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- EMDB-23613: Cryo-EM structure of the Sema3A/PlexinA4/Neuropilin 1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-23613
TitleCryo-EM structure of the Sema3A/PlexinA4/Neuropilin 1 complex
Map data
Sample
  • Complex: Ternary complex of Sema3A, PlexinA4 and neuropilin 1
    • Protein or peptide: Neuropilin-1
    • Protein or peptide: Semaphorin-3A
    • Protein or peptide: Plexin-A4
  • Ligand: CALCIUM ION
Keywordsplexin / semaphorin / neuropilin / signaling / SIGNALING PROTEIN
Function / homology
Function and homology information


Neurophilin interactions with VEGF and VEGFR / neural crest cell migration involved in sympathetic nervous system development / glossopharyngeal nerve morphogenesis / chemorepulsion of branchiomotor axon / regulation of negative chemotaxis / vagus nerve morphogenesis / cell migration involved in coronary vasculogenesis / cranial nerve morphogenesis / trigeminal nerve morphogenesis / Signal transduction by L1 ...Neurophilin interactions with VEGF and VEGFR / neural crest cell migration involved in sympathetic nervous system development / glossopharyngeal nerve morphogenesis / chemorepulsion of branchiomotor axon / regulation of negative chemotaxis / vagus nerve morphogenesis / cell migration involved in coronary vasculogenesis / cranial nerve morphogenesis / trigeminal nerve morphogenesis / Signal transduction by L1 / anterior commissure morphogenesis / regulation of axon extension involved in axon guidance / postganglionic parasympathetic fiber development / facial nerve morphogenesis / basal dendrite development / otic placode development / CRMPs in Sema3A signaling / positive regulation of smooth muscle cell chemotaxis / protein localization to early endosome / Sema3A PAK dependent Axon repulsion / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / sympathetic neuron axon guidance / retina vasculature morphogenesis in camera-type eye / vestibulocochlear nerve structural organization / semaphorin receptor binding / regulation of vascular endothelial growth factor receptor signaling pathway / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / epithelial cell migration / neurofilament / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / branchiomotor neuron axon guidance / renal artery morphogenesis / postsynapse organization / positive regulation of male gonad development / cerebellar climbing fiber to Purkinje cell synapse / negative regulation of axon extension involved in axon guidance / maintenance of synapse structure / VEGF-activated neuropilin signaling pathway / axon extension involved in axon guidance / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / synaptic target recognition / sympathetic neuron projection extension / blood vessel endothelial cell migration / negative regulation of epithelial cell migration / vascular endothelial growth factor binding / retina vasculature development in camera-type eye / endothelial cell chemotaxis / motor neuron migration / neural crest cell migration involved in autonomic nervous system development / sympathetic ganglion development / positive regulation of axon extension involved in axon guidance / positive regulation of platelet-derived growth factor receptor signaling pathway / axonogenesis involved in innervation / vascular endothelial growth factor receptor activity / negative regulation of axon extension / outflow tract septum morphogenesis / nerve development / positive regulation of neuron migration / semaphorin receptor complex / angiogenesis involved in coronary vascular morphogenesis / olfactory bulb development / neuropilin signaling pathway / neuropilin binding / sympathetic nervous system development / hepatocyte growth factor receptor signaling pathway / coronary artery morphogenesis / substrate-dependent cell migration, cell extension / chemorepellent activity / semaphorin receptor activity / commissural neuron axon guidance / negative regulation of cell adhesion / embryonic heart tube development / axon extension / axonal fasciculation / positive regulation of vascular associated smooth muscle cell migration / cell migration involved in sprouting angiogenesis / regulation of Cdc42 protein signal transduction / motor neuron axon guidance / sprouting angiogenesis / neural crest cell migration / dendrite morphogenesis / positive regulation of filopodium assembly / artery morphogenesis / negative chemotaxis / positive regulation of axonogenesis / positive regulation of cell migration involved in sprouting angiogenesis / cellular response to hepatocyte growth factor stimulus / branching involved in blood vessel morphogenesis / retinal ganglion cell axon guidance / positive chemotaxis / dendrite development / growth factor binding
Similarity search - Function
Semaphorin-3A, sema domain / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Semaphorin / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Neuropilin / Neuropilin, C-terminal ...Semaphorin-3A, sema domain / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Semaphorin / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / : / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Plexin family / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Plexin repeat / Plexin repeat / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Sema domain / semaphorin domain / Sema domain / Spermadhesin, CUB domain superfamily / Sema domain superfamily / Sema domain profile. / Coagulation factor 5/8 C-terminal domain, discoidin domain / IPT/TIG domain / Coagulation factors 5/8 type C domain (FA58C) profile. / ig-like, plexins, transcription factors / Rho GTPase activation protein / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Galactose-binding-like domain superfamily / Immunoglobulin E-set / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Semaphorin-3A / Neuropilin-1 / Plexin-A4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLu D / Shang G
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130289 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM136976 United States
Robert A. Welch FoundationI-1702 United States
Robert A. Welch FoundationI-1944 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP160082 United States
CitationJournal: Nat Commun / Year: 2021
Title: Architecture of the Sema3A/PlexinA4/Neuropilin tripartite complex.
Authors: Defen Lu / Guijun Shang / Xiaojing He / Xiao-Chen Bai / Xuewu Zhang /
Abstract: Secreted class 3 semaphorins (Sema3s) form tripartite complexes with the plexin receptor and neuropilin coreceptor, which are both transmembrane proteins that together mediate semaphorin signal for ...Secreted class 3 semaphorins (Sema3s) form tripartite complexes with the plexin receptor and neuropilin coreceptor, which are both transmembrane proteins that together mediate semaphorin signal for neuronal axon guidance and other processes. Despite extensive investigations, the overall architecture of and the molecular interactions in the Sema3/plexin/neuropilin complex are incompletely understood. Here we present the cryo-EM structure of a near intact extracellular region complex of Sema3A, PlexinA4 and Neuropilin 1 (Nrp1) at 3.7 Å resolution. The structure shows a large symmetric 2:2:2 assembly in which each subunit makes multiple interactions with others. The two PlexinA4 molecules in the complex do not interact directly, but their membrane proximal regions are close to each other and poised to promote the formation of the intracellular active dimer for signaling. The structure reveals a previously unknown interface between the a2b1b2 module in Nrp1 and the Sema domain of Sema3A. This interaction places the a2b1b2 module at the top of the complex, far away from the plasma membrane where the transmembrane regions of Nrp1 and PlexinA4 embed. As a result, the region following the a2b1b2 module in Nrp1 must span a large distance to allow the connection to the transmembrane region, suggesting an essential role for the long non-conserved linkers and the MAM domain in neuropilin in the semaphorin/plexin/neuropilin complex.
History
DepositionMar 11, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-7m0r
  • Surface level: 0.01
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23613.png

Downloads & links

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Map

FileDownload / File: emd_23613.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 280 pix.
= 302.4 Å		1.08 Å/pix.
x 280 pix.
= 302.4 Å		1.08 Å/pix.
x 280 pix.
= 302.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.015544364 - 0.04804559
Average (Standard dev.)0.0005064486 (±0.002195016)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 302.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z302.400302.400302.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0160.0480.001

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Supplemental data

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Sample components

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Entire : Ternary complex of Sema3A, PlexinA4 and neuropilin 1

EntireName: Ternary complex of Sema3A, PlexinA4 and neuropilin 1
Components
  • Complex: Ternary complex of Sema3A, PlexinA4 and neuropilin 1
    • Protein or peptide: Neuropilin-1
    • Protein or peptide: Semaphorin-3A
    • Protein or peptide: Plexin-A4
  • Ligand: CALCIUM ION

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Supramolecule #1: Ternary complex of Sema3A, PlexinA4 and neuropilin 1

SupramoleculeName: Ternary complex of Sema3A, PlexinA4 and neuropilin 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 600 kDa/nm

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Macromolecule #1: Neuropilin-1

MacromoleculeName: Neuropilin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 64.132211 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FRSDKCGGTI KIENPGYLTS PGYPHSYHPS EKCEWLIQAP EPYQRIMINF NPHFDLEDRD CKYDYVEVID GENEGGRLWG KFCGKIAPS PVVSSGPFLF IKFVSDYETH GAGFSIRYEI FKRGPECSQN YTAPTGVIKS PGFPEKYPNS LECTYIIFAP K MSEIILEF ...String:
FRSDKCGGTI KIENPGYLTS PGYPHSYHPS EKCEWLIQAP EPYQRIMINF NPHFDLEDRD CKYDYVEVID GENEGGRLWG KFCGKIAPS PVVSSGPFLF IKFVSDYETH GAGFSIRYEI FKRGPECSQN YTAPTGVIKS PGFPEKYPNS LECTYIIFAP K MSEIILEF ESFDLEQDSN PPGGMFCRYD RLEIWDGFPE VGPHIGRYCG QKTPGRIRSS SGVLSMVFYT DSAIAKEGFS AN YSVLQSS ISEDFKCMEA LGMESGEIHS DQITASSQYG TNWSVERSRL NYPENGWTPG EDSYKEWIQV DLGLLRFVTA VGT QGAISK ETKKKYYVKT YRVDISSNGE DWISLKEGNK AIIFQGNTNP TDVVLGVFSK PLITRFVRIK PVSWETGISM RFEV YGCKI TDYPCSGMLG MVSGLISDSQ ITASNQADRN WMPENIRLVT SRTGWALPPS PHPYTNEWLQ VDLGDEKIVR GVIIQ GGKH RENKVFMRKF KIAYSNNGSD WKTIMDDSKR KAKSFEGNNN YDTPELRTFS PLSTRFIRIY PERATHSGLG LRMELL GCE VEAP

UniProtKB: Neuropilin-1

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Macromolecule #2: Semaphorin-3A

MacromoleculeName: Semaphorin-3A / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 67.931812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NYANGKNNVP RLKLSYKEML ESNNVITFNG LANSSSYHTF LLDEERSRLY VGAKDHIFSF NLVNIKDFQK IVWPVSYTRR DECKWKGKD ILKECANFIK VLEAYNQTHL YACGTGAFHP ICTYIEVGHH PEDNIFKLQD SHFENGRGKS PYDPKLLTAS L LIDGELYS ...String:
NYANGKNNVP RLKLSYKEML ESNNVITFNG LANSSSYHTF LLDEERSRLY VGAKDHIFSF NLVNIKDFQK IVWPVSYTRR DECKWKGKD ILKECANFIK VLEAYNQTHL YACGTGAFHP ICTYIEVGHH PEDNIFKLQD SHFENGRGKS PYDPKLLTAS L LIDGELYS GTAADFMGRD FAIFRTLGHH HPIRTEQHDS RWLNDPRFIS AHLIPESDNP EDDKVYFFFR ENAIDGEHSG KA THARIGQ ICKNDFGGHR SLVNKWTTFL KARLICSVPG PNGIDTHFDE LQDVFLMNSK DPKNPIVYGV FTTSSNIFKG SAV CMYSMS DVRRVFLGPY AHRDGPNYQW VPYQGRVPYP RPGTCPSKTF GGFDSTKDLP DDVITFARSH PAMYNPVFPI NNRP IMIKT DVNYQFTQIV VDRVDAEDGQ YDVMFIGTDV GTVLKVVSVP KETWHDLEEV LLEEMTVFRE PTTISAMELS TKQQQ LYIG STAGVAQLPL HRCDIYGKAC AECCLARDPY CAWDGSSCSR YFPTAKARTR AQDIRNGDPL THCSD(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

UniProtKB: Semaphorin-3A

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Macromolecule #3: Plexin-A4

MacromoleculeName: Plexin-A4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 133.253203 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KPSFVTFRGE PAEGFNHLVV DERTGHIYLG AVNRIYKLSS DLKVLVTHQT GPDEDNPKCY PPRIVQTCNE PLASTNNVNK MLLIDYKEN RLIACGSLYQ GICKLLRLED LFKLGEPFHK KEHYLSGVNE SGSVFGVIVS YSNFDDKLFI ATAVDGKPEY F PTISSRKL ...String:
KPSFVTFRGE PAEGFNHLVV DERTGHIYLG AVNRIYKLSS DLKVLVTHQT GPDEDNPKCY PPRIVQTCNE PLASTNNVNK MLLIDYKEN RLIACGSLYQ GICKLLRLED LFKLGEPFHK KEHYLSGVNE SGSVFGVIVS YSNFDDKLFI ATAVDGKPEY F PTISSRKL TKNSEADGMF AYVFHDEFVA SMIKIPSDTF TVIPDFDIYY VYGFSSGNFV YFLTLQPEMV SPPGSTTKEQ VY TSKLVRL CKEDTAFNSY VEVPIGCERN GVEYRLLQAA YLSKAGAVLG RTLGVRPDDD LLFTVFSKGQ KRKMKSLDES ALC IFILKQ INDRIKDRLQ SCYRGEGTLD LAWLKVKDIP CSSALLTIDD NFCGLDMNAP LGVSEMVRGI PVFTEDRDRM TSVI AYVYK NHSLAFVGTK SGKLKKIRVD GPKGNALQYE TVQVVDSGPV LRDMAFSKDH EQLYIMSERQ LTRVPVESCG QYRSC GECL GSGDPHCGWC VLHNTCTRKE RCERSREPRR FASEMKQCVR LTVHPNNISV SQYNVLLVLE TYNVPELSAG VNCTFE DLS EMDGLVIGNQ IQCYSPAAKE VPRIITENGD HHVVQLQLKS KETGMTFAST SFVFYNCSVH NSCLSCVESP YRCHWCK YR HVCTHDPNTC SFQEGRVKLP EDCPQLLRVD KILVPVEVIK PITLKAKNLP QPQSGQRGYE CILNIQGIEQ RVPALRFN S SSVQCQNTSY SYEGMEINNL PVELTVVWNG HFNIDNPAQN KVYLYKCGAM RESCGLCLKA DPDFECGWCQ SPGQCTLRQ HCPAHESRWL ELSGANSKCT NPRITEIIPV TGPREGGTKV TIRGENLGLE FRDIASHVKV AGVECSPLVD GYIPAEQIVC EMGEAKPSQ HAGFVEICVA VCRPEFMARS SQLYYFMTLT LADLKPNRGP MSGGTQVTIT GTNLNAGSNV VVMFGSQPCL F HRRSPSYI ICNTTSSEEV LDMKVTVQVD RARIRQDLVF QYVEDPTIVR IEPEWSIVSG NTPIAVWGTH LDLIQNPQIR AK HGGKEHI NICEVLNATE MTCQAPALAL GPDHQSDLTE RPEEFGFILD NVQSLLILNK TNFTYYPNPV FEAFSPSGIL ELK PGTPII LKGKNLIPPV AGGNVKLNYT VLVGEKPCTV TVSDVQLLCE SPNLIGRHKV MARVGGMEYS PGMVYIAP

UniProtKB: Plexin-A4

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1453090
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4gza

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26741
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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