8XQX | pdb_00008xqx

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

Validation slider image for 8XQX

This is version 3.0 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 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.

Macromolecule Content 

  • Total Structure Weight: 1,553.13 kDa 
  • Atom Count: 73,189 
  • Modeled Residue Count: 9,468 
  • Deposited Residue Count: 14,147 
  • Unique protein chains: 21

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fhl11,182Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fhl3
B, C
1,112Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Ycf22,971Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A218N8A7 (Chlamydomonas reinhardtii)
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Entity Groups
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UniProt GroupA0A218N8A7
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Ctap1982Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Ctap61,024Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
ARHL495Chlamydomonas reinhardtiiMutation(s): 0 
EC: 3.2.1.143
UniProt
Find proteins for A0A2K3DLI2 (Chlamydomonas reinhardtii)
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UniProt GroupA0A2K3DLI2
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
PcyA555Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8HUP3 (Chlamydomonas reinhardtii)
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UniProt GroupA8HUP3
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
CrTam39366Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
ACP117Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q6UKY5 (Chlamydomonas reinhardtii)
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UniProt GroupQ6UKY5
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
CrTam29255Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3CY83 (Chlamydomonas reinhardtii)
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UniProt GroupA0A2K3CY83
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
CrTam34303Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3CZ99 (Chlamydomonas reinhardtii)
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UniProt GroupA0A2K3CZ99
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
FADL682Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DQ46 (Chlamydomonas reinhardtii)
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UniProt GroupA0A2K3DQ46
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
CrTam15137Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8ISA4 (Chlamydomonas reinhardtii)
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UniProt GroupA8ISA4
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
CrTam49471Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DVJ8 (Chlamydomonas reinhardtii)
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UniProt GroupA0A2K3DVJ8
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Ctap7691Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DHV6 (Chlamydomonas reinhardtii)
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UniProt GroupA0A2K3DHV6
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Tic22365Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
DnaJ462Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DGW6 (Chlamydomonas reinhardtii)
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UniProt GroupA0A2K3DGW6
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
CrTam35324Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3E633 (Chlamydomonas reinhardtii)
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
CrTam31299Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
UNK156Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
UNK86Chlamydomonas reinhardtiiMutation(s): 0 

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
UNK
Query on UNK
U
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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
  • Version 3.0: 2025-06-18
    Changes: Data collection, Non-polymer description, Structure summary