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

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Basic information

Entry
Database: PDB / ID: 9wv1
TitleHuman TIM22 complex wtih substrate GGC1-sfGFP
Components
  • (Mitochondrial import inner membrane translocase subunit ...) x 5
  • Acylglycerol kinase, mitochondrial
KeywordsTRANSLOCASE / Mitochondria / Protein translocation
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
1,2-Distearoyl-sn-glycerophosphoethanolamine / HEXADECANE / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLiu, X.L. / Cai, H.J. / Li, L.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial import inner membrane translocase subunit Tim22
B: Acylglycerol kinase, mitochondrial
C: Mitochondrial import inner membrane translocase subunit Tim29
D: Mitochondrial import inner membrane translocase subunit Tim9
E: Mitochondrial import inner membrane translocase subunit Tim9
F: Mitochondrial import inner membrane translocase subunit Tim9
G: Mitochondrial import inner membrane translocase subunit Tim10
H: Mitochondrial import inner membrane translocase subunit Tim10
I: Mitochondrial import inner membrane translocase subunit Tim10
J: Mitochondrial import inner membrane translocase subunit Tim10 B
K: Mitochondrial import inner membrane translocase subunit Tim9
L: Mitochondrial import inner membrane translocase subunit Tim9
M: Mitochondrial import inner membrane translocase subunit Tim10
N: Mitochondrial import inner membrane translocase subunit Tim10
O: Mitochondrial import inner membrane translocase subunit Tim10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,19720
Polymers225,02215
Non-polymers2,1755
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Mitochondrial import inner membrane translocase subunit ... , 5 types, 14 molecules ACDEFKLGHIMNOJ

#1: Protein Mitochondrial import inner membrane translocase subunit Tim22 / Testis-expressed protein 4


Mass: 22898.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMM22, TEX4, TIM22 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9Y584
#3: Protein Mitochondrial import inner membrane translocase subunit Tim29 / TIM29


Mass: 29272.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMM29, c19orf52 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9BSF4
#4: Protein
Mitochondrial import inner membrane translocase subunit Tim9


Mass: 10391.906 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMM9, TIM9, TIM9A, TIMM9A / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9Y5J7
#5: Protein
Mitochondrial import inner membrane translocase subunit Tim10


Mass: 10348.999 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMM10, TIM10 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P62072
#6: Protein Mitochondrial import inner membrane translocase subunit Tim10 B / Fracture callus protein 1 / FxC1 / Mitochondrial import inner membrane translocase subunit Tim9 B / ...Fracture callus protein 1 / FxC1 / Mitochondrial import inner membrane translocase subunit Tim9 B / TIMM10B / Tim10b


Mass: 11601.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMM10B, FXC1, TIM9B, TIMM9B / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9Y5J6

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Protein , 1 types, 1 molecules B

#2: Protein Acylglycerol kinase, mitochondrial / hAGK / Multiple substrate lipid kinase / HsMuLK / MuLK / Multi-substrate lipid kinase


Mass: 47196.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGK, MULK / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
References: UniProt: Q53H12, diacylglycerol kinase (ATP), ceramide kinase, acylglycerol kinase

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Non-polymers , 2 types, 5 molecules

#7: Chemical ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34
#8: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human TIM22 complex wtih substrate GGC1-sfGFP / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293F / Cellular location: mitochondria / Organelle: mitochondria
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293F
Buffer solutionpH: 7.4
Details: 20 mM HEPES-NaOH pH 7.4, 100 mM NaCl, 0.06% digitonin
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2100 mMsodium chlorideNaCl1
30.6 mg/mLdigitonin1
SpecimenConc.: 3.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K
Details: 1.5 s blot time, 5 s wait time, 100% humidity, and 6 degree centigrade

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5.44 sec. / Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 31755
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.6particle selectionTemplate Picker
2EPU3 5 1.6034image acquisition
4cryoSPARC4.6CTF correctionPatch CTF Estimation
7UCSF ChimeraX1.8model fitting
8Coot0.9.8.96model fitting
10cryoSPARC4.6initial Euler assignmentAb-Initio Reconstruction
13cryoSPARC4.63D reconstructionNon-uniform Refinement
14PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5385617
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 250094 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: Rigid body fitting in ChimeraX and then flexible fitting in Coot
Atomic model buildingSource name: AlphaFold / Type: in silico model

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