8XKS | pdb_00008xks

The cryo-EM structure of Orf2971-FtsHi motor complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Architecture of the ATP-driven motor for protein import into chloroplasts.

Wang, N.Xing, J.Su, X.Pan, J.Chen, H.Shi, L.Si, L.Yang, W.Li, M.

(2024) Mol Plant 17: 1702-1718

  • DOI: https://doi.org/10.1016/j.molp.2024.09.010
  • Primary Citation of Related Structures:  
    8XKS

  • PubMed Abstract: 

    Thousands of nuclear-encoded proteins are transported into chloroplasts through the TOC-TIC translocon that spans the chloroplast envelope membranes. A motor complex pulls the translocated proteins out of the TOC-TIC complex into the chloroplast stroma by hydrolyzing ATP. The Orf2971-FtsHi complex has been suggested to serve as the ATP-hydrolyzing motor in Chlamydomonas reinhardtii, but little is known about its architecture and assembly. Here, we report the 3.2-Å resolution structure of the Chlamydomonas Orf2971-FtsHi complex. The 20-subunit complex spans the chloroplast inner envelope, with two bulky modules protruding into the intermembrane space and stromal matrix. Six subunits form a hetero-hexamer that potentially provides the pulling force through ATP hydrolysis. The remaining subunits, including potential enzymes/chaperones, likely facilitate the complex assembly and regulate its proper function. Taken together, our results provide the structural foundation for a mechanistic understanding of chloroplast protein translocation.


  • Organizational Affiliation
    • Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ctap1982Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3CRM9 (Chlamydomonas reinhardtii)
Explore A0A2K3CRM9 
Go to UniProtKB:  A0A2K3CRM9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K3CRM9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fhl21,024Chlamydomonas 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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
4Fe-4S ferredoxin-type domain-containing protein462Chlamydomonas 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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
AAA+ ATPase domain-containing protein1,178Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DZD9 (Chlamydomonas reinhardtii)
Explore A0A2K3DZD9 
Go to UniProtKB:  A0A2K3DZD9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K3DZD9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized 341.7 kDa protein in psbD-psbC intergenic region2,971Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q32065 (Chlamydomonas reinhardtii)
Explore Q32065 
Go to UniProtKB:  Q32065
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ32065
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
AAA+ ATPase domain-containing protein
F, G
1,058Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DLF7 (Chlamydomonas reinhardtii)
Explore A0A2K3DLF7 
Go to UniProtKB:  A0A2K3DLF7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K3DLF7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Flagellar associated protein691Chlamydomonas 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: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Tic22330Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3CYB6 (Chlamydomonas reinhardtii)
Explore A0A2K3CYB6 
Go to UniProtKB:  A0A2K3CYB6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K3CYB6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
FaxL365Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DM81 (Chlamydomonas reinhardtii)
Explore A0A2K3DM81 
Go to UniProtKB:  A0A2K3DM81
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K3DM81
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Fatty acid desaturase domain-containing protein682Chlamydomonas 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: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Moc25255Chlamydomonas 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: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Moc29303Chlamydomonas 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: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Moc34324Chlamydomonas 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: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Moc45471Chlamydomonas 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
PcyA1555Chlamydomonas 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: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosylglycohydrolase495Chlamydomonas reinhardtiiMutation(s): 0 
EC: 3.2.1.143
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: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein117Chlamydomonas 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: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Moc13137Chlamydomonas 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: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Moc31299Chlamydomonas reinhardtiiMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

Download Ideal Coordinates CCD File 
BA [auth L],
X [auth J]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
SQD
Query on SQD

Download Ideal Coordinates CCD File 
CA [auth L]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 
AA [auth L],
Y [auth J]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
DGA (Subject of Investigation/LOI)
Query on DGA

Download Ideal Coordinates CCD File 
W [auth H]DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
ACD (Subject of Investigation/LOI)
Query on ACD

Download Ideal Coordinates CCD File 
Z [auth K]ARACHIDONIC ACID
C20 H32 O2
YZXBAPSDXZZRGB-DOFZRALJSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
U [auth C],
V [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
R
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release