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- PDB-7cgp: Cryo-EM structure of the human mitochondrial translocase TIM22 co... -

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Basic information

Entry
Database: PDB / ID: 7cgp
TitleCryo-EM structure of the human mitochondrial translocase TIM22 complex at 3.7 angstrom.
Components
  • (Mitochondrial import inner membrane translocase subunit ...) x 5
  • Acylglycerol kinase, mitochondrial
KeywordsTRANSLOCASE / human mitochondrial translocase TIM22 complex / inner membrane / chaperone Tim9/10a / chaperone Tim9/10a/10b
Function / homology
Function and homology information


ceramide kinase / acylglycerol kinase / ceramide kinase activity / acylglycerol kinase activity / dihydroceramide kinase activity / Glycerophospholipid biosynthesis / mitochondrial intermembrane space protein transporter complex / glycerolipid metabolic process / : / lipid kinase activity ...ceramide kinase / acylglycerol kinase / ceramide kinase activity / acylglycerol kinase activity / dihydroceramide kinase activity / Glycerophospholipid biosynthesis / mitochondrial intermembrane space protein transporter complex / glycerolipid metabolic process / : / lipid kinase activity / diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / membrane insertase activity / TIM23 mitochondrial import inner membrane translocase complex / mitochondrion targeting sequence binding / TIM22 mitochondrial import inner membrane insertion complex / NAD+ kinase activity / protein transporter activity / protein insertion into mitochondrial inner membrane / sphingolipid metabolic process / ceramide biosynthetic process / Mitochondrial protein import / protein targeting to mitochondrion / protein transmembrane transporter activity / Mitochondrial protein degradation / cell-matrix adhesion / mitochondrial membrane / sensory perception of sound / mitochondrial intermembrane space / Signaling by BRAF and RAF1 fusions / protein-folding chaperone binding / mitochondrial outer membrane / mitochondrial inner membrane / membrane => GO:0016020 / phosphorylation / intracellular membrane-bounded organelle / protein homodimerization activity / mitochondrion / zinc ion binding / ATP binding / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Acylglycerol kinase C-terminal / Mitochondrial import inner membrane translocase subunit Tim29 / Translocase of the Inner Mitochondrial membrane 29 / Mitochondrial import inner membrane translocase subunit TIM22 / Tim10-like / Tim10-like domain superfamily / Tim10/DDP family zinc finger / Diacylglycerol kinase, catalytic domain / Diacylglycerol kinase catalytic domain / DAG-kinase catalytic (DAGKc) domain profile. ...Acylglycerol kinase C-terminal / Mitochondrial import inner membrane translocase subunit Tim29 / Translocase of the Inner Mitochondrial membrane 29 / Mitochondrial import inner membrane translocase subunit TIM22 / Tim10-like / Tim10-like domain superfamily / Tim10/DDP family zinc finger / Diacylglycerol kinase, catalytic domain / Diacylglycerol kinase catalytic domain / DAG-kinase catalytic (DAGKc) domain profile. / Diacylglycerol kinase catalytic domain (presumed) / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily / Tim17/Tim22/Tim23/Pmp24 family
Similarity search - Domain/homology
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / 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: 3.7 Å
AuthorsQi, L. / Wang, Q. / Guan, Z. / Yan, C. / Yin, P.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0507700 China
National Natural Science Foundation of China (NSFC)31722017 China
CitationJournal: Cell Res / Year: 2021
Title: Cryo-EM structure of the human mitochondrial translocase TIM22 complex.
Authors: Liangbo Qi / Qiang Wang / Zeyuan Guan / Yan Wu / Cuicui Shen / Sixing Hong / Jianbo Cao / Xing Zhang / Chuangye Yan / Ping Yin /
History
DepositionJul 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

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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)222,92116
Polymers222,17215
Non-polymers7491
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area44100 Å2
ΔGint-297 kcal/mol
Surface area84430 Å2

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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: 20048.930 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): HEK293 / 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): HEK293 / 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): HEK293 / 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): HEK293 / 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): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9Y5J6

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Protein / Non-polymers , 2 types, 2 molecules B

#2: Protein Acylglycerol kinase, mitochondrial / hAGK / Multiple substrate lipid kinase / 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): HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q53H12, diacylglycerol kinase (ATP), ceramide kinase, acylglycerol kinase
#7: Chemical ChemComp-PEE / 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 749.073 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H83NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM

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Details

Has ligand of interestY

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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: TIM22 translocase / Type: COMPLEX / Entity ID: #1-#2, #4-#5 / Source: RECOMBINANT
Molecular weightValue: 220 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 6
SpecimenConc.: 7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 482959 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01212746
ELECTRON MICROSCOPYf_angle_d0.92317157
ELECTRON MICROSCOPYf_dihedral_angle_d20.8981743
ELECTRON MICROSCOPYf_chiral_restr0.0531911
ELECTRON MICROSCOPYf_plane_restr0.0052183

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