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 7VCF | pdb_00007vcf

Cryo-EM structure of Chlamydomonas TOC-TIC supercomplex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.4 of the entry. See complete history. 

Literature

Structure of a TOC-TIC supercomplex spanning two chloroplast envelope membranes.

Jin, Z., Wan, L., Zhang, Y., Li, X., Cao, Y., Liu, H., Fan, S., Cao, D., Wang, Z., Li, X., Pan, J., Dong, M.Q., Wu, J., Yan, Z.

(2022) Cell 185: 4788-4800.e13

  • DOI: https://doi.org/10.1016/j.cell.2022.10.030
  • Primary Citation Related Structures: 
    7VCF

  • PubMed Abstract: 

    The TOC and TIC complexes are essential translocons that facilitate the import of the nuclear genome-encoded preproteins across the two envelope membranes of chloroplast, but their exact molecular identities and assembly remain unclear. Here, we report a cryoelectron microscopy structure of TOC-TIC supercomplex from Chlamydomonas, containing a total of 14 identified components. The preprotein-conducting pore of TOC is a hybrid β-barrel co-assembled by Toc120 and Toc75, while the potential translocation path of TIC is formed by transmembrane helices from Tic20 and YlmG, rather than a classic model of Tic110. A rigid intermembrane space (IMS) scaffold bridges two chloroplast membranes, and a large hydrophilic cleft on the IMS scaffold connects TOC and TIC, forming a pathway for preprotein translocation. Our study provides structural insights into the TOC-TIC supercomplex composition, assembly, and preprotein translocation mechanism, and lays a foundation to interpret the evolutionary conservation and diversity of this fundamental translocon machinery.


  • Organizational Affiliation: 
    • Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China.

Macromolecule Content 

  • Total Structure Weight: 855.7 kDa 
  • Atom Count: 39,626 
  • Modeled Residue Count: 4,841 
  • Deposited Residue Count: 7,611 
  • Unique protein chains: 15

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tic2141,995Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: ycf78
Membrane Entity: Yes 
UniProt
Find proteins for P36495 (Chlamydomonas reinhardtii)
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UniProt GroupP36495
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Toc75798Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: TOC75, CHLRE_03g175200v5, CHLREDRAFT_195512
Membrane Entity: Yes 
UniProt
Find proteins for A8IE32 (Chlamydomonas reinhardtii)
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UniProt GroupA8IE32
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Toc52477Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: CHLRE_12g532100v5
UniProt
Find proteins for A0A2K3D4W3 (Chlamydomonas reinhardtii)
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UniProt GroupA0A2K3D4W3
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Tic13124Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: CHLRE_12g527550v5, CHLREDRAFT_184901
UniProt
Find proteins for A8J5D4 (Chlamydomonas reinhardtii)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Toc120E [auth F]967Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: CHLRE_17g734300v5
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K3CR90 (Chlamydomonas reinhardtii)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Toc34F [auth G]397Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: TOC34, CHLREDRAFT_187290
EC: 3.6.5
Membrane Entity: Yes 
UniProt
Find proteins for A8HYJ1 (Chlamydomonas reinhardtii)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
YlmGG [auth H]187Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: CHLRE_02g080250v5
UniProt
Find proteins for A0A2K3E0K3 (Chlamydomonas reinhardtii)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Toc39H [auth I]363Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: CHLRE_17g722750v5, CHLREDRAFT_192448
UniProt
Find proteins for A8J6H7 (Chlamydomonas reinhardtii)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Toc10I [auth K]98Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: CHLRE_02g142246v5
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Tic12J [auth M]127Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: CHLRE_09g402100v5, CHLREDRAFT_184536
UniProt
Find proteins for A8J1J3 (Chlamydomonas reinhardtii)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown fragmentK [auth N]18Chlamydomonas reinhardtiiMutation(s): 0 
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Tic35L [auth O]329Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: CHLRE_03g164700v5
UniProt
Find proteins for A0A2K3DWN5 (Chlamydomonas reinhardtii)
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Tic56M [auth Q]244Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: CHLRE_17g727100v5, CHLREDRAFT_184868
UniProt
Find proteins for A8J6R5 (Chlamydomonas reinhardtii)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Tic100N [auth T]955Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: CHLRE_06g300550v5
UniProt
Find proteins for A0A2K3DQY7 (Chlamydomonas reinhardtii)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Tic20-Venus-FlagO [auth W]532Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: TIC20, CHLRE_08g379650v5, CHLREDRAFT_33679
Membrane Entity: Yes 
UniProt
Find proteins for A8IZ79 (Chlamydomonas reinhardtii)
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMG

Query on LMG



Download:Ideal Coordinates CCD File
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
IHP

Query on IHP



Download:Ideal Coordinates CCD File
T [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
U [auth F],
V [auth T]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
SEP
Query on SEP
B
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.0
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2022-12-21
    Changes: Database references
  • Version 1.3: 2024-10-09
    Changes: Data collection, Structure summary
  • Version 1.4: 2025-07-02
    Changes: Data collection