[English] 日本語
Yorodumi
- PDB-9fyq: Cryo-EM structure of native SV2A in complex with TeNT-Hc, ganglio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fyq
TitleCryo-EM structure of native SV2A in complex with TeNT-Hc, gangliosides and Pro-Macrobody 5
Components
  • Pro-Macrobody 5,Maltose/maltodextrin-binding periplasmic protein
  • Synaptic vesicle glycoprotein 2A
  • Tetanus toxin heavy chain
KeywordsMEMBRANE PROTEIN / synaptic vesicles / MFS transporter / neurotransmission / clostridial neurotoxins
Function / homology
Function and homology information


tentoxilysin / symbiont-mediated perturbation of host neurotransmitter secretion / Toxicity of tetanus toxin (tetX) / synaptic vesicle priming / detection of maltose stimulus / maltose transport complex / carbohydrate transport / presynaptic active zone / transmembrane transporter activity / protein transmembrane transporter activity ...tentoxilysin / symbiont-mediated perturbation of host neurotransmitter secretion / Toxicity of tetanus toxin (tetX) / synaptic vesicle priming / detection of maltose stimulus / maltose transport complex / carbohydrate transport / presynaptic active zone / transmembrane transporter activity / protein transmembrane transporter activity / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / GABA-ergic synapse / cell chemotaxis / clathrin-coated endocytic vesicle membrane / neuromuscular junction / metalloendopeptidase activity / intracellular calcium ion homeostasis / synaptic vesicle membrane / endocytic vesicle membrane / cell-cell junction / outer membrane-bounded periplasmic space / toxin activity / periplasmic space / neuron projection / DNA damage response / protein kinase binding / glutamatergic synapse / endoplasmic reticulum / proteolysis / extracellular region / zinc ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / SV2A/B/C luminal domain / Synaptic vesicle protein SV2 / Sugar transport proteins signature 2. / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain ...: / SV2A/B/C luminal domain / Synaptic vesicle protein SV2 / Sugar transport proteins signature 2. / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / MFS transporter superfamily / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
omega-undecylenyl-beta-D-maltopyranoside / : / : / Synaptic vesicle glycoprotein 2A / Tetanus toxin / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesClostridium tetani E88 (bacteria)
Lama glama (llama)
Escherichia coli (E. coli)
Ovis aries (sheep)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsSchenck, S. / Brunner, J.D.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Vrije Universiteit Brussel Belgium
CitationJournal: Nat Commun / Year: 2025
Title: Structures of native SV2A reveal the binding mode for tetanus neurotoxin and anti-epileptic racetams.
Authors: Stephan Schenck / Toon Laeremans / Jan Steyaert / Janine D Brunner /
Abstract: The synaptic vesicle glycoprotein 2A (SV2A) is a synaptic vesicle (SV) resident with homology to the major facilitator superfamily (MFS) and essential in vertebrate neurotransmission. Despite its ...The synaptic vesicle glycoprotein 2A (SV2A) is a synaptic vesicle (SV) resident with homology to the major facilitator superfamily (MFS) and essential in vertebrate neurotransmission. Despite its unclear physiological role, SV2A is of high medical relevance as it is the target of the anti-epileptic drug Levetiracetam (LEV) and a receptor for clostridial neurotoxins (CNTs), among them presumably tetanus neurotoxin (TeNT). To obtain detailed insights about these molecular interactions we subjected native SV2A, purified from brain tissue, to cryo-EM. We discover that TeNT binds SV2A strikingly different from botulinum neurotoxin A and unveil the precise geometry of TeNT binding to dipartite SV2-ganglioside receptors. The structures deliver compelling support for SV2A as the protein receptor for TeNT in central neurons and reinforce the concepts of the dual receptor hypothesis for CNT entry into neurons. Further, our LEV-bound structure of SV2A reveals the drug-interacting residues, delineates a putative substrate pocket in SV2A and provides insights into the SV2-isoform-specificity of LEV. Our work has implications for CNT engineering from a hitherto unrecognized SV2 binding interface and for improved designs of anti-convulsant drugs in epilepsy treatment.
History
DepositionJul 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Synaptic vesicle glycoprotein 2A
C: Tetanus toxin heavy chain
D: Pro-Macrobody 5,Maltose/maltodextrin-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,3769
Polymers190,0343
Non-polymers5,3426
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 2 types, 2 molecules AC

#1: Protein Synaptic vesicle glycoprotein 2A


Mass: 82640.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A836APF1
#2: Protein Tetanus toxin heavy chain / Tetanus toxin chain H


Mass: 53718.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal domain of the heavy chain of tetanus toxin (TeNT-Hc)
Source: (gene. exp.) Clostridium tetani E88 (bacteria) / Strain: Clostridium tetani / Gene: tetX, CTC_p60 / Plasmid: pET 28a / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P04958

-
Antibody , 1 types, 1 molecules D

#3: Antibody Pro-Macrobody 5,Maltose/maltodextrin-binding periplasmic protein / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 53674.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fusion between a nanobody (Nb) and an N-terminally truncated maltose binding protein at the Nb C-terminus,Fusion between a nanobody (Nb) and an N-terminally truncated maltose binding protein at the Nb C-terminus
Source: (gene. exp.) Lama glama (llama), (gene. exp.) Escherichia coli (strain K12) (bacteria)
Plasmid: pBXNPHM3 / Gene: malE, b4034, JW3994 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): MC1061 / References: UniProt: P0AEX9

-
Sugars , 2 types, 3 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

-
Non-polymers , 3 types, 3 molecules

#6: Chemical ChemComp-6UZ / omega-undecylenyl-beta-D-maltopyranoside / (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[(2~{R},3~{S},4~{R},5~{R},6~{R})-2-(hydroxymethyl)-4,5-bis(oxidanyl )-6-undec-10-enoxy-oxan-3-yl]oxy-oxane-3,4,5-triol


Mass: 494.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H42O11
#7: Chemical ChemComp-A1IHM / (2~{R},4~{R},5~{S},6~{S})-2-[(2~{R},3~{R})-3-[(2~{R},3~{S},4~{S},6~{S})-6-[(2~{S},3~{S},4~{R},5~{S},6~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-(hydroxymethyl)-6-[(2~{R},3~{R},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-[2-(octadecanoylamino)-3-oxidanyl-octadec-4-enoxy]-4,5-bis(oxidanyl)oxan-3-yl]oxy-5-oxidanyl-oxan-4-yl]oxy-3-azanyl-6-carboxy-4-oxidanyl-oxan-2-yl]-2,3-bis(oxidanyl)propoxy]-5-azanyl-4-oxidanyl-6-[(1~{R},2~{S})-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid


Mass: 1591.863 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C74H134N4O32 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-A1IHN / (2~{S},4~{S},5~{R},6~{S})-5-acetamido-2-[(2~{R},3~{R},4~{R},5~{S},6~{R})-2-[(2~{R},3~{R},4~{S},5~{R},6~{S})-2-[(2~{R},3~{S},4~{R},5~{R},6~{R})-4-[(2~{S},4~{S},5~{S},6~{S})-5-acetamido-2-carboxy-4-oxidanyl-6-[(1~{S},2~{R})-1,2,3-tris(oxidanyl)propyl]oxan-2-yl]oxy-6-[(2~{R},3~{S},4~{R},5~{R},6~{R})-6-[2-(docosanoylamino)-3-oxidanyl-octadec-4-enoxy]-2-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]oxy-2-(hydroxymethyl)-5-oxidanyl-oxan-3-yl]oxy-6-(hydroxymethyl)-5-oxidanyl-3-(2-oxidanylidenepropyl)oxan-4-yl]oxy-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-4-yl]oxy-4-oxidanyl-6-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid


Mass: 1893.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C89H157N3O39 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1SV2A bound to TeNT-Hc, gangliosides and Pro-Macrobody 5COMPLEX#2-#30MULTIPLE SOURCES
2Synaptic vesicle glycoprotein 2ACOMPLEX#11NATURAL
3TeNT-HcCOMPLEX#21RECOMBINANT
4Pro-Macrobody 5COMPLEX#31RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.189 MDaNO
210.082 MDaNO
310.0536 MDaNO
410.0536 MDaNO
54
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Ovis aries (sheep)9940
32Ovis aries (sheep)9940
43Clostridium tetani E88 (bacteria)212717
54Lama glama (llama)9844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainPlasmid
33Escherichia coli K-12 (bacteria)83333BL21DE3pET28a
44Escherichia coli K-12 (bacteria)83333MC1061pBXNPHM3
Buffer solutionpH: 7.5
Details: 10 mM Hepes-NaOH 7.5, 150 mM NaCl, 3 mM maltose, 0.03 % n-dodecyl-beta-D-maltopyranoside, 0.006% cholesterol hemisuccinate
SpecimenConc.: 7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K

-
Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingAverage exposure time: 2.796 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 22295

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEM4.1.0 beta26image acquisition
3cryoSPARCPatch Motion596 correctionimage acquisition
4cryoSPARCCryoSPARC CTF estimationimage acquisition
5cryoSPARCcryoSPARC-v.4image acquisition
7cryoSPARCCTF correction
16cryoSPARCcryoSPARC-v.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 89713 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049410
ELECTRON MICROSCOPYf_angle_d0.71412766
ELECTRON MICROSCOPYf_dihedral_angle_d10.3491764
ELECTRON MICROSCOPYf_chiral_restr0.0451453
ELECTRON MICROSCOPYf_plane_restr0.0041575

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more