[English] 日本語
Yorodumi
- PDB-6ssi: Structure of the pentameric ligand-gated ion channel ELIC in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ssi
TitleStructure of the pentameric ligand-gated ion channel ELIC in complex with a PAM nanobody
Components
  • Cys-loop ligand-gated ion channel
  • NANOBODY 22
KeywordsTRANSPORT PROTEIN / ION CHANNEL / CYS-LOOP RECEPTOR / PENTAMERIC LIGAND GATED ION CHANNEL / LGIC / ELIC / NANOBODY
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
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
GAMMA-AMINO-BUTANOIC ACID / ACETATE ION / Cys-loop ligand-gated ion channel
Similarity search - Component
Biological speciesDickeya chrysanthemi (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsUlens, C. / Brams, M. / Evans, G.L. / Spurny, R. / Govaerts, C. / Pardon, E. / Steyaert, J.
Funding support Belgium, 5items
OrganizationGrant numberCountry
Research Foundation - Flanders1200261 Belgium
Research Foundation - FlandersG.0762.13 Belgium
KU LeuvenOT/13/095 Belgium
KU LeuvenC32/16/035 Belgium
KU LeuvenC14/17/093 Belgium
CitationJournal: Elife / Year: 2020
Title: Modulation of the Erwinia ligand-gated ion channel (ELIC) and the 5-HT 3 receptor via a common vestibule site.
Authors: Brams, M. / Govaerts, C. / Kambara, K. / Price, K.L. / Spurny, R. / Gharpure, A. / Pardon, E. / Evans, G.L. / Bertrand, D. / Lummis, S.C. / Hibbs, R.E. / Steyaert, J. / Ulens, C.
History
DepositionSep 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cys-loop ligand-gated ion channel
B: Cys-loop ligand-gated ion channel
C: Cys-loop ligand-gated ion channel
D: Cys-loop ligand-gated ion channel
E: Cys-loop ligand-gated ion channel
F: NANOBODY 22
G: NANOBODY 22
H: NANOBODY 22
I: NANOBODY 22
J: NANOBODY 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,53442
Polymers248,91210
Non-polymers5,62332
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42980 Å2
ΔGint-212 kcal/mol
Surface area85600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.604, 146.563, 140.242
Angle α, β, γ (deg.)90.000, 111.390, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Antibody , 2 types, 10 molecules ABCDEFGHIJ

#1: Protein
Cys-loop ligand-gated ion channel / ELIC


Mass: 36465.578 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C7B7
#2: Antibody
NANOBODY 22


Mass: 13316.725 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 8 types, 177 molecules

#3: Chemical
ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H9NO2
#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical
ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H3O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.27 Å3/Da / Density % sol: 71.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M GABA, 0.2 M Ca(OAc)2, 0.1 M MES buffer, 10% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.58→49.35 Å / Num. obs: 123740 / % possible obs: 99.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 87.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.035 / Rrim(I) all: 0.077 / Net I/σ(I): 13.4 / Num. measured all: 594559
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.58-2.634.61.3942695757990.4580.7191.572195.2
14.16-49.354.30.02731777440.9990.0140.0314593.4

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
MxCuBEdata collection
XDSMar 15, 2019data reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vl0, 3p0g

2vl0

3p0g


Resolution: 2.59→47.06 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 0.327 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.306 / SU Rfree Blow DPI: 0.226 / SU Rfree Cruickshank DPI: 0.235
RfactorNum. reflection% reflectionSelection details
Rfree0.246 6188 5 %RANDOM
Rwork0.23 ---
obs0.231 123710 99.8 %-
Displacement parametersBiso max: 167.99 Å2 / Biso mean: 77.43 Å2 / Biso min: 36.34 Å2
Baniso -1Baniso -2Baniso -3
1--1.9344 Å20 Å22.5217 Å2
2--9.4869 Å20 Å2
3----7.5524 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 2.59→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16423 0 356 145 16924
Biso mean--101.57 61.9 -
Num. residues----2081
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5834SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2868HARMONIC5
X-RAY DIFFRACTIONt_it17176HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2288SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact19025SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d17176HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg23331HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion15.26
LS refinement shellResolution: 2.59→2.6 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3329 124 5.01 %
Rwork0.2784 2351 -
all0.2809 2475 -
obs--94.43 %

+
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