8XQX

Cryo-EM structure of the Ycf2-FtsHi motor complex from Chlamydomonas reinhardtii in apo state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Conservation and specialization of the Ycf2-FtsHi chloroplast protein import motor in green algae.

Liang, K.Zhan, X.Li, Y.Yang, Y.Xie, Y.Jin, Z.Xu, X.Zhang, W.Lu, Y.Zhang, S.Zou, Y.Feng, S.Wu, J.Yan, Z.

(2024) Cell 187: 5638-5650.e18

  • DOI: https://doi.org/10.1016/j.cell.2024.08.002
  • Primary Citation of Related Structures:  
    8XQW, 8XQX

  • PubMed Abstract: 

    The protein import motor in chloroplasts plays a pivotal role in their biogenesis and homeostasis by driving the translocation of preproteins into chloroplasts. While the Ycf2-FtsHi complex serves as the import motor in land plants, its evolutionary conservation, specialization, and mechanisms across photosynthetic organisms are largely unexplored. Here, we isolated and determined the cryogenic electron microscopy (cryo-EM) structures of the native Ycf2-FtsHi complex from Chlamydomonas reinhardtii, uncovering a complex composed of up to 19 subunits, including multiple green-algae-specific components. The heterohexameric AAA+ ATPase motor module is tilted, potentially facilitating preprotein handover from the translocon at the inner chloroplast membrane (TIC) complex. Preprotein interacts with Ycf2-FtsHi and enhances its ATPase activity in vitro. Integrating Ycf2-FtsHi and translocon at the outer chloroplast membrane (TOC)-TIC supercomplex structures reveals insights into their physical and functional interplay during preprotein translocation. By comparing these findings with those from land plants, our study establishes a structural foundation for understanding the assembly, function, evolutionary conservation, and diversity of chloroplast protein import motors.


  • Organizational Affiliation

    College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310024, China; 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fhl11,182Chlamydomonas reinhardtiiMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fhl3
B, C
1,112Chlamydomonas reinhardtiiMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ycf22,971Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A218N8A7 (Chlamydomonas reinhardtii)
Explore A0A218N8A7 
Go to UniProtKB:  A0A218N8A7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A218N8A7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ctap1982Chlamydomonas reinhardtiiMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ctap61,024Chlamydomonas reinhardtiiMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ARHL495Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DLI2 (Chlamydomonas reinhardtii)
Explore A0A2K3DLI2 
Go to UniProtKB:  A0A2K3DLI2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K3DLI2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PcyA555Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8HUP3 (Chlamydomonas reinhardtii)
Explore A8HUP3 
Go to UniProtKB:  A8HUP3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8HUP3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
CrTam39366Chlamydomonas reinhardtiiMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ACP117Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q6UKY5 (Chlamydomonas reinhardtii)
Explore Q6UKY5 
Go to UniProtKB:  Q6UKY5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6UKY5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
CrTam29255Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3CY83 (Chlamydomonas reinhardtii)
Explore A0A2K3CY83 
Go to UniProtKB:  A0A2K3CY83
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K3CY83
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
CrTam34303Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3CZ99 (Chlamydomonas reinhardtii)
Explore A0A2K3CZ99 
Go to UniProtKB:  A0A2K3CZ99
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K3CZ99
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
FADL682Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DQ46 (Chlamydomonas reinhardtii)
Explore A0A2K3DQ46 
Go to UniProtKB:  A0A2K3DQ46
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K3DQ46
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
CrTam15137Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8ISA4 (Chlamydomonas reinhardtii)
Explore A8ISA4 
Go to UniProtKB:  A8ISA4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8ISA4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
CrTam49471Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DVJ8 (Chlamydomonas reinhardtii)
Explore A0A2K3DVJ8 
Go to UniProtKB:  A0A2K3DVJ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K3DVJ8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ctap7691Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DHV6 (Chlamydomonas reinhardtii)
Explore A0A2K3DHV6 
Go to UniProtKB:  A0A2K3DHV6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K3DHV6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Tic22365Chlamydomonas reinhardtiiMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
DnaJ462Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DGW6 (Chlamydomonas reinhardtii)
Explore A0A2K3DGW6 
Go to UniProtKB:  A0A2K3DGW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K3DGW6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
CrTam35324Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3E633 (Chlamydomonas reinhardtii)
Explore A0A2K3E633 
Go to UniProtKB:  A0A2K3E633
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K3E633
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
CrTam31299Chlamydomonas reinhardtiiMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
UNK156Chlamydomonas reinhardtiiMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
UNK86Chlamydomonas reinhardtiiMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

Download Ideal Coordinates CCD File 
EA [auth I],
KA [auth N]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
SQD
Query on SQD

Download Ideal Coordinates CCD File 
CA [auth I],
GA [auth K],
Y [auth B]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG

Download Ideal Coordinates CCD File 
DA [auth I],
FA [auth K],
IA [auth M],
W [auth A],
Z [auth C]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
DGA
Query on DGA

Download Ideal Coordinates CCD File 
AA [auth D],
HA [auth L]
DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
Y01
Query on Y01

Download Ideal Coordinates CCD File 
BA [auth D],
JA [auth M]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
A1LXL
Query on A1LXL

Download Ideal Coordinates CCD File 
LA [auth P],
MA [auth P]
Beta-Sitosterol
C29 H50 O
KZJWDPNRJALLNS-VJSFXXLFSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
NA [auth R],
OA [auth R]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
X [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
B, C
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
4HH
Query on 4HH
J
L-PEPTIDE LINKINGC14 H28 N3 O9 P SSER
SEP
Query on SEP
R
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32271239

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 2.0: 2024-11-27
    Type: Coordinate replacement
    Reason: Chirality error
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary