtih substrate GGC1-sfGFP
Map dataHuman TIM22 complex engaged with GGC1-sfGFP
Sample
  • Complex: Human TIM22 complex wtih substrate GGC1-sfGFP
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit Tim22
    • Protein or peptide: Acylglycerol kinase, mitochondrial
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit Tim29
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit Tim9
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit Tim10
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit Tim10 B
  • Ligand: HEXADECANE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
KeywordsMitochondria / Protein translocation / TRANSLOCASE
Function / homology
Function and homology information


ceramide kinase / acylglycerol kinase / ceramide kinase activity / acylglycerol kinase activity / : / Glycerophospholipid biosynthesis / glycerolipid metabolic process / lipid phosphorylation / mitochondrial intermembrane space chaperone complex / TIM22 mitochondrial import inner membrane insertion complex ...ceramide kinase / acylglycerol kinase / ceramide kinase activity / acylglycerol kinase activity / : / Glycerophospholipid biosynthesis / glycerolipid metabolic process / lipid phosphorylation / mitochondrial intermembrane space chaperone complex / TIM22 mitochondrial import inner membrane insertion complex / diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / TIM23 mitochondrial import inner membrane translocase complex / membrane insertase activity / mitochondrion targeting sequence binding / protein transporter activity / protein insertion into mitochondrial inner membrane / ceramide biosynthetic process / Mitochondrial protein import / : / intracellular membrane-bounded organelle / transmembrane protein transporter activity / cell-matrix adhesion / sensory perception of sound / Mitochondrial protein degradation / mitochondrial intermembrane space / mitochondrial membrane / : / Signaling by BRAF and RAF1 fusions / protein transport / protein-folding chaperone binding / mitochondrial outer membrane / mitochondrial inner membrane / protein homodimerization activity / mitochondrion / zinc ion binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
Mitochondrial import inner membrane translocase subunit Tim29 / Acylglycerol kinase, C-terminal / Translocase of the Inner Mitochondrial membrane 29 / Acylglycerol kinase C-terminal / : / : / Tim10-like / Tim10-like domain superfamily / Tim10/DDP family zinc finger / Diacylglycerol kinase, catalytic domain ...Mitochondrial import inner membrane translocase subunit Tim29 / Acylglycerol kinase, C-terminal / Translocase of the Inner Mitochondrial membrane 29 / Acylglycerol kinase C-terminal / : / : / Tim10-like / Tim10-like domain superfamily / Tim10/DDP family zinc finger / Diacylglycerol kinase, catalytic domain / Mitochondrial import inner membrane translocase subunit TIM22 / Diacylglycerol kinase catalytic domain / DAG-kinase catalytic (DAGKc) domain profile. / Diacylglycerol kinase catalytic domain (presumed) / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / Tim17/Tim22/Tim23/Pmp24 family
Similarity search - Domain/homology
Mitochondrial import inner membrane translocase subunit Tim10 / Acylglycerol kinase, mitochondrial / Mitochondrial import inner membrane translocase subunit Tim29 / Mitochondrial import inner membrane translocase subunit Tim22 / Mitochondrial import inner membrane translocase subunit Tim10 B / Mitochondrial import inner membrane translocase subunit Tim9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLiu XL / Cai HJ / Li L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271269 China
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: Direct coupling of human TOM and TIM22 complexes drives mitochondrial carrier import.
Authors: Xiaolong Liu / Hongjun Cai / Hao Wang / Xueyin Zhou / Yutong Zhang / Shuai Liu / Jiajun Zhu / Long Li /
Abstract: Metabolite carriers that control essential metabolite transport are imported into mitochondria through the TOM and TIM22 complexes. How TOM and TIM22 coordinate in human mitochondria has remained ...Metabolite carriers that control essential metabolite transport are imported into mitochondria through the TOM and TIM22 complexes. How TOM and TIM22 coordinate in human mitochondria has remained largely unknown. Here we show that human TOM and TIM22 assemble into a supercomplex that seamlessly couples carrier translocation across the outer and inner membranes, unlike in yeast where the two complexes appear to function separately. Cryo-electron microscopy structures of the human TOM-TIM22 supercomplex reveal unpaired carrier transmembrane segments traversing the TOM channel along a hydrophobic path and exiting through an unexpected lateral groove outside the channel. The membrane-bound small Tim subunits provide the substrate entry site for TIM22, while a membrane-exposed groove of TIM22 serves as the exit for carrier insertion into the inner membrane. These findings provide insights into the human carrier translocation pathway at molecular resolution and establish the TOM-TIM22 supercomplex as a central organizing unit of mitochondrial carrier import.
History
DepositionSep 19, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_66279.png

Downloads & links

-
Map

FileDownload / File: emd_66279.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman TIM22 complex engaged with GGC1-sfGFP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 320 pix.
= 304. Å		0.95 Å/pix.
x 320 pix.
= 304. Å		0.95 Å/pix.
x 320 pix.
= 304. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-2.4393373 - 4.2589192
Average (Standard dev.)0.0049407976 (±0.07223415)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 304.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_66279_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Human TIM22 complex engaged with GGC1-sfGFP half map 2

Fileemd_66279_half_map_1.map
AnnotationHuman TIM22 complex engaged with GGC1-sfGFP half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Human TIM22 complex engaged with GGC1-sfGFP half map 1

Fileemd_66279_half_map_2.map
AnnotationHuman TIM22 complex engaged with GGC1-sfGFP half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human TIM22 complex wtih substrate GGC1-sfGFP

EntireName: Human TIM22 complex wtih substrate GGC1-sfGFP
Components
  • Complex: Human TIM22 complex wtih substrate GGC1-sfGFP
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit Tim22
    • Protein or peptide: Acylglycerol kinase, mitochondrial
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit Tim29
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit Tim9
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit Tim10
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit Tim10 B
  • Ligand: HEXADECANE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine

-
Supramolecule #1: Human TIM22 complex wtih substrate GGC1-sfGFP

SupramoleculeName: Human TIM22 complex wtih substrate GGC1-sfGFP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293F / Organelle: mitochondria / Location in cell: mitochondria

-
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: Homo sapiens (human)
Molecular weightTheoretical: 22.89884 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDHDGDY KDHDIDYKDD DDKMAAAAPN AGGSAPETAG SAEAPLQYSL LLQYLVGDKR QPRLLEPGSL GGIPSPAKSE EQKMIEKAM ESCAFKAALA CVGGFVLGGA FGVFTAGIDT NVGFDPKDPY RTPTAKEVLK DMGQRGMSYA KNFAIVGAMF S CTECLIES ...String:
MDYKDHDGDY KDHDIDYKDD DDKMAAAAPN AGGSAPETAG SAEAPLQYSL LLQYLVGDKR QPRLLEPGSL GGIPSPAKSE EQKMIEKAM ESCAFKAALA CVGGFVLGGA FGVFTAGIDT NVGFDPKDPY RTPTAKEVLK DMGQRGMSYA KNFAIVGAMF S CTECLIES YRGTSDWKNS VISGCITGGA IGFRAGLKAG AIGCGGFAAF SAAIDYYLR

UniProtKB: Mitochondrial import inner membrane translocase subunit Tim22

-
Macromolecule #2: Acylglycerol kinase, mitochondrial

MacromoleculeName: Acylglycerol kinase, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: diacylglycerol kinase (ATP)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.196008 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTVFFKTLRN HWKKTTAGLC LLTWGGHWLY GKHCDNLLRR AACQEAQVFG NQLIPPNAQV KKATVFLNPA ACKGKARTLF EKNAAPILH LSGMDVTIVK TDYEGQAKKL LELMENTDVI IVAGGDGTLQ EVVTGVLRRT DEATFSKIPI GFIPLGETSS L SHTLFAES ...String:
MTVFFKTLRN HWKKTTAGLC LLTWGGHWLY GKHCDNLLRR AACQEAQVFG NQLIPPNAQV KKATVFLNPA ACKGKARTLF EKNAAPILH LSGMDVTIVK TDYEGQAKKL LELMENTDVI IVAGGDGTLQ EVVTGVLRRT DEATFSKIPI GFIPLGETSS L SHTLFAES GNKVQHITDA TLAIVKGETV PLDVLQIKGE KEQPVFAMTG LRWGSFRDAG VKVSKYWYLG PLKIKAAHFF ST LKEWPQT HQASISYTGP TERPPNEPEE TPVQRPSLYR RILRRLASYW AQPQDALSQE VSPEVWKDVQ LSTIELSITT RNN QLDPTS KEDFLNICIE PDTISKGDFI TIGSRKVRNP KLHVEGTECL QASQCTLLIP EGAGGSFSID SEEYEAMPVE VKLL PRKLQ FFCDPRKREQ MLTSPTQ

UniProtKB: Acylglycerol kinase, mitochondrial

-
Macromolecule #3: Mitochondrial import inner membrane translocase subunit Tim29

MacromoleculeName: Mitochondrial import inner membrane translocase subunit Tim29
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.272336 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAAALRRFW SRRRAEAGDA VVAKPGVWAR LGSWARALLR DYAEACRDAS AEARARPGRA AVYVGLLGGA AACFTLAPSE GAFEEALLE ASGTLLLLAP ATRNRESEAF VQRLLWLRGR GRLRYVNLGL CSLVYEAPFD AQASLYQARC RYLQPRWTDF P GRVLDVGF ...String:
MAAAALRRFW SRRRAEAGDA VVAKPGVWAR LGSWARALLR DYAEACRDAS AEARARPGRA AVYVGLLGGA AACFTLAPSE GAFEEALLE ASGTLLLLAP ATRNRESEAF VQRLLWLRGR GRLRYVNLGL CSLVYEAPFD AQASLYQARC RYLQPRWTDF P GRVLDVGF VGRWWVLGAW MRDCDINDDE FLHLPAHLRV VGPQQLHSET NERLFDEKYK PVVLTDDQVD QALWEEQVLQ KE KKDRLAL SQAHSLVQAE APR

UniProtKB: Mitochondrial import inner membrane translocase subunit Tim29

-
Macromolecule #4: Mitochondrial import inner membrane translocase subunit Tim9

MacromoleculeName: Mitochondrial import inner membrane translocase subunit Tim9
type: protein_or_peptide / ID: 4 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.391906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAAQIPESDQ IKQFKEFLGT YNKLTETCFL DCVKDFTTRE VKPEETTCSE HCLQKYLKMT QRISMRFQEY HIQQNEALAA KAGLLGQPR

UniProtKB: Mitochondrial import inner membrane translocase subunit Tim9

-
Macromolecule #5: Mitochondrial import inner membrane translocase subunit Tim10

MacromoleculeName: Mitochondrial import inner membrane translocase subunit Tim10
type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.348999 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MDPLRAQQLA AELEVEMMAD MYNRMTSACH RKCVPPHYKE AELSKGESVC LDRCVSKYLD IHERMGKKLT ELSMQDEELM KRVQQSSGP A

UniProtKB: Mitochondrial import inner membrane translocase subunit Tim10

-
Macromolecule #6: Mitochondrial import inner membrane translocase subunit Tim10 B

MacromoleculeName: Mitochondrial import inner membrane translocase subunit Tim10 B
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.601244 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MERQQQQQQQ LRNLRDFLLV YNRMTELCFQ RCVPSLHHRA LDAEEEACLH SCAGKLIHSN HRLMAAYVQL MPALVQRRIA DYEAASAVP GVAAEQPGVS PSGS

UniProtKB: Mitochondrial import inner membrane translocase subunit Tim10 B

-
Macromolecule #7: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 7 / Number of copies: 3 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

-
Macromolecule #8: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 8 / Number of copies: 2 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.6 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
100.0 mMNaClsodium chloride
0.6 mg/mLdigitonin

Details: 20 mM HEPES-NaOH pH 7.4, 100 mM NaCl, 0.06% digitonin
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV
Details: 1.5 s blot time, 5 s wait time, 100% humidity, and 6 degree centigrade.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 31755 / Average exposure time: 5.44 sec. / 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 / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 5385617
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6) / Software - details: Patch CTF Estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Software - details: Non-uniform Refinement / Number images used: 250094
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6) / Software - details: Ab-Initio Reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsRigid body fitting in ChimeraX and then flexible fitting in Coot
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9wv1:
Human TIM22 complex wtih substrate GGC1-sfGFP

+
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