+Open data
-Basic information
Entry | Database: PDB / ID: 6vxk | ||||||||||||||||||
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Title | Cryo-EM Structure of the full-length A39R/PlexinC1 complex | ||||||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / receptor / signaling / plexin | ||||||||||||||||||
Function / homology | Function and homology information semaphorin receptor binding / regulation of synapse pruning / cerebellar climbing fiber to Purkinje cell synapse / Other semaphorin interactions / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / positive regulation of axonogenesis / regulation of cell migration / regulation of cell shape ...semaphorin receptor binding / regulation of synapse pruning / cerebellar climbing fiber to Purkinje cell synapse / Other semaphorin interactions / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / positive regulation of axonogenesis / regulation of cell migration / regulation of cell shape / cell adhesion / signaling receptor binding / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Ectromelia virus Homo sapiens (human) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||
Authors | Kuo, Y.-C. / Chen, H. / Shang, G. / Uchikawa, E. / Tian, H. / Bai, X. / Zhang, X. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: Nat Commun / Year: 2020 Title: Cryo-EM structure of the PlexinC1/A39R complex reveals inter-domain interactions critical for ligand-induced activation. Authors: Yi-Chun Kuo / Hua Chen / Guijun Shang / Emiko Uchikawa / Hui Tian / Xiao-Chen Bai / Xuewu Zhang / Abstract: Plexins are receptors for semaphorins that transduce signals for regulating neuronal development and other processes. Plexins are single-pass transmembrane proteins with multiple domains in both the ...Plexins are receptors for semaphorins that transduce signals for regulating neuronal development and other processes. Plexins are single-pass transmembrane proteins with multiple domains in both the extracellular and intracellular regions. Semaphorin activates plexin by binding to its extracellular N-terminal Sema domain, inducing the active dimer of the plexin intracellular region. The mechanism underlying this activation process of plexin is incompletely understood. We present cryo-electron microscopic structure of full-length human PlexinC1 in complex with the viral semaphorin mimic A39R. The structure shows that A39R induces a specific dimer of PlexinC1 where the membrane-proximal domains from the two PlexinC1 protomers are placed close to each other, poised to promote the active dimer of the intracellular region. This configuration is imposed by a distinct conformation of the PlexinC1 extracellular region, stabilized by inter-domain interactions among the Sema and membrane-proximal domains. Our mutational analyses support the critical role of this conformation in PlexinC1 activation. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6vxk.cif.gz | 434.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vxk.ent.gz | 324.5 KB | Display | PDB format |
PDBx/mmJSON format | 6vxk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vxk_validation.pdf.gz | 844.8 KB | Display | wwPDB validaton report |
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Full document | 6vxk_full_validation.pdf.gz | 894.3 KB | Display | |
Data in XML | 6vxk_validation.xml.gz | 65.9 KB | Display | |
Data in CIF | 6vxk_validation.cif.gz | 100.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/6vxk ftp://data.pdbj.org/pub/pdb/validation_reports/vx/6vxk | HTTPS FTP |
-Related structure data
Related structure data | 21442MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 45330.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ectromelia virus (strain Moscow) / Strain: Moscow / Gene: EVM139, SEMA / Production host: Homo sapiens (human) / References: UniProt: Q8JL80 #2: Protein | Mass: 173487.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNC1, VESPR / Production host: Homo sapiens (human) / References: UniProt: O60486 #3: Sugar | ChemComp-NAG / 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
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Specimen support | Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 | ||||||||||||||||||||||||||||
Vitrification | Cryogen name: NITROGEN |
-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 |
Image recording | Electron dose: 2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143750 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 3NVN | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 100.65 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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