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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 / anchoring junction / protein sumoylation / 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 / cell adhesion / hydrolase activity / 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: To Be Published
Title: Structures of distinct human acetylcholinesterase tetramers form in complex with synaptic anchoring proteins
Authors: Cheung, J. / Karasawa, A.
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

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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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