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- PDB-8z9y: Cryo-EM Structure of the Arabidopsis thaliana TIC Complex -

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Basic information

Entry
Database: PDB / ID: 8z9y
TitleCryo-EM Structure of the Arabidopsis thaliana TIC Complex
Components
  • Actin T1-like protein
  • Nucleusenvelope protein
  • Protein TIC 100
  • Protein TIC 20-I, chloroplastic
  • Protein TIC 214
  • Protein TIC 56, chloroplastic
KeywordsTRANSLOCASE / Complex / Channel / Membrane protein.
Function / homology
Function and homology information


chloroplast targeting sequence binding / Tic complex / protein import into chloroplast stroma / chloroplast inner membrane / chloroplast organization / embryo development ending in seed dormancy / chloroplast envelope / plastid / chloroplast thylakoid membrane / protein transmembrane transporter activity ...chloroplast targeting sequence binding / Tic complex / protein import into chloroplast stroma / chloroplast inner membrane / chloroplast organization / embryo development ending in seed dormancy / chloroplast envelope / plastid / chloroplast thylakoid membrane / protein transmembrane transporter activity / chloroplast / nucleus / plasma membrane / cytosol
Similarity search - Function
Protein TIC214 / Ycf1 / Chloroplast protein import component Tic20 / Protein TIC56 / Chloroplast import apparatus Tic20-like / GYF domain 2 / GYF domain 2 / MORN motif / MORN repeat
Similarity search - Domain/homology
Protein TIC 214 / Actin T1-like protein / Protein TIC 56, chloroplastic / Protein TIC 20-I, chloroplastic / Protein TIC 100 / Nucleusenvelope protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsWu, J. / Yan, Z. / Jin, Z. / Xu, Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2024
Title: Structural insights into the chloroplast protein import in land plants.
Authors: Ke Liang / Zeyu Jin / Xiechao Zhan / Yuxin Li / Qikui Xu / Yanqiu Xie / Yi Yang / Shaojie Wang / Jianping Wu / Zhen Yan /
Abstract: Chloroplast proteins are imported via the translocon at the outer chloroplast membrane (TOC)-translocon at the inner chloroplast membrane (TIC) supercomplex, driven by an ATPase motor. The Ycf2-FtsHi ...Chloroplast proteins are imported via the translocon at the outer chloroplast membrane (TOC)-translocon at the inner chloroplast membrane (TIC) supercomplex, driven by an ATPase motor. The Ycf2-FtsHi complex has been identified as the chloroplast import motor. However, its assembly and cooperation with the TIC complex during preprotein translocation remain unclear. Here, we present the structures of the Ycf2-FtsHi and TIC complexes from Arabidopsis and an ultracomplex formed between them from Pisum. The Ycf2-FtsHi structure reveals a heterohexameric AAA+ ATPase motor module with characteristic features. Four previously uncharacterized components of Ycf2-FtsHi were identified, which aid in complex assembly and anchoring of the motor module at a tilted angle relative to the membrane. When considering the structures of the TIC complex and the TIC-Ycf2-FtsHi ultracomplex together, it becomes evident that the tilted motor module of Ycf2-FtsHi enables its close contact with the TIC complex, thereby facilitating efficient preprotein translocation. Our study provides valuable structural insights into the chloroplast protein import process in land plants.
History
DepositionApr 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein TIC 214
B: Protein TIC 20-I, chloroplastic
C: Actin T1-like protein
D: Protein TIC 100
E: Protein TIC 56, chloroplastic
F: Nucleusenvelope protein


Theoretical massNumber of molelcules
Total (without water)449,9346
Polymers449,9346
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 6 molecules ABCDEF

#1: Protein Protein TIC 214 / Translocon at the inner envelope membrane of chloroplasts 214 / AtTIC214


Mass: 214072.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56785
#2: Protein Protein TIC 20-I, chloroplastic / Translocon at the inner envelope membrane of chloroplasts 20-I / AtTIC20-I


Mass: 31235.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8GZ79
#3: Protein Actin T1-like protein / Tic12 / At3g09860


Mass: 12114.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q6IDB3
#4: Protein Protein TIC 100 / Protein EMBRYO DEFECTIVE 1211 / Translocon at the inner envelope membrane of chloroplasts 100 / AtTIC100


Mass: 100060.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LPR8
#5: Protein Protein TIC 56, chloroplastic / Tic35 / Translocon at the inner envelope membrane of chloroplasts 56 / AtTIC56


Mass: 61710.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q7Y1W1
#6: Protein Nucleusenvelope protein


Mass: 30739.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8VYY8

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Arabidopsis thaliana TIC Complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 316225 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00317191
ELECTRON MICROSCOPYf_angle_d0.62823282
ELECTRON MICROSCOPYf_dihedral_angle_d4.5252184
ELECTRON MICROSCOPYf_chiral_restr0.0432368
ELECTRON MICROSCOPYf_plane_restr0.0052951

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