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- PDB-7vcf: Cryo-EM structure of Chlamydomonas TOC-TIC supercomplex -

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Basic information

Entry
Database: PDB / ID: 7vcf
TitleCryo-EM structure of Chlamydomonas TOC-TIC supercomplex
Components
  • Tic100
  • Tic12
  • Tic13
  • Tic20-Venus-Flag
  • Tic214
  • Tic35
  • Tic56
  • Toc10
  • Toc120
  • Toc34
  • Toc39
  • Toc52
  • Toc75
  • Unknown fragment
  • YlmG
KeywordsTRANSLOCASE / Complex / Channel
Function / homology
Function and homology information


protein import into chloroplast stroma / chloroplast inner membrane / chloroplast outer membrane / chloroplast membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein transport / membrane => GO:0016020 / hydrolase activity / GTP binding / membrane / metal ion binding
Similarity search - Function
CCB3/YggT / Chloroplast protein import component Tic20 / Protein TIC56 / YGGT family / Chloroplast import apparatus Tic20-like / GYF domain 2 / GYF domain 2 / GTPase GIMA/IAN/Toc / AIG1-type guanine nucleotide-binding (G) domain / AIG1 family ...CCB3/YggT / Chloroplast protein import component Tic20 / Protein TIC56 / YGGT family / Chloroplast import apparatus Tic20-like / GYF domain 2 / GYF domain 2 / GTPase GIMA/IAN/Toc / AIG1-type guanine nucleotide-binding (G) domain / AIG1 family / AIG1-type G domain profile. / Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / MORN motif / MORN repeat / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / AIG1-type G domain-containing protein / Flagellar associated protein / Uncharacterized protein / J domain-containing protein / YggT family protein / YtxH domain-containing protein / Translocase of chloroplast 34 homolog, chloroplastic / Bacterial surface antigen (D15) domain-containing protein ...INOSITOL HEXAKISPHOSPHATE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / AIG1-type G domain-containing protein / Flagellar associated protein / Uncharacterized protein / J domain-containing protein / YggT family protein / YtxH domain-containing protein / Translocase of chloroplast 34 homolog, chloroplastic / Bacterial surface antigen (D15) domain-containing protein / Protein TIC 20 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized membrane protein ycf78
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsWu, J. / Yan, Z. / Jin, Z. / Zhang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2022
Title: Structure of a TOC-TIC supercomplex spanning two chloroplast envelope membranes.
Authors: Zeyu Jin / Li Wan / Yuqi Zhang / Xuecheng Li / Yong Cao / Haobin Liu / Shengyao Fan / Du Cao / Zhengmao Wang / Xiaobo Li / Junmin Pan / Meng-Qiu Dong / Jianping Wu / Zhen Yan /
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 ...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.
History
DepositionSep 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 21, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tic214
B: Toc75
C: Toc52
D: Tic13
F: Toc120
G: Toc34
H: YlmG
I: Toc39
K: Toc10
M: Tic12
N: Unknown fragment
O: Tic35
Q: Tic56
T: Tic100
W: Tic20-Venus-Flag
hetero molecules


Theoretical massNumber of molelcules
Total (without water)855,69722
Polymers851,84015
Non-polymers3,8577
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 14 types, 14 molecules ABCDFGHIKMOQTW

#1: Protein Tic214 / Uncharacterized membrane protein ycf78


Mass: 232615.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: ycf78 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: P36495
#2: Protein Toc75 / 75 kDa chloroplast membrane translocon


Mass: 87493.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: TOC75, CHLRE_03g175200v5, CHLREDRAFT_195512 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: A8IE32
#3: Protein Toc52


Mass: 52062.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_12g532100v5 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D4W3
#4: Protein Tic13


Mass: 13426.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_12g527550v5, CHLREDRAFT_184901 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: A8J5D4
#5: Protein Toc120 / AIG1-type G domain-containing protein


Mass: 102495.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_17g734300v5 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CR90
#6: Protein Toc34 / Translocase of chloroplast 34 homolog / chloroplastic


Mass: 44598.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: TOC34, CHLREDRAFT_187290 / Production host: Chlamydomonas reinhardtii (plant)
References: UniProt: A8HYJ1, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#7: Protein YlmG


Mass: 21425.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_02g080250v5 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3E0K3
#8: Protein Toc39


Mass: 39025.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_17g722750v5, CHLREDRAFT_192448 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: A8J6H7
#9: Protein Toc10


Mass: 10569.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_02g142246v5 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3E4D9
#10: Protein Tic12


Mass: 14662.776 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_09g402100v5, CHLREDRAFT_184536 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: A8J1J3
#12: Protein Tic35


Mass: 35633.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_03g164700v5 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DWN5
#13: Protein Tic56


Mass: 28046.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_17g727100v5, CHLREDRAFT_184868 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: A8J6R5
#14: Protein Tic100


Mass: 107337.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_06g300550v5 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DQY7
#15: Protein Tic20-Venus-Flag


Mass: 60260.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: TIC20, CHLRE_08g379650v5, CHLREDRAFT_33679 / Production host: Chlamydomonas reinhardtii (plant) / References: UniProt: A8IZ79

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Protein/peptide , 1 types, 1 molecules N

#11: Protein/peptide Unknown fragment


Mass: 2188.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: Chlamydomonas reinhardtii (plant)

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Non-polymers , 4 types, 9 molecules

#16: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H86O10
#17: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#18: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#19: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: TOC-TIC supercomplex / Type: COMPLEX / Entity ID: #1-#15 / Source: RECOMBINANT
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Source (recombinant)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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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 FIELDBright-field microscopy / Nominal magnification: 82000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1400 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.1_3865: / Classification: refinement
EM softwareName: cryoSPARC / Version: 3.3.0 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 595638 / Algorithm: BACK PROJECTION / Symmetry type: POINT
RefinementHighest resolution: 2.5 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00639780
ELECTRON MICROSCOPYf_angle_d0.99453823
ELECTRON MICROSCOPYf_dihedral_angle_d23.1645485
ELECTRON MICROSCOPYf_chiral_restr0.065678
ELECTRON MICROSCOPYf_plane_restr0.0086897

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