[English] 日本語
Yorodumi
- PDB-7rpm: Structures of the Intracellular Domain and Transmembrane Domain o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rpm
TitleStructures of the Intracellular Domain and Transmembrane Domain of the Human alpha7 Nicotinic Acetylcholine Receptors
ComponentsNeuronal acetylcholine receptor subunit alpha-7
KeywordsMEMBRANE PROTEIN / nAChRs / intracellular domains / ion channels / Cys-loop receptors / intrinsically disordered regions / intrinsically disordered proteins
Function / homology
Function and homology information


sensory processing / dendrite arborization / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / response to acetylcholine / acetylcholine-gated channel complex / acetylcholine-gated monoatomic cation-selective channel activity / regulation of amyloid fibril formation / short-term memory / positive regulation of CoA-transferase activity ...sensory processing / dendrite arborization / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / response to acetylcholine / acetylcholine-gated channel complex / acetylcholine-gated monoatomic cation-selective channel activity / regulation of amyloid fibril formation / short-term memory / positive regulation of CoA-transferase activity / dendritic spine organization / acetylcholine binding / chloride channel regulator activity / regulation of amyloid precursor protein catabolic process / acetylcholine receptor signaling pathway / positive regulation of amyloid-beta formation / negative regulation of amyloid-beta formation / plasma membrane raft / modulation of excitatory postsynaptic potential / response to amyloid-beta / monoatomic ion channel activity / negative regulation of tumor necrosis factor production / positive regulation of excitatory postsynaptic potential / toxic substance binding / monoatomic ion transport / positive regulation of protein metabolic process / positive regulation of long-term synaptic potentiation / response to nicotine / synapse organization / calcium channel activity / memory / cognition / intracellular calcium ion homeostasis / positive regulation of angiogenesis / calcium ion transport / amyloid-beta binding / monoatomic ion transmembrane transport / postsynaptic membrane / postsynapse / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / learning or memory / response to hypoxia / neuron projection / positive regulation of protein phosphorylation / positive regulation of cell population proliferation / synapse / signal transduction / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Nicotinic acetylcholine receptor / 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
Similarity search - Domain/homology
Neuronal acetylcholine receptor subunit alpha-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / na
AuthorsBondarenko, V. / Chen, Q. / Tang, P.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01DA046939 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM075770 United States
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)T32EB009403 United States
National Science Foundation (NSF, United States)1148698 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structures of highly flexible intracellular domain of human alpha 7 nicotinic acetylcholine receptor.
Authors: Bondarenko, V. / Wells, M.M. / Chen, Q. / Tillman, T.S. / Singewald, K. / Lawless, M.J. / Caporoso, J. / Brandon, N. / Coleman, J.A. / Saxena, S. / Lindahl, E. / Xu, Y. / Tang, P.
History
DepositionAug 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

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


Theoretical massNumber of molelcules
Total (without water)149,1595
Polymers149,1595
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area22570 Å2
ΔGint-206 kcal/mol
Surface area81700 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein
Neuronal acetylcholine receptor subunit alpha-7


Mass: 29831.779 Da / Num. of mol.: 5
Fragment: Transmembrane domain and intracellular domain residues 231-496
Mutation: A263S, V268S, L270S, A474E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRNA7, NACHRA7 / Plasmid: pTBSG1-TMD+ICD / Cell (production host): E. coli / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) pLysS / References: UniProt: P36544

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N TROSY-HSQC
121isotropic23D BEST-HNCA
131isotropic23D BEST-HN(CO)CA
141isotropic23D TROSY-CBCA(CO)NH
151isotropic23D BEST-HNCO
262isotropic22D 1H-15N TROSY-HSQC
272isotropic23D TROSY-HNCA
282isotropic23D TROSY-HN(CO)CA
292isotropic33D TROSY-HN(CA)CB
2102isotropic33D TROSY-CBCA(CO)NH
2112isotropic33D TROSY-HNCO
3123isotropic32D 1H-13C HSQC
3133isotropic33D 13C-edited NOESY-HSQC
4144isotropic12D 1H-15N TROSY-HSQC
4154isotropic13D 15N-edited NOESY-TROSY-HSQC
5165isotropic12D 1H-15N TROSY-HSQC
6176isotropic22D 1H-15N TROSY-HSQC
7187isotropic22D 1H-15N TROSY-HSQC
8198isotropic12D 1H-15N TROSY-HSQC
9209isotropic12D 1H-15N TROSY-HSQC
102110isotropic12D 1H-15N TROSY-HSQC
112211isotropic22D 1H-15N TROSY-HSQC
122312isotropic22D 1H-15N TROSY-HSQC
132413isotropic22D 1H-15N TROSY-HSQC
142514isotropic12D 1H-15N TROSY-HSQC
152615isotropic22D 1H-15N TROSY-HSQC
162716isotropic22D 1H-15N TROSY-HSQC
172817isotropic12D 1H-15N TROSY-HSQC
182918isotropic22D 1H-15N TROSY-HSQC
193019isotropic12D 1H-15N TROSY-HSQC
203120isotropic12D 1H-15N TROSY-HSQC
213221isotropic12D 1H-15N IPAP
223322isotropic12D 1H-15N TROSY-HSQC
233423isotropic12D 1H-15N IPAP
243524isotropic12D 1H-15N TROSY-HSQC
253625isotropic12D 1H-15N IPAP
263726isotropic22D 1H-15N TROSY-HSQC
263826isotropic23D TROSY-HNCA
263926isotropic23D TROSY-HN(CO)CA
274016isotropic22D 1H-15N TROSY-HSQC
284118isotropic22D 1H-15N TROSY-HSQC
294217isotropic12D 1H-15N TROSY-HSQC
304319isotropic12D 1H-15N TROSY-HSQC
30441isotropic22D 1H-15N TROSY-HSQC
30451isotropic23D BEST-HNCA
30461isotropic23D BEST-HN(CO)CA
30471isotropic23D TROSY-CBCA(CO)NH
30481isotropic23D BEST-HNCO

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
micelle10.24 mM [U-13C; U-15N] alpha7nAChR TMD+ICD, 5 mM sodium acetate, 66 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-, 13C-labeled alpha7 TMD+ICD for backbone 1H, 15N, 13C chemical shift assignment.15N_13C_a795% H2O/5% D2O
micelle20.25 mM [U-13C; U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-, 13C-labeled single-cysteine C317 alpha7 TMD+ICD for backbone 1H, 15N, 13C chemical shift assignment. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_13C_a7_C317_195% H2O/5% D2O
micelle260.35 mM [U-13C; U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-, 13C-labeled single-cysteine C317 alpha7 TMD+ICD for backbone 1H, 15N, 13C chemical shift assignment. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_13C_a7_C317_295% H2O/5% D2O
micelle30.25 mM [U-13C; U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-, 13C-labeled single-cysteine C317 alpha7 TMD+ICD for 3D 13C-edited NOESY-HSQC. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_13C_a7_C317_395% H2O/5% D2O
micelle40.35 mM [U-15N] alpha7nAChR C317 TMD+ICD, 5 mM sodium acetate, 66 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled single-cysteine C317 alpha7 TMD+ICD for 3D 15N-edited NOESY-TROSY-HSQC. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C31795% H2O/5% D2O
micelle50.22 mM [U-15N] V311C-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine V311C-MTSL-labeled alpha7 TMD+ICD with 0 and 2.2 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_V311C-MTSL95% H2O/5% D2O
micelle60.22 mM [U-15N] C317-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C317-MTSL-labeled alpha7 TMD+ICD with 0 and 2.2 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C317-MTSL95% H2O/5% D2O
micelle70.3 mM [U-15N] C335-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 53 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C335-MTSL-labeled alpha7 TMD+ICD with 0 and 3.0 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C335-MTSL95% H2O/5% D2O
micelle80.3 mM [U-15N] C342-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 66 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C342-MTSL-labeled alpha7 TMD+ICD with 0 and 3.0 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C335S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C342-MTSL95% H2O/5% D2O
micelle90.3 mM [U-15N] S350C-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 53 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine S350C-MTSL-labeled alpha7 TMD+ICD with 0 and 3.0 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_S350C-MTSL95% H2O/5% D2O
micelle100.25 mM [U-15N] S358C-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine S358C-MTSL-labeled alpha7 TMD+ICD with 0 and 2.5 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_S358C-MTSL95% H2O/5% D2O
micelle110.25 mM [U-15N] C375-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 66 mM LDAO, 20 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C375-MTSL-labeled alpha7 TMD+ICD with 0 and 2.5 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C375-MTSL95% H2O/5% D2O
micelle120.22 mM [U-15N] C390-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 53 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C390-MTSL-labeled alpha7 TMD+ICD with 0 and 2.2 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C427S, C435S, C443S, C449A, C460A.15N_a7_C390-MTSL95% H2O/5% D2O
micelle130.25 mM [U-15N] L415C-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine L415C-MTSL-labeled alpha7 TMD+ICD with 0 and 2.5 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_L415C-MTSL95% H2O/5% D2O
micelle140.25 mM [U-15N] C427-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C427-MTSL-labeled alpha7 TMD+ICD with 0 and 2.5 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C435S, C443S, C449A, C460A.15N_a7_C427-MTSL95% H2O/5% D2O
micelle150.25 mM [U-15N] C435-MTSL alpha7nAChR TMD+ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, single-cysteine C435-MTSL-labeled alpha7 TMD+ICD with 0 and 2.5 mM ascorbic acid for PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C443S, C449A, C460A.15N_a7_C435-MTSL95% H2O/5% D2O
micelle160.28 mM V311C-MTSL alpha7 TMD-ICD, 0.07 mM [U-15N] V311C alpha7 TMD-ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O0.28 mM V311C-MTSL-labeled alpha7 TMD-ICD mixed with 0.07 mM 15N-labeled V311C alpha7 TMD-ICD with 0 and 2.5 mM ascorbic acid for intersubunit PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_V311-MTSL_inter95% H2O/5% D2O
micelle180.28 mM V311C alpha7 TMD-ICD, 0.07 mM [U-15N] V311C-MTSL alpha7 TMD-ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O0.28 mM V311C alpha7 TMD-ICD mixed with 0.07 mM 15N-labeled, V311C-MTSL-labeled alpha7 TMD-ICD with 0 and 1.4 mM ascorbic acid for intrasubunit PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_V311-MTSL_intra95% H2O/5% D2O
micelle170.24 mM C427-MTSL alpha7 TMD-ICD, 0.06 mM [U-15N] C427 alpha7 TMD-ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O0.24 mM C427-MTSL-labeled alpha7 TMD-ICD mixed with 0.06 mM 15N-labeled C427 alpha7 TMD-ICD with 0 and 2.4 mM ascorbic acid for intersubunit PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C435S, C443S, C449A, C460A.15N_a7_C427-MTSL_inter95% H2O/5% D2O
micelle190.24 mM C427 alpha7 TMD-ICD, 0.06 mM [U-15N] C427-MTSL alpha7 TMD-ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O0.24 mM C427 alpha7 TMD-ICD mixed with 0.06 mM 15N-labeled, C427-MTSL-labeled alpha7 TMD-ICD with 0 and 1.2 mM ascorbic acid for intrasubunit PRE NMR. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C435S, C443S, C449A, C460A.15N_a7_C427-MTSL_intra95% H2O/5% D2O
micelle200.25 mM [U-15N] C427-EDTA-Lu3+ alpha7 TMD-ICD, 5 mM sodium acetate, 53 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, C427-labeled with a diamagnetic tag N-[S-(2-Pyridylthio)cysteaminyl]EDTA-Lu3+ alpha7 TMD-ICD. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C435S, C443S, C449A, C460A.15N_a7_C427_RDC_Lu3+95% H2O/5% D2O
micelle210.2 mM [U-15N] C427-EDTA-Tm3+ alpha7 TMD-ICD, 5 mM sodium acetate, 66 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, C427-labeled with a paramagnetic tag N-[S-(2-Pyridylthio)cysteaminyl]EDTA-Tm3+ alpha7 TMD-ICD. Additional mutations include C219A, C317S, C335S, C342S, C375S, C385S, C390S, C435S, C443S, C449A, C460A.15N_a7_C427_RDC_Tm3+95% H2O/5% D2O
micelle220.25 mM [U-15N] C317-EDTA-Lu3+ alpha7 TMD-ICD, 5 mM sodium acetate, 66 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, C317-labeled with a diamagnetic tag N-[S-(2-Pyridylthio)cysteaminyl]EDTA-Lu3+ alpha7 TMD-ICD. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C317_RDC_Lu3+95% H2O/5% D2O
micelle230.25 mM [U-15N] C317-EDTA-Tm3+ alpha7 TMD-ICD, 5 mM sodium acetate, 53 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, C317-labeled with a paramagnetic tag N-[S-(2-Pyridylthio)cysteaminyl]EDTA-Tm3+ alpha7 TMD-ICD. Additional mutations include C219A, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C317_RDC_Tm3+95% H2O/5% D2O
micelle240.24 mM [U-15N] C219-EDTA-Lu3+ alpha7 TMD-ICD, 5 mM sodium acetate, 44 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, C219-labeled with a diamagnetic tag N-[S-(2-Pyridylthio)cysteaminyl]EDTA-Lu3+ alpha7 TMD-ICD. Additional mutations include C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C219_RDC_Lu3+95% H2O/5% D2O
micelle250.22 mM [U-15N] C219-EDTA-Tm3+ alpha7 TMD-ICD, 5 mM sodium acetate, 53 mM LDAO, 25 mM NaCl, 5 % D2O, 20 uM DSS, 95% H2O/5% D2O15N-labeled, C219-labeled with a paramagnetic tag N-[S-(2-Pyridylthio)cysteaminyl]EDTA-Tm3+ alpha7 TMD-ICD. Additional mutations include C317S, C335S, C342S, C375S, C385S, C390S, C427S, C435S, C443S, C449A, C460A.15N_a7_C219_RDC_Tm3+95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.24 mMalpha7nAChR TMD+ICD[U-13C; U-15N]1
5 mMsodium acetatenatural abundance1
66 mMLDAOnatural abundance1
25 mMNaClnatural abundance1
5 %D2Onatural abundance1
20 uMDSSnatural abundance1
0.25 mMalpha7nAChR C317 TMD+ICD[U-13C; U-15N]2
5 mMsodium acetatenatural abundance2
44 mMLDAOnatural abundance2
25 mMNaClnatural abundance2
5 %D2Onatural abundance2
20 uMDSSnatural abundance2
0.35 mMalpha7nAChR C317 TMD+ICD[U-13C; U-15N]26
5 mMsodium acetatenatural abundance26
44 mMLDAOnatural abundance26
25 mMNaClnatural abundance26
5 %D2Onatural abundance26
20 uMDSSnatural abundance26
0.25 mMalpha7nAChR C317 TMD+ICD[U-13C; U-15N]3
5 mMsodium acetatenatural abundance3
44 mMLDAOnatural abundance3
25 mMNaClnatural abundance3
5 %D2Onatural abundance3
20 uMDSSnatural abundance3
0.35 mMalpha7nAChR C317 TMD+ICD[U-15N]4
5 mMsodium acetatenatural abundance4
66 mMLDAOnatural abundance4
25 mMNaClnatural abundance4
5 %D2Onatural abundance4
20 uMDSSnatural abundance4
0.22 mMV311C-MTSL alpha7nAChR TMD+ICD[U-15N]5
5 mMsodium acetatenatural abundance5
44 mMLDAOnatural abundance5
25 mMNaClnatural abundance5
5 %D2Onatural abundance5
20 uMDSSnatural abundance5
0.22 mMC317-MTSL alpha7nAChR TMD+ICD[U-15N]6
5 mMsodium acetatenatural abundance6
44 mMLDAOnatural abundance6
25 mMNaClnatural abundance6
5 %D2Onatural abundance6
20 uMDSSnatural abundance6
0.3 mMC335-MTSL alpha7nAChR TMD+ICD[U-15N]7
5 mMsodium acetatenatural abundance7
53 mMLDAOnatural abundance7
25 mMNaClnatural abundance7
5 %D2Onatural abundance7
20 uMDSSnatural abundance7
0.3 mMC342-MTSL alpha7nAChR TMD+ICD[U-15N]8
5 mMsodium acetatenatural abundance8
66 mMLDAOnatural abundance8
25 mMNaClnatural abundance8
5 %D2Onatural abundance8
20 uMDSSnatural abundance8
0.3 mMS350C-MTSL alpha7nAChR TMD+ICD[U-15N]9
5 mMsodium acetatenatural abundance9
53 mMLDAOnatural abundance9
25 mMNaClnatural abundance9
5 %D2Onatural abundance9
20 uMDSSnatural abundance9
0.25 mMS358C-MTSL alpha7nAChR TMD+ICD[U-15N]10
5 mMsodium acetatenatural abundance10
44 mMLDAOnatural abundance10
25 mMNaClnatural abundance10
5 %D2Onatural abundance10
20 uMDSSnatural abundance10
0.25 mMC375-MTSL alpha7nAChR TMD+ICD[U-15N]11
5 mMsodium acetatenatural abundance11
66 mMLDAOnatural abundance11
20 mMNaClnatural abundance11
5 %D2Onatural abundance11
20 uMDSSnatural abundance11
0.22 mMC390-MTSL alpha7nAChR TMD+ICD[U-15N]12
5 mMsodium acetatenatural abundance12
53 mMLDAOnatural abundance12
25 mMNaClnatural abundance12
5 %D2Onatural abundance12
20 uMDSSnatural abundance12
0.25 mML415C-MTSL alpha7nAChR TMD+ICD[U-15N]13
5 mMsodium acetatenatural abundance13
44 mMLDAOnatural abundance13
25 mMNaClnatural abundance13
5 %D2Onatural abundance13
20 uMDSSnatural abundance13
0.25 mMC427-MTSL alpha7nAChR TMD+ICD[U-15N]14
5 mMsodium acetatenatural abundance14
44 mMLDAOnatural abundance14
25 mMNaClnatural abundance14
5 %D2Onatural abundance14
20 uMDSSnatural abundance14
0.25 mMC435-MTSL alpha7nAChR TMD+ICD[U-15N]15
5 mMsodium acetatenatural abundance15
44 mMLDAOnatural abundance15
25 mMNaClnatural abundance15
5 %D2Onatural abundance15
20 uMDSSnatural abundance15
0.28 mMV311C-MTSL alpha7 TMD-ICDnatural abundance16
0.07 mMV311C alpha7 TMD-ICD[U-15N]16
5 mMsodium acetatenatural abundance16
44 mMLDAOnatural abundance16
25 mMNaClnatural abundance16
5 %D2Onatural abundance16
20 uMDSSnatural abundance16
0.28 mMV311C alpha7 TMD-ICDnatural abundance18
0.07 mMV311C-MTSL alpha7 TMD-ICD[U-15N]18
5 mMsodium acetatenatural abundance18
44 mMLDAOnatural abundance18
25 mMNaClnatural abundance18
5 %D2Onatural abundance18
20 uMDSSnatural abundance18
0.24 mMC427-MTSL alpha7 TMD-ICDnatural abundance17
0.06 mMC427 alpha7 TMD-ICD[U-15N]17
5 mMsodium acetatenatural abundance17
44 mMLDAOnatural abundance17
25 mMNaClnatural abundance17
5 %D2Onatural abundance17
20 uMDSSnatural abundance17
0.24 mMC427 alpha7 TMD-ICDnatural abundance19
0.06 mMC427-MTSL alpha7 TMD-ICD[U-15N]19
5 mMsodium acetatenatural abundance19
44 mMLDAOnatural abundance19
25 mMNaClnatural abundance19
5 %D2Onatural abundance19
20 uMDSSnatural abundance19
0.25 mMC427-EDTA-Lu3+ alpha7 TMD-ICD[U-15N]20
5 mMsodium acetatenatural abundance20
53 mMLDAOnatural abundance20
25 mMNaClnatural abundance20
5 %D2Onatural abundance20
20 uMDSSnatural abundance20
0.2 mMC427-EDTA-Tm3+ alpha7 TMD-ICD[U-15N]21
5 mMsodium acetatenatural abundance21
66 mMLDAOnatural abundance21
25 mMNaClnatural abundance21
5 %D2Onatural abundance21
20 uMDSSnatural abundance21
0.25 mMC317-EDTA-Lu3+ alpha7 TMD-ICD[U-15N]22
5 mMsodium acetatenatural abundance22
66 mMLDAOnatural abundance22
25 mMNaClnatural abundance22
5 %D2Onatural abundance22
20 uMDSSnatural abundance22
0.25 mMC317-EDTA-Tm3+ alpha7 TMD-ICD[U-15N]23
5 mMsodium acetatenatural abundance23
53 mMLDAOnatural abundance23
25 mMNaClnatural abundance23
5 %D2Onatural abundance23
20 uMDSSnatural abundance23
0.24 mMC219-EDTA-Lu3+ alpha7 TMD-ICD[U-15N]24
5 mMsodium acetatenatural abundance24
44 mMLDAOnatural abundance24
25 mMNaClnatural abundance24
5 %D2Onatural abundance24
20 uMDSSnatural abundance24
0.22 mMC219-EDTA-Tm3+ alpha7 TMD-ICD[U-15N]25
5 mMsodium acetatenatural abundance25
53 mMLDAOnatural abundance25
25 mMNaClnatural abundance25
5 %D2Onatural abundance25
20 uMDSSnatural abundance25
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
125 mMcondition_s14.71 atm318 K
225 mMcondition_s24.71 atm318 K
2625 mMcondition_s264.71 atm318 K
325 mMcondition_s34.71 atm318 K
425 mMcondition_s44.71 atm318 K
525 mMcondition_s54.71 atm318 K
625 mMcondition_s64.71 atm318 K
725 mMcondition_s74.71 atm318 K
825 mMcondition_s84.71 atm318 K
925 mMcondition_s94.71 atm318 K
1025 mMcondition_s104.71 atm318 K
1125 mMcondition_s114.71 atm318 K
1225 mMcondition_s124.71 atm318 K
1325 mMcondition_s134.71 atm318 K
1425 mMcondition_s144.71 atm318 K
1525 mMcondition_s154.71 atm318 K
1625 mMcondition_s164.71 atm318 K
2725 mMcondition_s274.71 atm298 K
1825 mMcondition_s184.71 atm318 K
2825 mMcondition_s284.71 atm298 K
1725 mMcondition_s174.71 atm318 K
2925 mMcondition_s294.71 atm298 K
1925 mMcondition_s194.71 atm318 K
3025 mMcondition_s304.71 atm298 K
2025 mMcondition_s204.71 atm308 K
2125 mMcondition_s214.71 atm308 K
2225 mMcondition_s224.71 atm308 K
2325 mMcondition_s234.71 atm308 K
2425 mMcondition_s244.71 atm308 K
2525 mMcondition_s254.71 atm308 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II9001
Bruker AVANCE IIBrukerAVANCE II8002
Bruker AVANCEBrukerAVANCE7003

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1 and 3.1Bruker Biospincollection
NMRPipe10.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.19Goddarddata analysis
NMRFAM-SPARKY1.47Lee, Tonelli and Markleydata analysis
CS-ROSETTA3.17Shen, Vernon, Baker and Baxstructure calculation
Rosetta3.7Leaver-Fay, Tyka, Lewis, Lange, Thompson, Jacak, Kaufman, Renfrew, Smith, Sheffler, Davis, Cooper, Treuille, Mandell, Richter, Ban, Fleishman, Corn, Kim, Lyskov, Berrondo, Mentzer, Popovic, Havranek, Karanicolas, Das, Meiler, Kortemme, Gray, Kuhlman, Baker, and Bradleystructure calculation
Rosetta3.7Leaver-Fay, Tyka, Lewis, Lange, Thompson, Jacak, Kaufman, Renfrew, Smith, Sheffler, Davis, Cooper, Treuille, Mandell, Richter, Ban, Fleishman, Corn, Kim, Lyskov, Berrondo, Mentzer, Popovic, Havranek, Karanicolas, Das, Meiler, Kortemme, Gray, Kuhlman, Baker, and Bradleyrefinement
PHENIX1.19Liebschner, Afonine, Baker, Bunkoczi, Chen, Croll, Hintze, Hung, Jain, McCoy, Moriarty, Oeffner, Poon, Prisant, Read, Richardson, Richardson, Sammito, Sobolev, Stockwell, Terwilliger, Urzhumtsev, Videau, Williams and Adamsrefinement
MolProbityRichardsondata analysis
Refinement
MethodSoftware ordinal
na8
na9
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 15

+
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