7XZI

Cryo-EM structure of TOC-TIC supercomplex from Chlamydomonas reinhardtii


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.77 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.3 of the entry. See complete history


Literature

Architecture of chloroplast TOC-TIC translocon supercomplex.

Liu, H.Li, A.Rochaix, J.D.Liu, Z.

(2023) Nature 615: 349-357

  • DOI: https://doi.org/10.1038/s41586-023-05744-y
  • Primary Citation of Related Structures:  
    7XZI, 7XZJ

  • PubMed Abstract: 

    Chloroplasts rely on the translocon complexes in the outer and inner envelope membranes (the TOC and TIC complexes, respectively) to import thousands of different nuclear-encoded proteins from the cytosol 1-4 . Although previous studies indicated that the TOC and TIC complexes may assemble into larger supercomplexes 5-7 , the overall architectures of the TOC-TIC supercomplexes and the mechanism of preprotein translocation are unclear. Here we report the cryo-electron microscopy structure of the TOC-TIC supercomplex from Chlamydomonas reinhardtii. The major subunits of the TOC complex (Toc75, Toc90 and Toc34) and TIC complex (Tic214, Tic20, Tic100 and Tic56), three chloroplast translocon-associated proteins (Ctap3, Ctap4 and Ctap5) and three newly identified small inner-membrane proteins (Simp1-3) have been located in the supercomplex. As the largest protein, Tic214 traverses the inner membrane, the intermembrane space and the outer membrane, connecting the TOC complex with the TIC proteins. An inositol hexaphosphate molecule is located at the Tic214-Toc90 interface and stabilizes their assembly. Four lipid molecules are located within or above an inner-membrane funnel formed by Tic214, Tic20, Simp1 and Ctap5. Multiple potential pathways found in the TOC-TIC supercomplex may support translocation of different substrate preproteins into chloroplasts.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ctap3A [auth 3]477Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3D4W3 (Chlamydomonas reinhardtii)
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UniProt GroupA0A2K3D4W3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ctap4B [auth 4]363Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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UniProt GroupA8J6H7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ctap5C [auth 5]383Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K3DWN0 (Chlamydomonas reinhardtii)
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Find proteins for A0A2K3DWN5 (Chlamydomonas reinhardtii)
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsA0A2K3DWN5A0A2K3DWN0
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Toc75D [auth 7]798Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8IE32 (Chlamydomonas reinhardtii)
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UniProt GroupA8IE32
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Toc90E [auth 9]967Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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UniProt GroupA0A2K3CR90
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Tic214F [auth A]1,995Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP36495
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Protein TIC 20G [auth B]259Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupA8IZ79
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Tic15H [auth C]127Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Simp3I [auth D]187Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Tic100J [auth E]955Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DQY7 (Chlamydomonas reinhardtii)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Tic56K [auth F]244Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Toc34L [auth G]397Chlamydomonas reinhardtiiMutation(s): 0 
EC: 3.6.5
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Simp2M [auth U]124Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown peptideN [auth X]21Chlamydomonas reinhardtiiMutation(s): 0 
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AJP
Query on AJP

Download Ideal Coordinates CCD File 
FA [auth B],
IA [auth D],
KA [auth D],
O [auth 4],
P [auth 5]
Digitonin
C56 H92 O29
UVYVLBIGDKGWPX-KUAJCENISA-N
LMG (Subject of Investigation/LOI)
Query on LMG

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AA [auth A],
BA [auth B],
Q [auth 5],
Y [auth A],
Z [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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EA [auth B],
GA [auth B],
HA [auth C],
LA [auth F],
U [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
IHP (Subject of Investigation/LOI)
Query on IHP

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T [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
R16
Query on R16

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R [auth 7]HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
D12
Query on D12

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CA [auth B]
DA [auth B]
JA [auth D]
S [auth 9]
V [auth A]
CA [auth B],
DA [auth B],
JA [auth D],
S [auth 9],
V [auth A],
W [auth A],
X [auth A]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.77 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaYSBR-015
National Natural Science Foundation of China (NSFC)China31925024
Chinese Academy of SciencesChinaXDB37020101
Ministry of Science and Technology (MoST, China)China2017YFA0503702

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-01-18
    Changes: Database references
  • Version 1.2: 2023-02-15
    Changes: Database references
  • Version 1.3: 2023-03-22
    Changes: Database references