[English] 日本語
Yorodumi
- EMDB-76971: Cryo-EM structure of an intact human acetylcholinesterase (T-form... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-76971
TitleCryo-EM structure of an intact human acetylcholinesterase (T-form) tetramer in complex with ColQ
Map datastructure of an intact human acetylcholinesterase (T-form) tetramer in complex with ColQ
Sample
  • Complex: Complex of human acetylcholinesterase tetramer bound to ColQ
    • Protein or peptide: Acetylcholinesterase
    • Protein or peptide: Small ubiquitin-related modifier,Acetylcholinesterase collagenic tail peptide
  • 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 / protein localization to synapse / 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 / extracellular matrix organization / collagen binding / synapse assembly / laminin binding / synaptic cleft / positive regulation of protein secretion / condensed nuclear chromosome / neuromuscular junction / protein tag activity / heparin binding / nervous system development / positive regulation of cold-induced thermogenesis / amyloid-beta binding / hydrolase activity / cell adhesion / extracellular matrix / molecular adaptor 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
Myxococcus cysteine-rich repeat / : / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / : / Cholinesterase ...Myxococcus cysteine-rich repeat / : / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / : / 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 / Acetylcholinesterase collagenic tail peptide
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsCheung J / Karasawa A
Funding support United States, 1 items
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, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_76971.png

Downloads & links

-
Map

FileDownload / File: emd_76971.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of an intact human acetylcholinesterase (T-form) tetramer in complex with ColQ
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 432 pix.
= 358.128 Å		0.83 Å/pix.
x 432 pix.
= 358.128 Å		0.83 Å/pix.
x 432 pix.
= 358.128 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.8
Minimum - Maximum-30.047186 - 48.263739999999999
Average (Standard dev.)-0.001689603 (±0.9839319)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 358.128 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Complex of human acetylcholinesterase tetramer bound to ColQ

EntireName: Complex of human acetylcholinesterase tetramer bound to ColQ
Components
  • Complex: Complex of human acetylcholinesterase tetramer bound to ColQ
    • Protein or peptide: Acetylcholinesterase
    • Protein or peptide: Small ubiquitin-related modifier,Acetylcholinesterase collagenic tail peptide
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Complex of human acetylcholinesterase tetramer bound to ColQ

SupramoleculeName: Complex of human acetylcholinesterase tetramer bound to ColQ
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: ColQ expressed with SUMO fused to N-terminus
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 279 KDa

-
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

-
Macromolecule #2: Small ubiquitin-related modifier,Acetylcholinesterase collagenic ...

MacromoleculeName: Small ubiquitin-related modifier,Acetylcholinesterase collagenic tail peptide
type: protein_or_peptide / ID: 2 / Details: ColQ fused to SUMO at N-terminus / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.010771 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EHHHHHHHHH HGSLQDSEVN QEAKPEVKPE VKPETHINLK VSDGSSEIFF KIKKTTPLRR LMEAFAKRQG KEMDSLTFLY DGIEIQADQ TPEDLDMEDN DIIEAHREQI GGENLYFQSQ PTFINSVLPI SAALPSLDQK KRGGHKACCL LTPPPPPLFP P PFFRGGRS PLLSPDMKNL MLELETS

UniProtKB: Small ubiquitin-related modifier, Acetylcholinesterase collagenic tail peptide

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5.6 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

-
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: 19935 / Average electron dose: 52.39 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

+
Image processing

Particle selectionNumber selected: 3806508
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: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 122083
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

-
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. 2.0_5936)
RefinementSpace: REAL / Protocol: OTHER
Output model

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

+
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