[English] 日本語
Yorodumi
- PDB-6hjy: X-ray structure of a pentameric ligand gated ion channel from Erw... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hjy
TitleX-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) Delta8 truncation mutant in complex with nanobody 72
Components
  • (Cys-loop ligand-gated ion ...) x 4
  • (nanobody 72) x 2
KeywordsMEMBRANE PROTEIN / ion channel / pentameric ligand-gated ion channel / cya-loop receptor
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / 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
Cys-loop ligand-gated ion channel
Similarity search - Component
Biological speciesDickeya chrysanthemi (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsSpurny, R. / Govaerts, C. / Evans, G.L. / Pardon, E. / Steyaert, J. / Ulens, C.
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: A lipid site shapes the agonist response of a pentameric ligand-gated ion channel.
Authors: Henault, C.M. / Govaerts, C. / Spurny, R. / Brams, M. / Estrada-Mondragon, A. / Lynch, J. / Bertrand, D. / Pardon, E. / Evans, G.L. / Woods, K. / Elberson, B.W. / Cuello, L.G. / Brannigan, G. ...Authors: Henault, C.M. / Govaerts, C. / Spurny, R. / Brams, M. / Estrada-Mondragon, A. / Lynch, J. / Bertrand, D. / Pardon, E. / Evans, G.L. / Woods, K. / Elberson, B.W. / Cuello, L.G. / Brannigan, G. / Nury, H. / Steyaert, J. / Baenziger, J.E. / Ulens, C.
History
DepositionSep 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 27, 2019Group: 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 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
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 72
G: nanobody 72
H: nanobody 72
I: nanobody 72
J: nanobody 72


Theoretical massNumber of molelcules
Total (without water)227,63410
Polymers227,63410
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35890 Å2
ΔGint-139 kcal/mol
Surface area79770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.675, 155.093, 101.618
Angle α, β, γ (deg.)90.000, 103.080, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Cys-loop ligand-gated ion ... , 4 types, 5 molecules ABCDE

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


Mass: 32102.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C7B7
#2: Protein Cys-loop ligand-gated ion channel / ELIC


Mass: 32413.795 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C7B7
#3: Protein Cys-loop ligand-gated ion channel / ELIC


Mass: 32031.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C7B7
#4: Protein Cys-loop ligand-gated ion channel / ELIC


Mass: 32217.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C7B7

-
Antibody , 2 types, 5 molecules FJGHI

#5: Antibody nanobody 72


Mass: 13367.960 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#6: Antibody nanobody 72


Mass: 13239.831 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 300 mM ammonium formate, 50 mM TRIS pH 9.0 and 33% PEG monomethylether 550

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9754 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 2.78→49.49 Å / Num. obs: 71824 / % possible obs: 99.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 88.12 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.094 / Rrim(I) all: 0.136 / Net I/av σ(I): 6.6 / Net I/σ(I): 6.6
Reflection shellResolution: 2.78→2.85 Å / Rmerge(I) obs: 1.442 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4318 / CC1/2: 0.281 / Rpim(I) all: 1.379 / Rrim(I) all: 1.998

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HJX

6hjx


Resolution: 2.78→49.49 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.919 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.712 / SU Rfree Blow DPI: 0.292 / SU Rfree Cruickshank DPI: 0.307
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3602 5.02 %RANDOM
Rwork0.225 ---
obs0.226 71790 99 %-
Displacement parametersBiso max: 253.68 Å2 / Biso mean: 101.39 Å2 / Biso min: 45.07 Å2
Baniso -1Baniso -2Baniso -3
1-21.464 Å20 Å2-6.2316 Å2
2---10.5398 Å20 Å2
3----10.9242 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: final / Resolution: 2.78→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16066 0 0 0 16066
Num. residues----2006
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5557SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes395HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2408HARMONIC5
X-RAY DIFFRACTIONt_it16497HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2113SEMIHARMONIC5
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_contact17956SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d16497HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg22427HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion17.24
LS refinement shellResolution: 2.78→2.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2296 246 5.13 %
Rwork0.2403 4553 -
all0.2397 4799 -
obs--89.42 %

+
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