[English] 日本語
Yorodumi
- PDB-7ekt: human alpha 7 nicotinic acetylcholine receptor bound to EVP-6124 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ekt
Titlehuman alpha 7 nicotinic acetylcholine receptor bound to EVP-6124 and PNU-120596
ComponentsNeuronal acetylcholine receptor subunit alpha-7
KeywordsMEMBRANE PROTEIN / alpha 7 / nicotinic acetylcholine receptor / agonist / PAM
Function / homology
Function and homology information


sensory processing / synaptic transmission involved in micturition / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / regulation of amyloid fibril formation / acetylcholine-gated monoatomic cation-selective channel activity / short-term memory ...sensory processing / synaptic transmission involved in micturition / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / regulation of amyloid fibril formation / acetylcholine-gated monoatomic cation-selective channel activity / short-term memory / cation channel complex / dendritic spine organization / chloride channel regulator activity / acetylcholine binding / regulation of amyloid precursor protein catabolic process / acetylcholine receptor signaling pathway / neurotransmitter receptor complex / positive regulation of amyloid-beta formation / negative regulation of amyloid-beta formation / positive regulation of protein metabolic process / modulation of excitatory postsynaptic potential / response to amyloid-beta / monoatomic ion channel activity / ligand-gated ion channel signaling pathway / plasma membrane raft / negative regulation of tumor necrosis factor production / positive regulation of excitatory postsynaptic potential / toxic substance binding / monoatomic ion transport / negative regulation of canonical NF-kappaB signal transduction / negative regulation of cytokine production involved in inflammatory response / positive regulation of long-term synaptic potentiation / excitatory postsynaptic potential / regulation of membrane potential / response to nicotine / synapse organization / calcium channel activity / cognition / memory / intracellular calcium ion homeostasis / positive regulation of angiogenesis / calcium ion transport / transmembrane signaling receptor activity / amyloid-beta binding / monoatomic ion transmembrane transport / chemical synaptic transmission / postsynaptic membrane / response to hypoxia / learning or memory / positive regulation of ERK1 and ERK2 cascade / postsynapse / neuron projection / positive regulation of MAPK cascade / positive regulation of cell population proliferation / synapse / dendrite / endoplasmic reticulum membrane / signal transduction / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Nicotinic acetylcholine receptor / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel ...Nicotinic acetylcholine receptor / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
CHOLESTEROL / Chem-I33 / Chem-I34 / Neuronal acetylcholine receptor subunit alpha-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsLiu, S. / Zhao, Y. / Sun, D. / Tian, C.
CitationJournal: Cell Res / Year: 2021
Title: Structural basis of human α7 nicotinic acetylcholine receptor activation.
Authors: Yue Zhao / Sanling Liu / Yingxin Zhou / Mengge Zhang / Haopeng Chen / H Eric Xu / Demeng Sun / Lei Liu / Changlin Tian /
History
DepositionApr 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-31176
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neuronal acetylcholine receptor subunit alpha-7
B: Neuronal acetylcholine receptor subunit alpha-7
C: Neuronal acetylcholine receptor subunit alpha-7
D: Neuronal acetylcholine receptor subunit alpha-7
E: Neuronal acetylcholine receptor subunit alpha-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,85030
Polymers282,5265
Non-polymers8,32425
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 23 through 136 or resid 138 through 621))
d_2ens_1(chain "B" and (resid 23 through 136 or resid 138 through 621))
d_3ens_1(chain "C" and (resid 23 through 136 or resid 138 through 621))
d_4ens_1(chain "D" and (resid 23 through 136 or resid 138 through 621))
d_5ens_1(chain "E" and (resid 23 through 136 or resid 138 through 621))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYGLYA1 - 114
d_12ens_1CYSALAA116 - 396
d_13ens_1I33I33M
d_14ens_1I34I34N
d_15ens_1NAGNAGF
d_16ens_1NAGNAGF
d_17ens_1NAGNAGK
d_18ens_1CLRCLRL
d_21ens_1GLYGLYB1 - 114
d_22ens_1CYSALAB116 - 396
d_23ens_1I33I33O
d_24ens_1I34I34P
d_25ens_1NAGNAGG
d_26ens_1NAGNAGG
d_27ens_1NAGNAGQ
d_28ens_1CLRCLRR
d_31ens_1GLYGLYC1 - 114
d_32ens_1CYSALAC116 - 396
d_33ens_1I33I33S
d_34ens_1I34I34T
d_35ens_1NAGNAGH
d_36ens_1NAGNAGH
d_37ens_1NAGNAGU
d_38ens_1CLRCLRV
d_41ens_1GLYGLYD1 - 114
d_42ens_1CYSALAD116 - 396
d_43ens_1I33I33W
d_44ens_1I34I34X
d_45ens_1NAGNAGI
d_46ens_1NAGNAGI
d_47ens_1NAGNAGY
d_48ens_1CLRCLRZ
d_51ens_1GLYGLYE1 - 114
d_52ens_1CYSALAE116 - 396
d_53ens_1I33I33AA
d_54ens_1I34I34BA
d_55ens_1NAGNAGJ
d_56ens_1NAGNAGJ
d_57ens_1NAGNAGCA
d_58ens_1CLRCLRDA

NCS oper:
IDCodeMatrixVector
1given(0.307606541786, -0.951513433975, 0.000632784120891), (0.951513639264, 0.307606403112, -0.000308317288429), (9.87195944938E-5, 0.000696943136604, 0.999999752262)199.9871394, -31.4531822951, -0.140004511822
2given(-0.809801808111, -0.586703192125, 0.000629230109493), (0.58670349574, -0.809801659798, 0.000529031616343), (0.000199167049019, 0.000797582264327, 0.999999662097)291.513986066, 148.794983646, -0.158325980636
3given(-0.808415300426, 0.588612517977, -7.56179662622E-5), (-0.588612490339, -0.808415206435, 0.000436144195689), (0.00019558921942, 0.000397095320423, 0.99999990203)148.388092839, 291.644250495, -0.0884314058769
4given(0.31010349826, 0.950702749497, -0.000320102622106), (-0.950702798014, 0.310103514726, 1.90233134549E-6), (0.000101073499829, 0.000303732538882, 0.999999948765)-31.7164452761, 199.580620021, -0.0587667708726

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
Neuronal acetylcholine receptor subunit alpha-7


Mass: 56505.176 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRNA7, NACHRA7 / Production host: Homo sapiens (human) / References: UniProt: P36544

-
Sugars , 2 types, 10 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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.: 5 / Source method: obtained synthetically / 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, 15 molecules

#4: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical
ChemComp-I33 / 7-chloro-N-(quinuclidin-3-yl)benzo[b]thiophene-2-carboxamide


Mass: 320.837 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H17ClN2OS / Feature type: SUBJECT OF INVESTIGATION / Comment: agonist*YM
#6: Chemical
ChemComp-I34 / N-(5-Chloro-2,4-dimethoxyphenyl)-N'-(5-methyl-3-isoxazolyl)-urea


Mass: 311.721 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C13H14ClN3O4 / 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

ComponentName: Human alpha7 nicotinic acetylcholine receptor bound to EVP-6124 and PNU-120596
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 62 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19_4092refinement
PHENIX1.19_4092refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46899 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 87.57 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002716665
ELECTRON MICROSCOPYf_angle_d0.589822795
ELECTRON MICROSCOPYf_chiral_restr0.04722635
ELECTRON MICROSCOPYf_plane_restr0.00422780
ELECTRON MICROSCOPYf_dihedral_angle_d11.25045845
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.000597027403305
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.000616055031402
ens_1d_4AELECTRON MICROSCOPYNCS constraints0.000686480994244
ens_1d_5AELECTRON MICROSCOPYNCS constraints0.000855280558509

+
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