[English] 日本語
Yorodumi
- PDB-6gl4: Structure of GluA2o ligand-binding domain (S1S2J) in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gl4
TitleStructure of GluA2o ligand-binding domain (S1S2J) in complex with glutamate and sodium bromide at 1.95 A resolution
ComponentsGlutamate receptor 2,Glutamate receptor 2
KeywordsMEMBRANE PROTEIN / Ionotropic glutamate receptor / GluA2o ligand-binding domain / agonist
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors ...spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / asymmetric synapse / ionotropic glutamate receptor complex / conditioned place preference / regulation of receptor recycling / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / glutamate-gated receptor activity / regulation of long-term synaptic depression / extracellular ligand-gated monoatomic ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / somatodendritic compartment / dendrite membrane / ionotropic glutamate receptor binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / synaptic membrane / dendritic shaft / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / establishment of protein localization / postsynaptic density membrane / cerebral cortex development / modulation of chemical synaptic transmission / receptor internalization / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / synaptic vesicle membrane / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / perikaryon / chemical synaptic transmission / dendritic spine / postsynaptic membrane / neuron projection / postsynaptic density / axon / external side of plasma membrane / neuronal cell body / dendrite / synapse / protein kinase binding / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / 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
ACETATE ION / BROMIDE ION / GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.948 Å
AuthorsVenskutonyte, R. / Frydenvang, K. / Kastrup, J.S.
CitationJournal: Neuron / Year: 2019
Title: Nanoscale Mobility of the Apo State and TARP Stoichiometry Dictate the Gating Behavior of Alternatively Spliced AMPA Receptors.
Authors: Dawe, G.B. / Kadir, M.F. / Venskutonyte, R. / Perozzo, A.M. / Yan, Y. / Alexander, R.P.D. / Navarrete, C. / Santander, E.A. / Arsenault, M. / Fuentes, C. / Aurousseau, M.R.P. / Frydenvang, K. ...Authors: Dawe, G.B. / Kadir, M.F. / Venskutonyte, R. / Perozzo, A.M. / Yan, Y. / Alexander, R.P.D. / Navarrete, C. / Santander, E.A. / Arsenault, M. / Fuentes, C. / Aurousseau, M.R.P. / Frydenvang, K. / Barrera, N.P. / Kastrup, J.S. / Edwardson, J.M. / Bowie, D.
History
DepositionMay 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.journal_volume / _citation.page_first
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 / struct_ncs_dom_lim
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr2_label_alt_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_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_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate receptor 2,Glutamate receptor 2
B: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,52814
Polymers58,5572
Non-polymers97112
Water7,584421
1
A: Glutamate receptor 2,Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,51512
Polymers58,5572
Non-polymers95810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area3490 Å2
ΔGint-6 kcal/mol
Surface area23590 Å2
MethodPISA
2
B: Glutamate receptor 2,Glutamate receptor 2
hetero molecules

B: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,54116
Polymers58,5572
Non-polymers98414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_856-x+3,y,-z+11
Buried area3920 Å2
ΔGint-54 kcal/mol
Surface area23770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.717, 47.715, 116.713
Angle α, β, γ (deg.)90.000, 93.790, 90.000
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 24 or resid 26...
21(chain B and (resid 1 through 24 or resid 26...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLU(chain A and (resid 1 through 24 or resid 26...AA1 - 241 - 24
12LEULEUGLUGLU(chain A and (resid 1 through 24 or resid 26...AA26 - 4226 - 42
13ALAALALEULEU(chain A and (resid 1 through 24 or resid 26...AA44 - 9444 - 94
14ARGARGILEILE(chain A and (resid 1 through 24 or resid 26...AA96 - 11596 - 115
15SERSERALAALA(chain A and (resid 1 through 24 or resid 26...AA142 - 165142 - 165
16ASNASNGLYGLY(chain A and (resid 1 through 24 or resid 26...AA197 - 231197 - 231
17ALAALASERSER(chain A and (resid 1 through 24 or resid 26...AA233 - 263233 - 263
21GLYGLYGLUGLU(chain B and (resid 1 through 24 or resid 26...BB1 - 241 - 24
22LEULEUGLUGLU(chain B and (resid 1 through 24 or resid 26...BB26 - 4226 - 42
23ALAALALEULEU(chain B and (resid 1 through 24 or resid 26...BB44 - 9444 - 94
24ARGARGILEILE(chain B and (resid 1 through 24 or resid 26...BB96 - 11596 - 115
25SERSERALAALA(chain B and (resid 1 through 24 or resid 26...BB142 - 165142 - 165
26ASNASNGLYGLY(chain B and (resid 1 through 24 or resid 26...BB197 - 231197 - 231
27ALAALASERSER(chain B and (resid 1 through 24 or resid 26...BB233 - 263233 - 263

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Glutamate receptor 2,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: 29278.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein crystallized is the extracellular ligand-binding domain of GluA2o. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residue 118-119). The ...Details: The protein crystallized is the extracellular ligand-binding domain of GluA2o. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residue 118-119). The sequence matches discontinously with the reference database (UNP residues 413-527 and 653-797, numbering with signal peptide of 21 amino acids). The two first residues (GLY, ALA) are cloning remnants.,The protein crystallized is the extracellular ligand-binding domain of GluA2o. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residue 118-119). The sequence matches discontinously with the reference database (UNP residues 413-527 and 653-797, numbering with signal peptide of 21 amino acids). The two first residues (GLY, ALA) are cloning remnants.,The protein crystallized is the extracellular ligand-binding domain of GluA2o. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residue 118-119). The sequence matches discontinously with the reference database (UNP residues 413-527 and 653-797, numbering with signal peptide of 21 amino acids). The two first residues (GLY, ALA) are cloning remnants.,The protein crystallized is the extracellular ligand-binding domain of GluA2o. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residue 118-119). The sequence matches discontinously with the reference database (UNP residues 413-527 and 653-797, numbering with signal peptide of 21 amino acids). The two first residues (GLY, ALA) are cloning remnants.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET-22B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B (DE3) / References: UniProt: P19491

-
Non-polymers , 6 types, 433 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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#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.: 421 / 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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG4000, 0.2M sodium sulfate, 0.1M sodium acetate pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.91949 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91949 Å / Relative weight: 1
ReflectionResolution: 1.948→116.457 Å / Num. all: 37848 / Num. obs: 37848 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 19.88 Å2 / Rpim(I) all: 0.035 / Rrim(I) all: 0.096 / Rsym value: 0.089 / Net I/av σ(I): 7.8 / Net I/σ(I): 16.2 / Num. measured all: 286755
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.95-2.067.60.4681.64132254500.1820.5020.4684.4100
2.06-2.187.60.2972.63948852050.1150.3190.2976.6100
2.18-2.337.60.213.63709248800.0810.2250.218.9100
2.33-2.527.60.1734.43473845600.0670.1860.17310.4100
2.52-2.767.60.1216.33192541940.0470.130.12114.1100
2.76-3.087.60.0858.62901238050.0330.0910.08519.5100
3.08-3.567.60.05712.32563533710.0220.0610.05728.9100
3.56-4.367.60.04415.32174028710.0170.0480.04437.6100
4.36-6.177.50.04215.61673622360.0160.0450.04236100
6.17-46.6157.10.0414.9906712760.0160.0440.0435.299.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.01 Å47.59 Å
Translation2.01 Å47.59 Å

-
Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.22data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TDJ

3tdj


Resolution: 1.948→46.615 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.22 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1985 1984 5.24 %
Rwork0.1628 35852 -
obs0.1648 37836 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.39 Å2 / Biso mean: 27.7342 Å2 / Biso min: 8.31 Å2
Refinement stepCycle: final / Resolution: 1.948→46.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4090 0 38 430 4558
Biso mean--29.67 31.51 -
Num. residues----526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054271
X-RAY DIFFRACTIONf_angle_d0.7365752
X-RAY DIFFRACTIONf_chiral_restr0.048633
X-RAY DIFFRACTIONf_plane_restr0.004726
X-RAY DIFFRACTIONf_dihedral_angle_d9.7172606
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2958X-RAY DIFFRACTION4.589TORSIONAL
12B2958X-RAY DIFFRACTION4.589TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9481-1.99690.2636850.19612509259499
1.9969-2.05080.23991100.182125952705100
2.0508-2.11120.23581200.180225582678100
2.1112-2.17930.21771860.165925192705100
2.1793-2.25720.2241810.167424962677100
2.2572-2.34760.23691570.171625282685100
2.3476-2.45440.21571070.170725962703100
2.4544-2.58380.19631170.174325842701100
2.5838-2.74570.25831450.171125532698100
2.7457-2.95770.26091340.171825492683100
2.9577-3.25520.21791800.168225212701100
3.2552-3.72610.15111570.149125892746100
3.7261-4.69380.15431670.128125842751100
4.6938-46.62850.171380.171426712809100
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)
12.93030.3801-0.89322.0053-0.10042.82390.1534-0.08330.13470.2635-0.06840.0791-0.1032-0.0621-0.06710.18040.01140.03540.11720.00650.131334.569518.58820.0532
20.48340.63930.27572.84460.63090.41940.02470.0054-0.04810.05420.0364-0.15150.00960.0417-0.03190.15430.03040.01180.16580.00460.102350.285818.649314.5385
32.9924-0.4144-0.08843.27790.30342.229-0.07590.0075-0.04740.14980.1966-0.30460.18710.5439-0.07530.19470.0936-0.0120.297-0.02440.135762.12432.289517.1811
40.93720.82240.42691.94210.79440.9578-0.00980.04750.10990.03720.00320.1293-0.0941-0.1270.01140.2380.04090.03190.19160.03050.126342.573928.274210.2381
52.6808-0.19020.35853.0408-0.24972.6497-0.05210.1567-0.0075-0.24450.0557-0.1920.10410.25430.00890.1173-0.00260.04290.1549-0.0130.171682.682540.960741.7558
60.6178-0.1735-0.06052.2737-0.21510.6129-0.00150.0968-0.0179-0.2497-0.00930.06750.0546-0.0160.01440.1293-0.0089-0.00170.16770.00010.11766.569740.840943.2409
74.4189-1.1763-0.3455.2651-1.00253.5355-0.23440.49170.1932-0.46650.40040.42910.0204-0.3146-0.09270.1649-0.0965-0.07690.32360.07820.251753.925453.507440.5945
80.8563-0.10240.18682.0432-1.08631.401-0.06490.0850.0741-0.22330.14120.06260.0146-0.11-0.0550.1649-0.03640.02030.1756-0.02220.127467.636652.611644.4527
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 47 )A1 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 123 )A48 - 123
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 187 )A124 - 187
4X-RAY DIFFRACTION4chain 'A' and (resid 188 through 263 )A188 - 263
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 47 )B1 - 47
6X-RAY DIFFRACTION6chain 'B' and (resid 48 through 123 )B48 - 123
7X-RAY DIFFRACTION7chain 'B' and (resid 124 through 152 )B124 - 152
8X-RAY DIFFRACTION8chain 'B' and (resid 153 through 263 )B153 - 263

+
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