+Open data
-Basic information
Entry | Database: PDB / ID: 7vcf | ||||||
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Title | Cryo-EM structure of Chlamydomonas TOC-TIC supercomplex | ||||||
Components |
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Keywords | TRANSLOCASE / Complex / Channel | ||||||
Function / homology | Function and homology information protein import into chloroplast stroma / protein targeting to chloroplast / chloroplast inner membrane / chloroplast outer membrane / chloroplast membrane / chloroplast organization / axoneme assembly / motile cilium / spermatid development / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement ...protein import into chloroplast stroma / protein targeting to chloroplast / chloroplast inner membrane / chloroplast outer membrane / chloroplast membrane / chloroplast organization / axoneme assembly / motile cilium / spermatid development / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein transport / membrane => GO:0016020 / hydrolase activity / GTP binding / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||
Authors | Wu, J. / Yan, Z. / Jin, Z. / Zhang, Y. | ||||||
Funding support | 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vcf.cif.gz | 926.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vcf.ent.gz | 728.5 KB | Display | PDB format |
PDBx/mmJSON format | 7vcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vcf_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7vcf_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7vcf_validation.xml.gz | 127.6 KB | Display | |
Data in CIF | 7vcf_validation.cif.gz | 196.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/7vcf ftp://data.pdbj.org/pub/pdb/validation_reports/vc/7vcf | HTTPS FTP |
-Related structure data
Related structure data | 31890MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 14 types, 14 molecules ABCDFGHIKMOQTW
#1: Protein | 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 |
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#2: Protein | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 |
-Protein/peptide , 1 types, 1 molecules N
#11: Protein/peptide | 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 / #17: Chemical | ChemComp-IHP / | #18: Chemical | #19: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: TOC-TIC supercomplex / Type: COMPLEX / Entity ID: #1-#15 / Source: RECOMBINANT |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
Source (recombinant) | Organism: Chlamydomonas reinhardtii (plant) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / 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 holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.1_3865: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: cryoSPARC / Version: 3.3.0 / Category: 3D reconstruction | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 595638 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 2.5 Å | ||||||||||||||||||||||||
Refine LS restraints |
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