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- PDB-13cp: Cryo-EM structure of an intact human acetylcholinesterase (T-form... -

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Basic information

Entry
Database: PDB / ID: 13cp
TitleCryo-EM structure of an intact human acetylcholinesterase (T-form) tetramer in complex with PRiMA
Components
  • Acetylcholinesterase
  • Small ubiquitin-related modifier,Proline-rich membrane anchor 1
KeywordsHYDROLASE
Function / homology
Function and homology information


negative regulation of synaptic transmission, cholinergic / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of SUMOylation proteins / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / septin ring ...negative regulation of synaptic transmission, cholinergic / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of SUMOylation proteins / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / septin ring / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / Neurotransmitter clearance / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / osteoblast development / SUMOylation of chromatin organization proteins / acetylcholine catabolic process / amyloid precursor protein metabolic process / acetylcholinesterase / cholinesterase activity / acetylcholine binding / acetylcholinesterase activity / Synthesis of PC / basement membrane / ubiquitin-like protein ligase binding / Synthesis, secretion, and deacylation of Ghrelin / protein sumoylation / anchoring junction / collagen binding / synapse assembly / laminin binding / synaptic cleft / positive regulation of protein secretion / condensed nuclear chromosome / neuromuscular junction / protein tag activity / nervous system development / positive regulation of cold-induced thermogenesis / amyloid-beta binding / hydrolase activity / cell adhesion / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular region / membrane / identical protein binding / nucleus / plasma membrane
Similarity search - Function
: / Proline-rich membrane anchor 1 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. ...: / Proline-rich membrane anchor 1 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Acetylcholinesterase / Small ubiquitin-related modifier / Proline-rich membrane anchor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsCheung, J. / Karasawa, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Structure / Year: 2026
Title: Structures of distinct human acetylcholinesterase tetramer forms in complex with synaptic anchoring proteins.
Authors: Jonah Cheung / Akira Karasawa /
Abstract: Acetylcholinesterase (AChE) hydrolyzes the neurotransmitter acetylcholine in the nervous system. Higher order oligomeric forms of AChE are specific to synapses in vertebrates. The enzyme is anchored ...Acetylcholinesterase (AChE) hydrolyzes the neurotransmitter acetylcholine in the nervous system. Higher order oligomeric forms of AChE are specific to synapses in vertebrates. The enzyme is anchored to the basal lamina at neuromuscular junctions by ColQ and to neuronal membranes in the brain by the membrane protein PRiMA. We use cryo-electron microscopy to show that human AChE (hAChE) forms distinct tetramers in complex with the two synaptic anchors. The ColQ complex is more compact and square-like while the PRiMA complex is more open, asymmetric, and flexible. 3D variability analysis also reveals different flexibilities within the complexes, which are also different than AChE tetramers from other species. Binding of hAChE to the anchors occurs through a conserved mechanism but differences within the anchor sequences may lead to significantly different structures. Flexibility of hAChE tetramer form may be important for interactions with endogenous proteins in the nervous system.
History
DepositionApr 29, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
C: Acetylcholinesterase
D: Acetylcholinesterase
E: Small ubiquitin-related modifier,Proline-rich membrane anchor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,48717
Polymers278,4355
Non-polymers4,05212
Water00
1


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

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Components

#1: Protein
Acetylcholinesterase / AChE


Mass: 64641.738 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase
#2: Protein Small ubiquitin-related modifier,Proline-rich membrane anchor 1 / SUMO / Suppressor of mif two / Ubiquitin-like protein SMT3 / PRiMA


Mass: 19868.143 Da / Num. of mol.: 1 / Mutation: R64T, R71E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMT3, YDR510W, D9719.15, PRIMA1 / Production host: Homo sapiens (human) / References: UniProt: Q12306, UniProt: Q86XR5
#3: 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.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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.: 8 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 interestY
Has protein modificationY

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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

ComponentName: Complex of human acetylcholinesterase tetramer bound to PRiMA
Type: COMPLEX / Details: PRiMA expressed with SUMO fused to N-terminus / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.278 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5 / Details: 20 mM Tris pH 7.5 150 mM NaCl 0.015% NP-40
SpecimenConc.: 5.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Details: Blot force 2, 9.5 s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Image recordingElectron dose: 54.16 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 21758
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
4cryoSPARCCTF correction
7PHENIX1.21.2_5419model fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3018602
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 531169 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
14EY4

4ey4

14EY41PDBexperimental model
21VZJ

1vzj

11VZJ2PDBexperimental model
RefinementHighest resolution: 2.94 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00318883
ELECTRON MICROSCOPYf_angle_d0.51625816
ELECTRON MICROSCOPYf_dihedral_angle_d5.5142976
ELECTRON MICROSCOPYf_chiral_restr0.0442768
ELECTRON MICROSCOPYf_plane_restr0.0063392

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