[English] 日本語
Yorodumi
- PDB-4yki: Mnemiopsis leidyi ML032222a iGluR LBD glycine complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yki
TitleMnemiopsis leidyi ML032222a iGluR LBD glycine complex
ComponentsML032222a iGluR
KeywordsMEMBRANE PROTEIN / Glutamate Receptor / Ion Channel
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / metal ion binding / plasma membrane
Similarity search - Function
Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYCINE / ML032222a iGluR
Similarity search - Component
Biological speciesMnemiopsis leidyi (sea walnut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsAlberstein, R.G. / Mayer, M.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Glycine activated ion channel subunits encoded by ctenophore glutamate receptor genes.
Authors: Alberstein, R. / Grey, R. / Zimmet, A. / Simmons, D.K. / Mayer, M.L.
History
DepositionMar 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Nov 18, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ML032222a iGluR
B: ML032222a iGluR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1946
Polymers57,9232
Non-polymers2714
Water14,718817
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-19 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.944, 123.388, 54.319
Angle α, β, γ (deg.)90.00, 111.84, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ML032222a iGluR


Mass: 28961.559 Da / Num. of mol.: 2 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Details: The construct contains residues K409-E526 and T682-S815 of the ML032222a ligand binding domain connected by a synthetic GT linker
Source: (gene. exp.) Mnemiopsis leidyi (sea walnut) / Gene: ML032222a / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: A0A0R4I973*PLUS
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 817 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe construct contains residues K409-E526 and T682-S815 of the ML032222a ligand binding domain ...The construct contains residues K409-E526 and T682-S815 of the ML032222a ligand binding domain connected by a synthetic GT linker

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Reservoir: 18% PEG 8K, 100 mM Cacodylate, 150 mM MgS04. Protein buffer: 100 mM NaCl, 10 mM HEPES, pH 7.0, 0.5 mM EDTA, 2 mM Na glutamate, no added glycine
PH range: 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.21→40 Å / Num. obs: 169396 / % possible obs: 90.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 20.8
Reflection shellResolution: 1.21→1.23 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2 / % possible all: 64.8

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S50

1s50


Resolution: 1.21→31.871 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0.39 / Phase error: 16.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1613 14490 5.05 %Random selection
Rwork0.1335 ---
obs0.1349 144200 84.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.21→31.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4006 0 16 817 4839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084365
X-RAY DIFFRACTIONf_angle_d1.2185913
X-RAY DIFFRACTIONf_dihedral_angle_d12.7451629
X-RAY DIFFRACTIONf_chiral_restr0.072624
X-RAY DIFFRACTIONf_plane_restr0.006782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2104-1.22410.25181080.18662420X-RAY DIFFRACTION23
1.2241-1.23860.1692120.17513912X-RAY DIFFRACTION36
1.2386-1.25370.17692660.16865305X-RAY DIFFRACTION50
1.2537-1.26950.20263580.16346374X-RAY DIFFRACTION60
1.2695-1.28620.17924060.16687185X-RAY DIFFRACTION67
1.2862-1.30390.17554300.15647940X-RAY DIFFRACTION74
1.3039-1.32250.18464600.16158382X-RAY DIFFRACTION79
1.3225-1.34220.18674560.15498708X-RAY DIFFRACTION82
1.3422-1.36320.18814700.15158975X-RAY DIFFRACTION84
1.3632-1.38550.19325230.14249133X-RAY DIFFRACTION86
1.3855-1.40940.17174850.14359399X-RAY DIFFRACTION88
1.4094-1.43510.18055140.14239771X-RAY DIFFRACTION91
1.4351-1.46270.16075120.13359638X-RAY DIFFRACTION91
1.4627-1.49250.17675100.13449816X-RAY DIFFRACTION92
1.4925-1.5250.15215200.12859895X-RAY DIFFRACTION92
1.525-1.56040.17295320.124210006X-RAY DIFFRACTION94
1.5604-1.59950.1475530.124310058X-RAY DIFFRACTION94
1.5995-1.64270.17075170.120210131X-RAY DIFFRACTION95
1.6427-1.6910.16375520.126310165X-RAY DIFFRACTION95
1.691-1.74560.15075070.123410267X-RAY DIFFRACTION96
1.7456-1.8080.15555460.128210274X-RAY DIFFRACTION96
1.808-1.88040.14845540.128410379X-RAY DIFFRACTION97
1.8804-1.9660.15275360.127310379X-RAY DIFFRACTION97
1.966-2.06960.14575800.125510443X-RAY DIFFRACTION98
2.0696-2.19920.14365170.122910566X-RAY DIFFRACTION98
2.1992-2.3690.16215340.126210533X-RAY DIFFRACTION98
2.369-2.60730.17435060.137110600X-RAY DIFFRACTION99
2.6073-2.98430.17055870.141410548X-RAY DIFFRACTION99
2.9843-3.7590.15135730.133910624X-RAY DIFFRACTION99
3.759-31.88170.16356660.136310519X-RAY DIFFRACTION99

+
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://pdbjlvh1.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