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- EMDB-76975: Cryo-EM structure of an intact human acetylcholinesterase (T-form... -

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Basic information

Entry
Database: EMDB / ID: EMD-76975
TitleCryo-EM structure of an intact human acetylcholinesterase (T-form) tetramer in complex with PRiMA
Map dataComposite map
Sample
  • Complex: Complex of human acetylcholinesterase tetramer bound to PRiMA
    • Protein or peptide: Acetylcholinesterase
    • Protein or peptide: Small ubiquitin-related modifier,Proline-rich membrane anchor 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsCheung J / Karasawa A
Funding support United States, 1 items
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, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76975.png

Downloads & links

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Map

FileDownload / File: emd_76975.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 432 pix.
= 356.832 Å		0.83 Å/pix.
x 432 pix.
= 356.832 Å		0.83 Å/pix.
x 432 pix.
= 356.832 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.3
Minimum - Maximum-61.159668000000003 - 76.268969999999996
Average (Standard dev.)0.002696755 (±1.1428628)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 356.832 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Complex of human acetylcholinesterase tetramer bound to PRiMA

EntireName: Complex of human acetylcholinesterase tetramer bound to PRiMA
Components
  • Complex: Complex of human acetylcholinesterase tetramer bound to PRiMA
    • Protein or peptide: Acetylcholinesterase
    • Protein or peptide: Small ubiquitin-related modifier,Proline-rich membrane anchor 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of human acetylcholinesterase tetramer bound to PRiMA

SupramoleculeName: Complex of human acetylcholinesterase tetramer bound to PRiMA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: PRiMA expressed with SUMO fused to N-terminus
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 278 KDa

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Macromolecule #1: Acetylcholinesterase

MacromoleculeName: Acetylcholinesterase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: acetylcholinesterase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.641738 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EGREDAELLV TVRGGRLRGI RLKTPGGPVS AFLGIPFAEP PMGPRRFLPP EPKQPWSGVV DATTFQSVCY QYVDTLYPGF EGTEMWNPN RELSEDCLYL NVWTPYPRPT SPTPVLVWIY GGGFYSGASS LDVYDGRFLV QAERTVLVSM NYRVGAFGFL A LPGSREAP ...String:
EGREDAELLV TVRGGRLRGI RLKTPGGPVS AFLGIPFAEP PMGPRRFLPP EPKQPWSGVV DATTFQSVCY QYVDTLYPGF EGTEMWNPN RELSEDCLYL NVWTPYPRPT SPTPVLVWIY GGGFYSGASS LDVYDGRFLV QAERTVLVSM NYRVGAFGFL A LPGSREAP GNVGLLDQRL ALQWVQENVA AFGGDPTSVT LFGESAGAAS VGMHLLSPPS RGLFHRAVLQ SGAPNGPWAT VG MGEARRR ATQLAHLVGC PPGGTGGNDT ELVACLRTRP AQVLVNHEWH VLPQESVFRF SFVPVVDGDF LSDTPEALIN AGD FHGLQV LVGVVKDEGS YFLVYGAPGF SKDNESLISR AEFLAGVRVG VPQVSDLAAE AVVLHYTDWL HPEDPARLRE ALSD VVGDH NVVCPVAQLA GRLAAQGARV YAYVFEHRAS TLSWPLWMGV PHGYEIEFIF GIPLDPSRNY TAEEKIFAQR LMRYW ANFA RTGDPNEPRD PKAPQWPPYT AGAQQYVSLD LRPLEVRRGL RAQACAFWNR FLPKLLSATD TLDEAERQWK AEFHRW SSY MVHWKNQFDH YSKQDRCSDL

UniProtKB: Acetylcholinesterase

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Macromolecule #2: Small ubiquitin-related modifier,Proline-rich membrane anchor 1

MacromoleculeName: Small ubiquitin-related modifier,Proline-rich membrane anchor 1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.868143 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EHHHHHHHHH HGSLQDSEVN QEAKPEVKPE VKPETHINLK VSDGSSEIFF KIKKTTPLRR LMEAFAKRQG KEMDSLTFLY DGIEIQADQ TPEDLDMEDN DIIEAHREQI GGENLYFQSE PQKSCSKVTD SCRHVCQCRP PPPLPPPPPP PPPPRLLSAP A PNSTSCPT EESWWSG

UniProtKB: Small ubiquitin-related modifier, Proline-rich membrane anchor 1

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 8 / 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

Concentration5.7 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris pH 7.5 150 mM NaCl 0.015% NP-40
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Details: Blot force 2, 9.5 s.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 21758 / Average electron dose: 54.16 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3018602
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 531169
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial model
PDB IDChain

4ey4

source_name: PDB, initial_model_type: experimental model

1vzj

source_name: PDB, initial_model_type: experimental model
SoftwareName: PHENIX (ver. 1.21.2_5419)
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-13cp:
Cryo-EM structure of an intact human acetylcholinesterase (T-form) tetramer in complex with PRiMA

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