[English] 日本語
Yorodumi
- PDB-5o4f: Structure of GluK3 ligand-binding domain (S1S2) in complex with t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o4f
TitleStructure of GluK3 ligand-binding domain (S1S2) in complex with the agonist LM-12b at 2.10 A resolution
ComponentsGlutamate receptor ionotropic, kainate 3
KeywordsMEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR / KAINATE RECEPTOR / LIGAND-BINDING DOMAIN / GLUK3 / GLUR7 / AGONIST
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / G protein-coupled glutamate receptor signaling pathway / negative regulation of synaptic transmission, glutamatergic / glutamate receptor activity / glutamate receptor signaling pathway / kainate selective glutamate receptor activity ...Presynaptic function of Kainate receptors / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / G protein-coupled glutamate receptor signaling pathway / negative regulation of synaptic transmission, glutamatergic / glutamate receptor activity / glutamate receptor signaling pathway / kainate selective glutamate receptor activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / presynaptic membrane / chemical synaptic transmission / perikaryon / postsynaptic membrane / axon / dendrite / glutamatergic synapse / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / 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 / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region ...Ionotropic glutamate receptor, metazoa / 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 / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8VE / ACETATE ION / Glutamate receptor ionotropic, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsMoellerud, S. / Frydenvang, K. / Kastrup, J.S.
CitationJournal: ACS Chem Neurosci / Year: 2017
Title: Structure and Affinity of Two Bicyclic Glutamate Analogues at AMPA and Kainate Receptors.
Authors: Mllerud, S. / Pinto, A. / Marconi, L. / Frydenvang, K. / Thorsen, T.S. / Laulumaa, S. / Venskutonyte, R. / Winther, S. / Moral, A.M.C. / Tamborini, L. / Conti, P. / Pickering, D.S. / Kastrup, J.S.
History
DepositionMay 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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 / _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 / _struct_conn.ptnr2_symmetry
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Glutamate receptor ionotropic, kainate 3
A: Glutamate receptor ionotropic, kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,70121
Polymers58,1852
Non-polymers1,51619
Water2,990166
1
B: Glutamate receptor ionotropic, kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,97712
Polymers29,0921
Non-polymers88411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Glutamate receptor ionotropic, kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7249
Polymers29,0921
Non-polymers6318
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.392, 56.205, 87.462
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11B-307-

ZN

21B-482-

HOH

31A-476-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESSEQ 4:20 OR RESSEQ 22:26 OR RESSEQ...
211(CHAIN B AND (RESSEQ 4:20 OR RESSEQ 22:26 OR RESSEQ...

-
Components

-
Protein , 1 types, 2 molecules BA

#1: Protein Glutamate receptor ionotropic, kainate 3 / GluK3 / Glutamate receptor 7 / GluR7


Mass: 29092.453 Da / Num. of mol.: 2
Fragment: ligand-binding domain, UNP Residues 669-806,ligand-binding domain, UNP Residues 432-546
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER (RESIDUES 117-118). THE SEQUENCE MATCHES ...Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER (RESIDUES 117-118). THE SEQUENCE MATCHES DISCONTINOUSLY WITH REFERENCE DATABASE (432-546, 669-806). THE FIRST THREE RESIDUES GLY-PRO-GLY ARE CLONING REMNANTS.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik3, Glur7 / Production host: Escherichia coli (E. coli) / Variant (production host): Origami 2 / References: UniProt: P42264

-
Non-polymers , 6 types, 185 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-8VE / (3~{a}~{R},4~{S},6~{a}~{R})-1-methyl-4,5,6,6~{a}-tetrahydro-3~{a}~{H}-pyrrolo[3,4-c]pyrazole-3,4-dicarboxylic acid


Mass: 213.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11N3O4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 15% PEG4000, 0.3 M Lithium sulfate, 5 mM zinc acetate, 0.1 M Bis-Tris-Propane pH 8.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→131.392 Å / Num. obs: 38619 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 38.1 Å2 / Rsym value: 0.061 / Net I/σ(I): 16.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.562 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.53 Å44.49 Å
Translation5.53 Å44.49 Å

-
Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
PHASER2.5.1phasing
PDB_EXTRACT3.22data extraction
PHENIXmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U92

3u92


Resolution: 2.1→44.49 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.82
RfactorNum. reflection% reflection
Rfree0.215 1936 5.02 %
Rwork0.192 --
obs0.193 38592 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 60.15 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3993 0 75 166 4234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034157
X-RAY DIFFRACTIONf_angle_d0.6735594
X-RAY DIFFRACTIONf_dihedral_angle_d13.122514
X-RAY DIFFRACTIONf_chiral_restr0.042619
X-RAY DIFFRACTIONf_plane_restr0.004698
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A2656X-RAY DIFFRACTIONPOSITIONAL
12B2656X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.26041510.24782566X-RAY DIFFRACTION100
2.1525-2.21070.26961280.24032581X-RAY DIFFRACTION100
2.2107-2.27580.24671410.23242539X-RAY DIFFRACTION100
2.2758-2.34920.24841230.22812624X-RAY DIFFRACTION100
2.3492-2.43320.27361270.23012613X-RAY DIFFRACTION100
2.4332-2.53060.28381510.22462541X-RAY DIFFRACTION100
2.5306-2.64570.2451290.21342608X-RAY DIFFRACTION100
2.6457-2.78520.25531370.22292590X-RAY DIFFRACTION100
2.7852-2.95970.23711510.21862608X-RAY DIFFRACTION100
2.9597-3.18810.22261290.21552608X-RAY DIFFRACTION100
3.1881-3.50890.22761440.18752643X-RAY DIFFRACTION100
3.5089-4.01630.19781360.17052646X-RAY DIFFRACTION100
4.0163-5.0590.1571350.14512683X-RAY DIFFRACTION100
5.059-44.50030.19471540.18742806X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0627-0.01360.05590.02980.00320.0344-0.18120.1794-0.10060.10850.01650.04660.0105-0.1558-0.00010.3429-0.02480.01670.3850.03850.3027.993977.465110.2433
20.26220.0462-0.07720.06510.00730.0876-0.2501-0.0009-0.50690.07320.09220.02540.2362-0.10470.00550.4148-0.02280.12210.33480.03340.484715.854864.268715.1459
30.0017-0.0068-0.00120.00670.00880.0086-0.1239-0.1456-0.03660.0838-0.0444-0.0195-0.01410.0657-0.00020.75570.0861-0.01090.84180.0640.443123.363471.591144.8122
40.1690.08220.11850.0951-0.02130.1649-0.0736-0.4423-0.32480.09790.01360.0831-0.1386-0.0367-0.11840.38250.09920.07320.43950.2260.356717.719468.159733.6947
50.0435-0.02610.0060.0045-0.00050.0275-0.22220.1928-0.2023-0.0065-0.1201-0.0740.06010.2346-0.00050.382-0.04770.08620.40060.0110.40723.765170.82646.1469
60.00130.0102-0.00520.01460.00410.0085-0.10750.0741-0.0102-0.04310.02540.122-0.1932-0.06220.00010.3967-0.01530.00450.29080.04860.378719.664385.666116.6046
70.1875-0.1397-0.03380.0663-0.04390.35130.082-0.15420.54540.1323-0.0014-0.2898-0.086-0.0428-0.00060.3356-0.0456-0.01990.2986-0.02180.525343.311102.10413.401
80.1756-0.1676-0.08660.1850.02570.14710.7551-0.6579-0.42320.20750.2195-0.1570.6555-0.43020.78850.5527-0.3094-0.69120.7170.29230.147946.462778.619925.5105
90.4364-0.1065-0.1650.02390.05670.10350.5019-0.13520.10380.02980.0089-0.42910.48140.11490.21340.4716-0.0685-0.2950.3738-0.01260.428254.541684.217720.3954
100.00940.03890.04080.10910.12550.11870.11710.16280.30320.0841-0.0858-0.15240.0041-0.002200.32850.02850.02270.37260.07040.376243.11594.08063.0625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'B' AND (RESID 4 THROUGH 47 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 48 THROUGH 115 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 116 THROUGH 132 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 133 THROUGH 212 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 213 THROUGH 238 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 239 THROUGH 255 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 4 THROUGH 105 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 106 THROUGH 163 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 164 THROUGH 212 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 213 THROUGH 256 )

+
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