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- EMDB-21442: Cryo-EM Structure of the full-length A39R/PlexinC1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-21442
TitleCryo-EM Structure of the full-length A39R/PlexinC1 complex
Map dataDimeric map
Sample
  • Complex: Complex between A39R and PlexinC1
    • Complex: A39R dimer
      • Protein or peptide: Semaphorin-like protein 139
    • Complex: PlexinC1
      • Protein or peptide: Plexin-C1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsreceptor / signaling / plexin / MEMBRANE PROTEIN
Function / homology
Function and homology information


semaphorin receptor binding / Other semaphorin interactions / cerebellar climbing fiber to Purkinje cell synapse / regulation of synapse pruning / semaphorin receptor complex / negative regulation of cell adhesion / chemorepellent activity / semaphorin receptor activity / positive regulation of axonogenesis / semaphorin-plexin signaling pathway ...semaphorin receptor binding / Other semaphorin interactions / cerebellar climbing fiber to Purkinje cell synapse / regulation of synapse pruning / semaphorin receptor complex / negative regulation of cell adhesion / chemorepellent activity / semaphorin receptor activity / positive regulation of axonogenesis / semaphorin-plexin signaling pathway / synapse assembly / regulation of cell migration / integrin-mediated signaling pathway / integrin binding / regulation of cell shape / regulation of inflammatory response / cell adhesion / positive regulation of cell migration / signaling receptor binding / extracellular region / membrane / plasma membrane
Similarity search - Function
Plexin-C1, Sema domain / Semaphorin / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain ...Plexin-C1, Sema domain / Semaphorin / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding 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 / IPT domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Plexin-C1 / Semaphorin-like protein 139
Similarity search - Component
Biological speciesHomo sapiens (human) / Ectromelia virus / Ectromelia virus (strain Moscow)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKuo Y-C / Chen H
Funding support United States, 5 items
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, 2020-
Header (metadata) releaseMar 4, 2020-
Map releaseApr 29, 2020-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.009
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vxk
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21442.png

Downloads & links

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Map

FileDownload / File: emd_21442.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDimeric map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.009
Minimum - Maximum-0.019878436 - 0.058618017
Average (Standard dev.)0.00013637892 (±0.0016063284)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.08002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8280.8280.828
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z298.080298.080298.080
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ350350350
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0200.0590.000

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Supplemental data

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Additional map: Focused refined half map

Fileemd_21442_additional.map
AnnotationFocused refined half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex between A39R and PlexinC1

EntireName: Complex between A39R and PlexinC1
Components
  • Complex: Complex between A39R and PlexinC1
    • Complex: A39R dimer
      • Protein or peptide: Semaphorin-like protein 139
    • Complex: PlexinC1
      • Protein or peptide: Plexin-C1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex between A39R and PlexinC1

SupramoleculeName: Complex between A39R and PlexinC1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Full-length PlexinC1 in complex with A39R
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 400 KDa

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Supramolecule #2: A39R dimer

SupramoleculeName: A39R dimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Ectromelia virus

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Supramolecule #3: PlexinC1

SupramoleculeName: PlexinC1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Semaphorin-like protein 139

MacromoleculeName: Semaphorin-like protein 139 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Ectromelia virus (strain Moscow) / Strain: Moscow
Molecular weightTheoretical: 45.330195 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ELEIEWHKFE TSEEIISTYL IDDVLYTGVN GAVYTFSNNE LNKTGLTNNN NYITTSIKVE DTLVCGTNNG NPKCWKIDGS EDPKYRGRG YAPYQNSKVT IISHNECVLS DINISKEGIK RWRRFDGPCG YDLYTADNVI PKDGVRGAFV DKDGTYDKVY I LFTDTIDT ...String:
ELEIEWHKFE TSEEIISTYL IDDVLYTGVN GAVYTFSNNE LNKTGLTNNN NYITTSIKVE DTLVCGTNNG NPKCWKIDGS EDPKYRGRG YAPYQNSKVT IISHNECVLS DINISKEGIK RWRRFDGPCG YDLYTADNVI PKDGVRGAFV DKDGTYDKVY I LFTDTIDT KRIVKIPYIA QMCLNDEGGP SSLSSHRWST FLKVELECDI DGRSYRQIIH SKAIKTDNDT ILYVFFDSPY SK SALCTYS MNAIKHSFST SKLGGYTKQL PSPAPGICLP AGKVVPHTTF DIIEQYNELD DIIKPLSQPI FEGPSGVKWF DIK EKENEH REYRIYFIKE NTIYSFDTKS KQTRSAQVDA RLFSVMVTSK PLFIADIGIG VGIPRMKKIL KMGTHHHHHH HH

UniProtKB: Semaphorin-like protein 139

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Macromolecule #2: Plexin-C1

MacromoleculeName: Plexin-C1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 173.487 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ADEPVWRSEQ AIGAIAASQE DGVFVASGSC LDQLDYSLEH SLSRLYRDQA GNCTEPVSLA PPARPRPGSS FSKLLLPYRE GAAGLGGLL LTGWTFDRGA CEVRPLGNLS RNSLRNGTEV VSCHPQGSTA GVVYRAGRNN RWYLAVAATY VLPEPETASR C NPAASDHD ...String:
ADEPVWRSEQ AIGAIAASQE DGVFVASGSC LDQLDYSLEH SLSRLYRDQA GNCTEPVSLA PPARPRPGSS FSKLLLPYRE GAAGLGGLL LTGWTFDRGA CEVRPLGNLS RNSLRNGTEV VSCHPQGSTA GVVYRAGRNN RWYLAVAATY VLPEPETASR C NPAASDHD TAIALKDTEG RSLATQELGR LKLCEGAGSL HFVDAFLWNG SIYFPYYPYN YTSGAATGWP SMARIAQSTE VL FQGQASL DCGHGHPDGR RLLLSSSLVE ALDVWAGVFS AAAGEGQERR SPTTTALCLF RMSEIQARAK RVSWDFKTAE SHC KEGDQP ERVQPIASST LIHSDLTSVY GTVVMNRTVL FLGTGDGQLL KVILGENLTS NCPEVIYEIK EETPVFYKLV PDPV KNIYI YLTAGKEVRR IRVANCNKHK SCSECLTATD PHCGWCHSLQ RCTFQGDCVH SENLENWLDI SSGAKKCPKI QIIRS SKEK TTVTMVGSFS PRHSKCMVKN VDSSRELCQN KSQPNRTCTC SIPTRATYKD VSVVNVMFSF GSWNLSDRFN FTNCSS LKE CPACVETGCA WCKSARRCIH PFTACDPSDY ERNQEQCPVA VEKTSGGGRP KENKGNRTNQ ALQVFYIKSI EPQKVST LG KSNVIVTGAN FTRASNITMI LKGTSTCDKD VIQVSHVLND THMKFSLPSS RKEMKDVCIQ FDGGNCSSVG SLSYIALP H CSLIFPATTW ISGGQNITMM GRNFDVIDNL IISHELKGNI NVSEYCVATY CGFLAPSLKS SKVRTNVTVK LRVQDTYLD CGTLQYREDP RFTGYRVESE VDTELEVKIQ KENDNFNISK KDIEITLFHG ENGQLNCSFE NITRNQDLTT ILCKIKGIKT ASTIANSSK KVRVKLGNLE LYVEQESVPS TWYFLIVLPV LLVIVIFAAV GVTRHKSKEL SRKQSQQLEL LESELRKEIR D GFAELQMD KLDVVDSFGT VPFLDYKHFA LRTFFPESGG FTHIFTEDMH NRDANDKNES LTALDALICN KSFLVTVIHT LE KQKNFSV KDRCLFASFL TIALQTKLVY LTSILEVLTR DLMEQCSNMQ PKLMLRRTES VVEKLLTNWM SVCLSGFLRE TVG EPFYLL VTTLNQKINK GPVDVITCKA LYTLNEDWLL WQVPEFSTVA LNVVFEKIPE NESADVCRNI SVNVLDCDTI GQAK EKIFQ AFLSKNGSPY GLQLNEIGLE LQMGTRQKEL LDIDSSSVIL EDGITKLNTI GHYEISNGST IKVFKKIANF TSDVE YSDD HCHLILPDSE AFQDVQGKRH RGKHKFKVKE MYLTKLLSTK VAIHSVLEKL FRSIWSLPNS RAPFAIKYFF DFLDAQ AEN KKITDPDVVH IWKTNSLPLR FWVNILKNPQ FVFDIKKTPH IDGCLSVIAQ AFMDAFSLTE QQLGKEAPTN KLLYAKD IP TYKEEVKSYY KAIRDLPPLS SSEMEEFLTQ ESKKHENEFN EEVALTEIYK YIVKYFDEIL NKLERERGLE EAQKQLLH V KVLFDEKKKC KWMGTSSGLE VLFQ

UniProtKB: Plexin-C1

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 18 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
150.0 mMNaClNaCl
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 143750
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

3nvn


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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