[English] 日本語
Yorodumi
- PDB-5fti: Crystal structure of the GluA2 K738M-T744K LBD in complex with gl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fti
TitleCrystal structure of the GluA2 K738M-T744K LBD in complex with glutamate (lithium form)
ComponentsGLUTAMATE RECEPTOR 2
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / 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. ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / 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. / 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
GLUTAMIC ACID / : / Glutamate receptor 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsNayeem, N. / Green, T.
CitationJournal: Neuron / Year: 2016
Title: Distinct Structural Pathways Coordinate the Activation of Ampa Receptor-Auxiliary Subunit Complexes.
Authors: Dawe, G.B. / Musgaard, M. / Aurousseau, M.R.P. / Nayeem, N. / Green, T. / Biggin, P.C. / Bowie, D.
History
DepositionJan 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUTAMATE RECEPTOR 2
B: GLUTAMATE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,40512
Polymers64,5282
Non-polymers87710
Water12,394688
1
A: GLUTAMATE RECEPTOR 2
hetero molecules

A: GLUTAMATE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,40512
Polymers64,5282
Non-polymers87710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_457-x-1,y,-z+21
Buried area3120 Å2
ΔGint-76.1 kcal/mol
Surface area24290 Å2
MethodPISA
2
B: GLUTAMATE RECEPTOR 2
hetero molecules

B: GLUTAMATE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,40512
Polymers64,5282
Non-polymers87710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_358-x-2,y,-z+31
Buried area3020 Å2
ΔGint-65.5 kcal/mol
Surface area24050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.316, 47.562, 96.754
Angle α, β, γ (deg.)90.00, 95.65, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-2134-

HOH

21B-2113-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein GLUTAMATE RECEPTOR 2 / GLUR-2 / AMPA-SELECTIVE GLUTAMATE RECEPTOR 2 / GLUR-B / GLUR-K2 / GLUTAMATE RECEPTOR IONOTROPIC / ...GLUR-2 / AMPA-SELECTIVE GLUTAMATE RECEPTOR 2 / GLUR-B / GLUR-K2 / GLUTAMATE RECEPTOR IONOTROPIC / AMPA 2 / GLUA2


Mass: 32264.088 Da / Num. of mol.: 2
Fragment: LIGAND BINDING DOMAIN, UNP RESIDUES 404-527,653-796
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA-GAMI B / References: UniProt: P19491

-
Non-polymers , 5 types, 698 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsEXPRESSED FRAGMENT INCLUDES TWO NON-CONTIGUOUS REGIONS FROM GENE, JOINED BY GLYTHR LINKER MAPPED TO ...EXPRESSED FRAGMENT INCLUDES TWO NON-CONTIGUOUS REGIONS FROM GENE, JOINED BY GLYTHR LINKER MAPPED TO FLIP ISOFORM, P19491-2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 5
Details: 22% PEG 4,000, 200 MM LI SULPHATE, 100MM ACETATE PH 5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.35→67 Å / Num. obs: 126864 / % possible obs: 94.7 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 15.72 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.9
Reflection shellResolution: 1.35→1.39 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 1.88 / % possible all: 92.5

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UXA

2uxa


Resolution: 1.35→66.989 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 19.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1775 2538 2 %
Rwork0.1612 --
obs0.1615 126864 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→66.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4039 0 54 688 4781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114284
X-RAY DIFFRACTIONf_angle_d1.3915787
X-RAY DIFFRACTIONf_dihedral_angle_d12.1871653
X-RAY DIFFRACTIONf_chiral_restr0.094641
X-RAY DIFFRACTIONf_plane_restr0.007719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.3760.29051370.27996702X-RAY DIFFRACTION93
1.376-1.40410.27321380.27096767X-RAY DIFFRACTION93
1.4041-1.43460.28011370.25366731X-RAY DIFFRACTION93
1.4346-1.4680.26291380.24826767X-RAY DIFFRACTION93
1.468-1.50470.26371380.2296766X-RAY DIFFRACTION94
1.5047-1.54540.21961400.20286811X-RAY DIFFRACTION94
1.5454-1.59080.19791400.18366876X-RAY DIFFRACTION94
1.5908-1.64220.1981410.16846914X-RAY DIFFRACTION95
1.6422-1.70090.18651400.16196886X-RAY DIFFRACTION95
1.7009-1.7690.19891430.15946966X-RAY DIFFRACTION96
1.769-1.84950.18171420.15736951X-RAY DIFFRACTION96
1.8495-1.9470.17311420.15226983X-RAY DIFFRACTION96
1.947-2.0690.16751440.157078X-RAY DIFFRACTION96
2.069-2.22880.17231440.14467025X-RAY DIFFRACTION96
2.2288-2.45310.16541430.15177000X-RAY DIFFRACTION96
2.4531-2.80810.19031420.16156982X-RAY DIFFRACTION95
2.8081-3.53790.16931420.14896972X-RAY DIFFRACTION94
3.5379-67.07140.14571470.14667149X-RAY DIFFRACTION95
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)
12.4282-0.5601-0.30072.57110.34362.26120.175-0.39970.05110.3364-0.09540.0495-0.00910.0354-0.05540.1621-0.04540.01070.1687-0.0050.092-54.413546.8361116.5313
20.45470.4212-0.18182.0060.50310.69730.06310.00550.0786-0.0003-0.04770.1598-0.0542-0.0515-0.03010.1010.0115-0.00270.14570.00690.1258-57.510647.414100.6585
31.08220.3341-0.44041.3333-0.53092.6167-0.05990.1103-0.0039-0.05220.03620.03350.12-0.17360.02230.0689-0.0047-0.00680.1288-0.00440.1026-62.801632.232694.736
42.06250.34740.07642.7469-0.80191.67230.086-0.1304-0.0820.1332-0.0702-0.06740.01530.1272-0.00530.0904-0.00030.00090.1408-0.0120.0746-45.287944.0807107.6681
52.01061.99632.00092.00331.99861.99810.09330.35840.04610.6953-0.0760.76580.3408-0.1221-0.04450.15360.00450.00470.1553-0.00780.158-58.394942.452798.5826
62.22970.3933-1.13441.552-0.19132.68260.00620.01750.0012-0.1523-0.0136-0.12150.10830.1630.01610.19810.00020.04080.1308-0.01610.1057-72.789327.77124.1822
70.9246-0.53230.14313.8232-0.42871.0784-0.052-0.0284-0.0332-0.16080.08580.15780.0139-0.0883-0.0010.1716-0.02770.00850.1528-0.0040.1045-86.95129.9244131.4672
83.80210.22240.07362.4035-0.39482.3679-0.05830.0150.1621-0.0380.09670.14-0.1333-0.19-0.04170.24940.00690.0030.1499-0.00770.1505-92.998143.6031128.2369
92.66930.6505-0.43132.6407-1.15642.73010.0359-0.18350.11160.019-0.0214-0.1807-0.21720.39230.01770.1841-0.02840.03810.1957-0.03070.0881-73.068431.2065137.2582
106.6467-5.98134.29188.73690.38818.16570.2122-0.13370.4097-0.4663-0.23020.02250.0504-0.15560.01430.2983-0.01950.03330.1575-0.01450.1753-87.373333.4051130.106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 392:436 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 437:635 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 636:729 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 730:774 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 900:900 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 393:454 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 455:635 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 636:729 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 730:774 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 900:900 )

+
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