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- PDB-6vxk: Cryo-EM Structure of the full-length A39R/PlexinC1 complex -

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Basic information

Entry
Database: PDB / ID: 6vxk
TitleCryo-EM Structure of the full-length A39R/PlexinC1 complex
Components
  • Plexin-C1
  • Semaphorin-like protein 139
KeywordsMEMBRANE PROTEIN / receptor / signaling / plexin
Function / homology
Function and homology information


regulation of synapse pruning / semaphorin receptor binding / cerebellar climbing fiber to Purkinje cell synapse / Other semaphorin interactions / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / positive regulation of axonogenesis / regulation of cell migration ...regulation of synapse pruning / semaphorin receptor binding / cerebellar climbing fiber to Purkinje cell synapse / Other semaphorin interactions / semaphorin-plexin signaling pathway involved in axon guidance / 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
Plexin-C1, Sema domain / Semaphorin / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain ...Plexin-C1, Sema domain / Semaphorin / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / Rho GTPase activation protein / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Plexin-C1 / Semaphorin-like protein 139
Similarity search - Component
Biological speciesEctromelia virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKuo, Y.-C. / Chen, H. / Shang, G. / Uchikawa, E. / Tian, H. / Bai, X. / Zhang, X.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130289 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP160082 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP170644 United States
Welch FoundationI-1702 United States
Welch FoundationI-1944 United States
CitationJournal: 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
DepositionFeb 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

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Assembly

Deposited unit
A: Semaphorin-like protein 139
B: Plexin-C1
C: Semaphorin-like protein 139
D: Plexin-C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,61622
Polymers437,6344
Non-polymers3,98218
Water0
1


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

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Components

#1: Protein Semaphorin-like protein 139


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 Plexin-C1 / Virus-encoded semaphorin protein receptor


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 / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Complex between A39R and PlexinC1COMPLEXFull-length PlexinC1 in complex with A39R#1-#20RECOMBINANT
2A39R dimerCOMPLEX#11RECOMBINANT
3PlexinC1COMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.4 MDaNO
210.1 MDaNO
310.4 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Ectromelia virus12643
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESHEPES1
2150 mMNaClSodium chlorideNaClSodium chloride1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationCryogen name: NITROGEN

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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
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refinedev_3724refinement
PHENIXdev_3724refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143750 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 3NVN

3nvn

RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 100.65 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.011117764
ELECTRON MICROSCOPYf_angle_d0.772324110
ELECTRON MICROSCOPYf_chiral_restr0.05222800
ELECTRON MICROSCOPYf_plane_restr0.00413068
ELECTRON MICROSCOPYf_dihedral_angle_d14.54082518

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