[English] 日本語
Yorodumi
- PDB-4io7: Crystal Structure of the AvGluR1 ligand binding domain complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4io7
TitleCrystal Structure of the AvGluR1 ligand binding domain complex with phenylalanine at 1.9 Angstrom resolution
ComponentsAvGluR1 ligand binding domain
KeywordsMEMBRANE PROTEIN / Ion Channel
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / G protein-coupled receptor activity / postsynaptic membrane
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / GPCR, family 3 / 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 ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / GPCR, family 3 / 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
PHENYLALANINE / Glutamate receptor 1
Similarity search - Component
Biological speciesAdineta vaga (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.92 Å
AuthorsLomash, S. / Chittori, S. / Mayer, M.L.
CitationJournal: Structure / Year: 2013
Title: Anions Mediate Ligand Binding in Adineta vaga Glutamate Receptor Ion Channels.
Authors: Lomash, S. / Chittori, S. / Brown, P. / Mayer, M.L.
History
DepositionJan 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Sep 20, 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 / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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: AvGluR1 ligand binding domain
B: AvGluR1 ligand binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4578
Polymers54,9852
Non-polymers4726
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-51 kcal/mol
Surface area21250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.499, 100.235, 56.757
Angle α, β, γ (deg.)90.00, 116.49, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein AvGluR1 ligand binding domain


Mass: 27492.455 Da / Num. of mol.: 2 / Fragment: unp residues 457-567; 680-812
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adineta vaga (invertebrata) / Plasmid: pet22B modified / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: E9P5T5
#2: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF AvGluR1. TRANSMEMBRANE ...THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF AvGluR1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (457-567 AND 680-812)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15.5% PEG 3350, 0.05 M NaCitrate, 0.1 M, BisTris Propane 0.05 M Phenylalanine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
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: Dec 8, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→30 Å / Num. all: 42897 / Num. obs: 42897 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 19.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.92-1.953.80.72.61100
1.95-1.993.80.542.91100
1.99-2.033.80.433.61100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4IO2

4io2


Resolution: 1.92→29.535 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1868 1337 3.15 %Random
Rwork0.1552 ---
obs0.1563 42385 99.99 %-
all-42385 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.92→29.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3812 0 28 291 4131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114035
X-RAY DIFFRACTIONf_angle_d1.2845477
X-RAY DIFFRACTIONf_dihedral_angle_d11.4141513
X-RAY DIFFRACTIONf_chiral_restr0.077632
X-RAY DIFFRACTIONf_plane_restr0.006706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.98860.21251360.19074079X-RAY DIFFRACTION100
1.9886-2.06820.22511280.17214083X-RAY DIFFRACTION100
2.0682-2.16230.20251260.15714105X-RAY DIFFRACTION100
2.1623-2.27630.22641310.154103X-RAY DIFFRACTION100
2.2763-2.41880.16691300.14974090X-RAY DIFFRACTION100
2.4188-2.60550.18571230.15454108X-RAY DIFFRACTION100
2.6055-2.86750.17951350.15674103X-RAY DIFFRACTION100
2.8675-3.2820.1721440.15744119X-RAY DIFFRACTION100
3.282-4.13310.17421320.14334101X-RAY DIFFRACTION100
4.1331-29.5390.19031520.15774157X-RAY DIFFRACTION100
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)
13.4193-0.15820.70521.76491.42431.26590.0610.0259-0.0648-0.21530.01120.18150.0406-0.1336-0.11940.2001-0.0498-0.05350.21790.00360.0772-5.982239.1825-16.2405
22.2994-1.43892.26973.2737-3.39133.87060.121.42460.5011-0.9479-0.05160.0958-0.8812-0.01330.17871.0717-0.2123-0.15390.91820.04040.3884-3.09544.7686-33.7249
31.81840.6206-0.39921.984-0.1280.8188-0.00870.06070.072-0.17140.075-0.0308-0.01450.0509-0.05680.1234-0.0033-0.00610.1036-0.01250.07980.609346.2958-9.1905
42.4033-0.1153-0.70672.93050.21260.99890.11050.13420.2987-0.18070.0846-0.2604-0.20370.0521-0.16480.1842-0.0280.06710.1788-0.02280.230610.402158.5221-9.9781
51.7397-0.1307-0.54413.53380.13242.3224-0.0154-0.0075-0.116-0.00730.04250.15860.1961-0.0557-0.03260.127-0.0218-0.02570.12150.00390.0702-2.438434.3197-4.5265
63.79435.0814-1.30746.9779-1.2532.02180.0724-0.3111-0.35070.1943-0.1018-1.10380.28420.52070.33590.212-0.03330.08910.3164-0.07820.320615.842539.1664-16.956
72.89320.5087-0.45961.75730.14781.53650.2093-0.41020.03160.396-0.12040.06220.0653-0.0535-0.0140.2692-0.0029-0.02290.2625-0.05560.1243-0.54236.817525.302
86.9826-0.72780.32192.34640.81711.09980.0851-0.56950.96360.37780.0737-0.1055-0.56650.0180.01820.26120.03220.03360.1859-0.06650.17110.535445.521720.0977
91.5673-0.3771-0.13932.2301-0.01310.8419-0.0534-0.089-0.07710.12570.0767-0.15590.1090.1019-0.01920.16150.0005-0.02660.1255-0.01450.09475.399827.949611.2356
104.2755-0.40840.53643.2815-0.1762.3563-0.2119-0.4967-0.62820.07590.0166-0.26610.03870.23330.15810.23140.05650.02540.21860.07510.301713.715616.930611.4329
112.5269-0.8328-0.69022.66020.22791.1424-0.1019-0.25920.29250.17570.1502-0.49530.11380.1678-0.02520.14750.0159-0.03590.1739-0.05950.13839.843232.162410.801
122.6161-0.68782.43351.98-0.79562.7575-0.01490.31190.14930.2120.0363-0.4693-0.13610.45220.02250.1596-0.0252-0.01320.2093-0.07870.21638.534545.391112.8746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:26)
2X-RAY DIFFRACTION2(chain A and resid 27:36)
3X-RAY DIFFRACTION3(chain A and resid 37:126)
4X-RAY DIFFRACTION4(chain A and resid 127:203)
5X-RAY DIFFRACTION5(chain A and resid 204:237)
6X-RAY DIFFRACTION6(chain A and resid 238:248)
7X-RAY DIFFRACTION7(chain B and resid 1:37)
8X-RAY DIFFRACTION8(chain B and resid 38:53)
9X-RAY DIFFRACTION9(chain B and resid 54:127)
10X-RAY DIFFRACTION10(chain B and resid 128:176)
11X-RAY DIFFRACTION11(chain B and resid 177:219)
12X-RAY DIFFRACTION12(chain B and resid 220:248)

+
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