[English] 日本語
Yorodumi
- PDB-3hsy: High resolution structure of a dimeric GluR2 N-terminal domain (NTD) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hsy
TitleHigh resolution structure of a dimeric GluR2 N-terminal domain (NTD)
ComponentsGlutamate receptor 2GRIA2
KeywordsTRANSPORT PROTEIN / GLUTAMATE RECEPTOR / LIGAND-GATED ION CHANNEL / SYNAPSE / CELL JUNCTION / CELL MEMBRANE / ENDOPLASMIC RETICULUM / GLYCOPROTEIN / ION TRANSPORT / IONIC CHANNEL / LIPOPROTEIN / MEMBRANE / PALMITATE / PHOSPHOPROTEIN / POSTSYNAPTIC CELL MEMBRANE / RECEPTOR / RNA EDITING / TRANSMEMBRANE / TRANSPORT
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / 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 / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / cytoskeletal protein binding / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / protein tetramerization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / establishment of protein localization / terminal bouton / receptor internalization / synaptic vesicle membrane / cerebral cortex development / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / perikaryon / chemical synaptic transmission / postsynaptic membrane / scaffold protein binding / dendritic spine / postsynaptic density / neuron projection / axon / dendrite / neuronal cell body / glutamatergic synapse / synapse / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / 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 / : / Response regulator / 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 ...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 / : / Response regulator / 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 I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsRossmann, M. / Sukumaran, M. / Penn, A.C. / Veprintsev, D.B. / Greger, I.H.
CitationJournal: Embo J. / Year: 2011
Title: Subunit-selective N-terminal domain associations organize the formation of AMPA receptor heteromers
Authors: Rossmann, M. / Sukumaran, M. / Penn, A.C. / Veprintsev, D.B. / Babu, M.M. / Greger, I.H.
History
DepositionJun 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
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)86,4439
Polymers85,0302
Non-polymers1,4137
Water11,458636
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-15 kcal/mol
Surface area31440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.452, 93.695, 101.466
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Glutamate receptor 2 / GRIA2 / GluR-2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / AMPA-selective glutamate receptor 2


Mass: 42515.012 Da / Num. of mol.: 2 / Fragment: N-terminal Domain, UNP residues 25-400
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): High5 / References: UniProt: P19491
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 636 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.63 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 200mM ammonium phosphatre, 20% PEG3350, pH4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95294 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95294 Å / Relative weight: 1
ReflectionRedundancy: 5 % / Number: 35008 / Rmerge(I) obs: 0.123 / Rsym value: 0.064 / D res high: 2.1 Å / Num. obs: 30290 / % possible obs: 34.5
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsRsym valueRedundancy
6.2444.61106131.90.0240.0254.8
4.436.24209635.20.0360.034.9
3.624.43285337.10.040.0375
3.143.62348338.10.0670.0495.1
2.813.14386737.60.1590.0665.1
2.572.81416436.40.2770.0915.1
2.382.57443235.80.4740.1365.1
2.222.38463334.80.590.2075.1
2.12.223701261.0240.3565.1
ReflectionResolution: 1.75→68.84 Å / Num. obs: 79848 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 21.01 Å2 / Rsym value: 0.064
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 11530 / Rsym value: 0.581 / % possible all: 100

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.15data processing
SHARPphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementResolution: 1.75→42.533 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.887 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.46 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1588 1.99 %RANDOM
Rwork0.178 78175 --
obs0.178 79763 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.88 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 154.51 Å2 / Biso mean: 28.616 Å2 / Biso min: 6.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.185 Å2-0 Å20 Å2
2---0.252 Å20 Å2
3---0.067 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5785 0 87 636 6508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066101
X-RAY DIFFRACTIONf_angle_d1.0648282
X-RAY DIFFRACTIONf_chiral_restr0.131919
X-RAY DIFFRACTIONf_plane_restr0.0051067
X-RAY DIFFRACTIONf_dihedral_angle_d13.1862252
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.75-1.8130.2611560.22177157871
1.813-1.8850.2141620.19977117873
1.885-1.9710.2251570.17777317888
1.971-2.0750.1921360.16777877923
2.075-2.2050.2331400.16477847924
2.205-2.3750.171590.16177707929
2.375-2.6140.1991570.16878157972
2.614-2.9920.2141690.17978388007
2.992-3.770.1891810.16978948075
3.77-42.5460.1891710.16881308301
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)
10.47610.45050.21260.91510.67520.48710.0416-0.03580.0419-0.0269-0.07810.043-0.0385-0.07720.03760.03420.00010.00290.046-0.00150.0192-3.184-2.685-4.2335
21.06571.1144-0.2311.4551-0.30160.7634-0.0471-0.0093-0.0567-0.06510.012-0.03250.01540.14650.02930.04080.01060.0020.0674-0.02180.048711.0252-18.8997-25.3197
30.0482-0.0067-0.18510.6326-0.03431.14890.02820.0167-0.05650.0064-0.17460.1615-0.0533-0.38680.10170.0374-0.019-0.01740.1338-0.03840.085-11.8439-13.6961-5.5984
40.42680.1263-0.18930.3046-0.57860.97590.0384-0.2901-0.20160.3296-0.1781-0.00020.428-0.09880.07780.007-0.0015-0.0353-0.07970.0203-0.01992.2423-18.3533-4.4323
51.53620.2282-0.1081-0.0433-0.07870.4657-0.0313-0.04210.08590.03850.030.0035-0.0634-0.01110.00270.0840.00850.00170.047-0.00080.072920.562816.1179-7.9777
60.71550.3257-0.04720.5019-0.39970.515-0.0646-0.064-0.17670.01130.0131-0.10180.05960.04730.05180.05920.03210.00760.04820.01940.088235.5607-9.944-15.3479
70.15660.25630.03150.39740.02960.0827-0.00010.02040.0321-0.00440.0027-0.0297-0.00320.0272-0.01060.0202-0.0227-0.00080.0496-0.00040.029735.017620.9165-9.1129
80.6632-0.2641-0.21870.45070.20550.2516-0.00610.11820.0144-0.017-0.0245-0.0443-0.03410.00560.02040.0297-0.0008-0.00540.05210.01740.015927.735714.0958-20.196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:109)A4 - 109
2X-RAY DIFFRACTION2(chain A and resid 110:240)A110 - 240
3X-RAY DIFFRACTION3(chain A and resid 241:306)A241 - 306
4X-RAY DIFFRACTION4(chain A and resid 307:377)A307 - 377
5X-RAY DIFFRACTION5(chain B and resid 4:110)B4 - 110
6X-RAY DIFFRACTION6(chain B and resid 111:241)B111 - 241
7X-RAY DIFFRACTION7(chain B and resid 242:301)B242 - 301
8X-RAY DIFFRACTION8(chain B and resid 302:379)B302 - 379

+
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