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- EMDB-9958: Cryo-EM structure of the human mitochondrial translocase TIM22 co... -

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Basic information

Entry
Database: EMDB / ID: EMD-9958
TitleCryo-EM structure of the human mitochondrial translocase TIM22 complex at 3.7 angstrom.
Map dataThe overall cryo-EM map of TIM22 complex at 3.7 angstrom.
Sample
  • Complex: TIM22 translocase
    • 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: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
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 / membrane insertase activity / TIM23 mitochondrial import inner membrane translocase complex / mitochondrion targeting sequence binding / protein transporter activity / protein insertion into mitochondrial inner membrane / ceramide biosynthetic process / Mitochondrial protein import / protein targeting to mitochondrion / protein transmembrane transporter activity / Mitochondrial protein degradation / cell-matrix adhesion / sensory perception of sound / mitochondrial membrane / mitochondrial intermembrane space / Signaling by BRAF and RAF1 fusions / unfolded protein binding / protein-folding chaperone binding / mitochondrial outer membrane / mitochondrial inner membrane / intracellular membrane-bounded organelle / 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: 3.7 Å
AuthorsQi L / Wang Q / Guan Z / Yan C / Yin P
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2018YFA0507700 China
National Natural Science Foundation of China31722017 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
DepositionJun 27, 2019-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7cgp
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9958.png

Downloads & links

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Map

FileDownload / File: emd_9958.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe overall cryo-EM map of TIM22 complex at 3.7 angstrom.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 320 pix.
= 324.48 Å		1.01 Å/pix.
x 320 pix.
= 324.48 Å		1.01 Å/pix.
x 320 pix.
= 324.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0189 / Movie #1: 0.015
Minimum - Maximum-0.04588625 - 0.08768039
Average (Standard dev.)0.00009546748 (±0.0020129622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 324.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z324.480324.480324.480
α/β/γ90.00090.00090.000
start NX/NY/NZ-19-94-60
NX/NY/NZ114128118
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0460.0880.000

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Supplemental data

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Additional map: The cryo-EM map for inter-membrane region of TIM22...

Fileemd_9958_additional_1.map
AnnotationThe cryo-EM map for inter-membrane region of TIM22 complex at 3.5 angstrom.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TIM22 translocase

EntireName: TIM22 translocase
Components
  • Complex: TIM22 translocase
    • 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: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine

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Supramolecule #1: TIM22 translocase

SupramoleculeName: TIM22 translocase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293
Molecular weightTheoretical: 220 kDa/nm

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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: 20.04893 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAAAPNAGG SAPETAGSAE APLQYSLLLQ YLVGDKRQPR LLEPGSLGGI PSPAKSEEQK MIEKAMESCA FKAALACVGG FVLGGAFGV FTAGIDTNVG FDPKDPYRTP TAKEVLKDMG QRGMSYAKNF AIVGAMFSCT ECLIESYRGT SDWKNSVISG C ITGGAIGF ...String:
MAAAAPNAGG SAPETAGSAE APLQYSLLLQ YLVGDKRQPR LLEPGSLGGI PSPAKSEEQK MIEKAMESCA FKAALACVGG FVLGGAFGV FTAGIDTNVG FDPKDPYRTP TAKEVLKDMG QRGMSYAKNF AIVGAMFSCT ECLIESYRGT SDWKNSVISG C ITGGAIGF RAGLKAGAIG CGGFAAFSAA IDYYLR

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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

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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

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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

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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

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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

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Macromolecule #7: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 7 / Number of copies: 1 / Formula: PEE
Molecular weightTheoretical: 749.073 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration7 mg/mL
BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 482959
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)

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