[English] 日本語
Yorodumi
- PDB-3p3w: Structure of a dimeric GluA3 N-terminal domain (NTD) at 4.2 A res... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p3w
TitleStructure of a dimeric GluA3 N-terminal domain (NTD) at 4.2 A resolution
ComponentsGlutamate receptor 3
KeywordsTRANSPORT PROTEIN / Periplasmatic binding protein
Function / homology
Function and homology information


chemical synaptic transmission, postsynaptic / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor complex / ionotropic glutamate receptor complex ...chemical synaptic transmission, postsynaptic / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane potential / synaptic cleft / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / monoatomic ion transmembrane transport / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendritic shaft / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / amyloid-beta binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuronal cell body / glutamatergic synapse / dendrite / protein-containing complex / 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 I
Similarity search - Domain/homology
Glutamate receptor 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsRossmann, M. / Sukumaran, M. / Greger, I.H.
CitationJournal: Embo J. / Year: 2011
Title: Dynamics and allosteric potential of the AMPA receptor N-terminal domain
Authors: Sukumaran, M. / Rossmann, M. / Shrivastava, I. / Dutta, A. / Bahar, I. / Greger, I.H.
History
DepositionOct 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate receptor 3
B: Glutamate receptor 3
C: Glutamate receptor 3
D: Glutamate receptor 3


Theoretical massNumber of molelcules
Total (without water)179,8594
Polymers179,8594
Non-polymers00
Water00
1
A: Glutamate receptor 3
C: Glutamate receptor 3


Theoretical massNumber of molelcules
Total (without water)89,9302
Polymers89,9302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-13 kcal/mol
Surface area32110 Å2
MethodPISA
2
B: Glutamate receptor 3
D: Glutamate receptor 3


Theoretical massNumber of molelcules
Total (without water)89,9302
Polymers89,9302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-17 kcal/mol
Surface area32720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.960, 127.920, 130.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A3 - 380
2111B2 - 380
1124C3 - 380
2124D2 - 379

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Glutamate receptor 3 / GluR-3 / GluR-C / GluR-K3 / Glutamate receptor ionotropic / AMPA 3 / GluA3 / AMPA-selective ...GluR-3 / GluR-C / GluR-K3 / Glutamate receptor ionotropic / AMPA 3 / GluA3 / AMPA-selective glutamate receptor 3


Mass: 44964.773 Da / Num. of mol.: 4 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: HEK 293 Cell / Gene: Gria3, Glur3 / Production host: Homo sapiens (human) / References: UniProt: P19492

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.06 % / Mosaicity: 1.1 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.7
Details: 200mM ammonium phosphate, 20% PEG3350, pH 4.7, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 4.2→91.197 Å / Num. all: 13979 / Num. obs: 13979 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rsym value: 0.316 / Net I/σ(I): 3.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
4.2-4.433.60.9640.8220.9716820080.4940.9640.8221.799.8
4.43-4.73.70.7880.6741.1695118960.4010.7880.674299.9
4.7-5.023.70.6060.521.5665617940.3070.6060.522.5100
5.02-5.423.70.5620.4821.6623016850.2850.5620.4822.699.9
5.42-5.943.70.6210.5321.4571915480.3140.6210.5322.499.9
5.94-6.643.70.5790.4961.5516914060.2920.5790.4962.699.8
6.64-7.673.70.3510.3012.5459712450.1780.3510.3014.299.5
7.67-9.393.60.1690.1445391410750.0860.1690.1447.799.4
9.39-13.283.60.0980.0836.430038380.050.0980.08310.898.9
13.28-55.4133.30.0740.0625.815944840.040.0740.06212.196.5

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→55.41 Å / Cor.coef. Fo:Fc: 0.819 / Cor.coef. Fo:Fc free: 0.751 / WRfactor Rfree: 0.3529 / WRfactor Rwork: 0.3232 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7088 / SU B: 233.534 / SU ML: 1.339 / SU Rfree: 1.4609 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3377 688 4.9 %RANDOM
Rwork0.3059 ---
obs0.3075 13916 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.37 Å2 / Biso mean: 116.809 Å2 / Biso min: 54.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2---0.59 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 4.2→55.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11484 0 0 0 11484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02212188
X-RAY DIFFRACTIONr_angle_refined_deg0.8221.92416546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.12451482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45823.911629
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.377151936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.2471579
X-RAY DIFFRACTIONr_chiral_restr0.0580.21809
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219465
X-RAY DIFFRACTIONr_mcbond_it0.0271.57406
X-RAY DIFFRACTIONr_mcangle_it0.053211935
X-RAY DIFFRACTIONr_scbond_it0.0734782
X-RAY DIFFRACTIONr_scangle_it0.1254.54611
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2959TIGHT POSITIONAL0.010.05
1A2959TIGHT THERMAL0.010.5
2C2899MEDIUM POSITIONAL0.520.5
2C2899MEDIUM THERMAL0.042
LS refinement shellResolution: 4.2→4.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 52 -
Rwork0.342 946 -
all-998 -
obs--99.6 %
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)
17.02951.9631-2.629315.63621.21583.05120.34791.22640.1611-0.3736-0.71740.2320.8992-0.1190.36950.80960.25930.23540.54290.18560.352-28.9504-6.1089-3.7908
25.9255-14.749112.157140.3131-25.342531.7273-0.6081.1101-0.12720.5694-1.60762.2043-2.51314.01862.21560.4007-0.5768-0.35030.84540.44351.0805-25.99956.15450.5635
32.1706-0.2488-0.73483.0136-1.93057.02170.1411-0.13790.31890.49680.0351-0.2779-0.32420.4494-0.17620.401-0.0692-0.04060.2117-0.03030.3829-33.6711-4.459921.8387
417.094.0035-0.79414.53160.51262.9566-0.42461.30072.5041-1.35250.54760.8454-1.10520.4658-0.1231.1645-0.1478-0.02360.86740.03550.5428-37.88017.4691-7.1679
57.1888-2.36412.23355.6795.51538.6880.4888-0.3009-0.20110.3476-0.4291-0.00310.761-0.9748-0.05970.1093-0.1262-0.08380.7393-0.09140.4807-46.7538-3.803218.5006
67.1377-5.5372-3.21679.4817-1.0653.8983-0.01710.5813-0.23870.2012-0.2857-0.1436-0.1111-0.37470.30270.6816-0.1326-0.07430.39180.21240.445725.2033-5.74122.6447
76.00524.6697-9.51324.1182-7.73815.36711.8148-0.29350.73521.7384-0.51830.5561-3.23360.4387-1.29650.86370.01040.30320.75310.26160.258620.86814.895818.6363
811.4816-12.47014.482721.1431-10.38525.9222-0.375-0.6010.72520.87820.0962-1.1313-0.67430.18060.27881.1709-0.2202-0.27470.5375-0.26610.845126.2263.590739.0371
91.0851-0.9992-2.40944.1911-0.53628.9333-0.0987-0.2789-0.05480.18480.47430.30381.10640.2904-0.37560.7238-0.1703-0.07370.3942-0.01460.314919.762-11.427326.914
102.24590.7843-1.57713.0274-3.24398.86250.09880.1797-0.03170.16450.1607-0.1681-1.5221-0.7592-0.25950.41250.0263-0.03350.6234-0.00130.75111.52792.062113.4624
116.29353.6785-1.18439.18742.7725.5117-0.69350.4551-0.1409-0.29080.1911-0.150.1988-0.11190.50230.19710.15780.15470.4010.23530.2376-7.897325.03755.3428
1212.3465-0.3377-7.90420.5977-1.674211.47140.15220.47360.6536-0.56640.1247-0.17392.0523-0.9648-0.27691.0728-0.1814-0.05330.16870.18110.542-13.618718.797330.0401
1324.8148-2.2161-0.220711.5769-9.867118.12551.307-0.686-1.73960.274-0.30962.9166-0.4143-1.4161-0.99750.4884-0.4025-0.00040.6787-0.30050.9938-27.442119.746235.4587
1419.47631.83085.661911.37271.341816.91161.11920.794-0.17630.2502-0.53641.455-1.1802-0.8169-0.58280.38710.0137-0.140.3850.20490.5432-23.848532.688331.6306
153.99340.268-1.96084.6752-0.20861.65940.2344-0.2101-0.05080.1921-0.3747-0.6127-0.16580.73120.14030.22910.0747-0.12580.69810.05340.3644-2.608729.126319.3263
1612.248312.8844-0.278514.92910.56349.0123-0.82610.70251.0737-0.89920.73510.45440.03530.16690.09090.32750.0404-0.05430.08050.06920.461649.267227.528311.9483
175.6971-1.7853-6.54081.07910.503512.7491-1.28370.7083-1.60570.7577-0.57220.55350.0415-0.14351.85590.6803-0.29410.23830.4399-0.19770.703741.1117.184628.5093
184.0981.6713-4.63885.3623-0.82975.54940.16750.21540.1377-0.2943-0.15890.816-0.1495-0.4165-0.00870.3623-0.0773-0.0910.4935-0.08380.491930.930728.918336.8267
198.8659-2.20853.64562.1089-3.51865.9851-0.10080.3077-0.8033-0.256-0.0643-0.21850.50920.17040.16510.16540.0747-0.01740.4123-0.13060.527454.581120.206520.1482
2015.7238-12.8289-5.864932.070817.12739.239-2.8253-2.928-0.46230.73013.1345-0.42270.15081.5478-0.30921.13170.34830.0671.00780.2210.106547.011826.916943.4527
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 63
2X-RAY DIFFRACTION2A64 - 93
3X-RAY DIFFRACTION3A94 - 296
4X-RAY DIFFRACTION4A297 - 339
5X-RAY DIFFRACTION5A340 - 380
6X-RAY DIFFRACTION6B2 - 70
7X-RAY DIFFRACTION7B71 - 131
8X-RAY DIFFRACTION8B132 - 182
9X-RAY DIFFRACTION9B183 - 293
10X-RAY DIFFRACTION10B294 - 380
11X-RAY DIFFRACTION11C3 - 106
12X-RAY DIFFRACTION12C107 - 150
13X-RAY DIFFRACTION13C151 - 193
14X-RAY DIFFRACTION14C194 - 230
15X-RAY DIFFRACTION15C231 - 380
16X-RAY DIFFRACTION16D2 - 71
17X-RAY DIFFRACTION17D72 - 134
18X-RAY DIFFRACTION18D135 - 269
19X-RAY DIFFRACTION19D270 - 348
20X-RAY DIFFRACTION20D349 - 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://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