[English] 日本語
Yorodumi
- PDB-6q60: Structure of GluA2 ligand-binding domain (S1S2J) in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q60
TitleStructure of GluA2 ligand-binding domain (S1S2J) in complex with the agonist (S)-2-Amino-3-(2-methyl-5-hydroxy-2H-1,2,3-triazol-4-yl)propanoic acid at 1.55 A resolution
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / AMPA receptor / GluA2-S1S2 / 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 / cellular response to glycine / AMPA glutamate receptor complex / 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 / cellular response to brain-derived neurotrophic factor stimulus / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / 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 / signaling receptor activity / presynapse / amyloid-beta binding / growth cone / presynaptic membrane / scaffold protein binding / perikaryon / dendritic spine / chemical synaptic transmission / postsynaptic membrane / neuron projection / postsynaptic density / axon / external side of plasma membrane / neuronal cell body / synapse / dendrite / 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
Chem-HJH / : / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMoellerud, S. / Temperini, P. / Kastrup, J.S.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Use of the 4-Hydroxytriazole Moiety as a Bioisosteric Tool in the Development of Ionotropic Glutamate Receptor Ligands.
Authors: Sainas, S. / Temperini, P. / Farnsworth, J.C. / Yi, F. / Mollerud, S. / Jensen, A.A. / Nielsen, B. / Passoni, A. / Kastrup, J.S. / Hansen, K.B. / Boschi, D. / Pickering, D.S. / Clausen, R.P. / Lolli, M.L.
History
DepositionDec 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 24, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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
Revision 1.3Nov 20, 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
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,53925
Polymers58,5572
Non-polymers1,98223
Water13,241735
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-82 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.344, 122.254, 47.351
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-737-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 20 or resid 22...
21(chain B and (resid 1 through 20 or resid 22...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 20 or resid 22...A1 - 20
121(chain A and (resid 1 through 20 or resid 22...A22 - 24
131(chain A and (resid 1 through 20 or resid 22...A26 - 42
141(chain A and (resid 1 through 20 or resid 22...A44 - 53
151(chain A and (resid 1 through 20 or resid 22...A78 - 106
161(chain A and (resid 1 through 20 or resid 22...A1 - 264
171(chain A and (resid 1 through 20 or resid 22...A157 - 163
181(chain A and (resid 1 through 20 or resid 22...A165 - 200
191(chain A and (resid 1 through 20 or resid 22...A203 - 2091
1101(chain A and (resid 1 through 20 or resid 22...A223 - 21
1111(chain A and (resid 1 through 20 or resid 22...A223 - 229
1121(chain A and (resid 1 through 20 or resid 22...A231 - 247
1131(chain A and (resid 1 through 20 or resid 22...A249 - 251
1141(chain A and (resid 1 through 20 or resid 22...A254 - 263
211(chain B and (resid 1 through 20 or resid 22...B1 - 20
221(chain B and (resid 1 through 20 or resid 22...B22 - 24
231(chain B and (resid 1 through 20 or resid 22...B26 - 42
241(chain B and (resid 1 through 20 or resid 22...B44 - 53
251(chain B and (resid 1 through 20 or resid 22...B78 - 106
261(chain B and (resid 1 through 20 or resid 22...B1 - 263
271(chain B and (resid 1 through 20 or resid 22...B157 - 163
281(chain B and (resid 1 through 20 or resid 22...B165 - 200
291(chain B and (resid 1 through 20 or resid 22...B203 - 2091
2101(chain B and (resid 1 through 20 or resid 22...B223 - 21
2111(chain B and (resid 1 through 20 or resid 22...B223 - 229
2121(chain B and (resid 1 through 20 or resid 22...B231 - 247
2131(chain B and (resid 1 through 20 or resid 22...B249 - 251
2141(chain B and (resid 1 through 20 or resid 22...B254 - 263

-
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: 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 GluA2. Transmembrane regions were replaced with a Gly-Thr linker (118-119). Sequence matches discontinously with the ...Details: The protein crystallized is the extracellular ligand-binding domain of GluA2. Transmembrane regions were replaced with a Gly-Thr linker (118-119). Sequence matches discontinously with the reference database (413-527, 653-797). Residues 1-2 are cloning remnants.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B / References: UniProt: P19491

-
Non-polymers , 6 types, 758 molecules

#2: Chemical ChemComp-HJH / (2~{S})-2-azanyl-3-(2-methyl-5-oxidanyl-1,2,3-triazol-4-yl)propanoic acid


Type: L-peptide linking / Mass: 186.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N4O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 10% PEG4000, 0.1 M lithium sulfate, 0.1 M phosphate-citrate, pH 4.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.979988 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979988 Å / Relative weight: 1
ReflectionResolution: 1.55→44.15 Å / Num. obs: 83759 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 16.4 Å2 / Rpim(I) all: 0.036 / Rrim(I) all: 0.094 / Rsym value: 0.087 / Net I/av σ(I): 4.7 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.55-1.636.70.3681.6121030.1550.40.368100
1.63-1.736.70.272.1114200.1140.2940.27100
1.73-1.856.80.1962.9107640.0810.2120.196100
1.85-26.90.1453.9100470.060.1570.145100
2-2.196.80.1164.992700.0480.1260.116100
2.19-2.456.70.1035.684290.0420.1110.103100
2.45-2.836.70.0886.774700.0360.0950.088100
2.83-3.476.90.0757.763620.030.0810.075100
3.47-4.96.70.0638.950150.0260.0680.063100
4.9-44.1556.40.0518.928790.0230.0560.05199.5

-
Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M5B

1m5b


Resolution: 1.55→44.155 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.28 / Phase error: 18.27
RfactorNum. reflection% reflection
Rfree0.1752 4173 5.01 %
Rwork0.148 --
obs0.1494 83371 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.04 Å2 / Biso mean: 24.3901 Å2 / Biso min: 9.02 Å2
Refinement stepCycle: final / Resolution: 1.55→44.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4095 0 236 751 5082
Biso mean--53.55 30.82 -
Num. residues----527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094427
X-RAY DIFFRACTIONf_angle_d1.045973
X-RAY DIFFRACTIONf_chiral_restr0.064652
X-RAY DIFFRACTIONf_plane_restr0.007741
X-RAY DIFFRACTIONf_dihedral_angle_d14.6872716
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2804X-RAY DIFFRACTION5.651TORSIONAL
12B2804X-RAY DIFFRACTION5.651TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.56760.22961180.20162629274799
1.5676-1.58610.25011290.22599272899
1.5861-1.60540.20591320.19392570270299
1.6054-1.62570.19951270.18862599272699
1.6257-1.64710.23671440.17352580272499
1.6471-1.66970.22181130.17232622273599
1.6697-1.69350.22071580.16772587274599
1.6935-1.71880.18621220.17452605272799
1.7188-1.74570.20641400.162326442784100
1.7457-1.77430.1871390.15242586272599
1.7743-1.80490.20561310.15262598272999
1.8049-1.83770.17131290.159226342763100
1.8377-1.87310.20931310.156926382769100
1.8731-1.91130.21571570.155926022759100
1.9113-1.95290.19721440.154626202764100
1.9529-1.99830.18521350.153426312766100
1.9983-2.04830.18841600.150226112771100
2.0483-2.10360.17371460.140526172763100
2.1036-2.16550.16021340.139126462780100
2.1655-2.23540.15691380.133226412779100
2.2354-2.31530.16661400.13426402780100
2.3153-2.4080.17381270.134326642791100
2.408-2.51760.18051410.144126662807100
2.5176-2.65030.1711450.141826462791100
2.6503-2.81640.18731310.14226802811100
2.8164-3.03380.17381430.146526812824100
3.0338-3.3390.1521610.141726732834100
3.339-3.82190.15731510.137927022853100
3.8219-4.81420.14871510.123927382889100
4.8142-44.17270.17571560.1782849300599
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)
11.29720.0430.07572.8936-0.47092.1448-0.03610.0199-0.0767-0.11660.03450.00940.1138-0.0374-0.00490.11710.00170.00820.1086-0.00410.119229.835320.7421-32.9846
23.79340.18850.73141.87780.08072.99220.01050.1122-0.0586-0.08460.0102-0.29210.11820.4049-0.02070.11710.05080.02650.1226-0.00630.122242.129529.4474-39.066
30.42650.11240.08430.3273-0.22592.2961-0.019-0.03730.0226-0.0059-0.02940.0001-0.01340.1240.03870.11650.01990.01540.12890.0010.149338.526737.1569-28.0792
41.9450.3156-0.0612.9297-0.63272.57850.0027-0.08510.031-0.0174-0.083-0.2741-0.10730.52750.05270.1114-0.00840.01230.2470.00350.149349.163737.3921-18.497
51.0512-1.42551.00025.862-6.2088.9477-0.0863-0.1179-0.02820.1035-0.04550.13890.06970.09950.13410.13020.00780.0340.166-0.01630.169738.42334.9326-12.5154
62.7684-0.9615-1.42851.92250.36445.99620.00730.26950.0192-0.118-0.00590.0283-0.0138-0.15380.01520.10570.0051-0.00740.05340.00980.119427.107737.2395-38.045
72.9357-2.50433.96153.5932-4.34898.9168-0.0802-0.443-0.03870.21950.2530.08290.0638-0.551-0.2020.1841-0.00630.03990.1508-0.00070.160824.320428.7416-17.7927
81.6561-0.0471-0.35291.344-0.34451.76990.0386-0.01660.1032-0.0220.0012-0.0664-0.17440.0806-0.05540.1245-0.00920.01180.0979-0.01730.136729.668768.5266-32.7952
91.8271-0.31-0.70741.3041-0.0852.5950.06620.12280.0378-0.1150.00940.1859-0.0653-0.2978-0.07350.13510.0346-0.01160.12380.00790.146117.195559.8525-39.1715
100.25290.1095-0.39640.58640.10871.94960.0036-0.0076-0.01130.00730.01-0.01420.0006-0.0081-0.00780.10780.0125-0.0160.1053-0.00030.134220.607552.2307-28.1751
112.6060.6978-1.03514.67370.53153.2724-0.0930.0863-0.08050.0581-0.04180.27010.2746-0.30440.08130.1001-0.029-0.02320.1464-0.00040.18968.235447.3713-20.1519
122.94080.3196-0.47822.38251.16561.7168-0.0472-0.00550.0210.0194-0.00790.70410.1118-0.33290.06810.1078-0.0351-0.01950.17640.01510.23373.714449.8649-21.2951
133.69791.5183-1.62154.5784-0.31135.24950.1220.04080.18060.3482-0.07670.4514-0.1945-0.4246-0.12060.13420.01290.02230.1306-0.00730.18410.278361.8092-13.2119
140.642-0.2716-0.74690.5540.41651.29930.0089-0.08720.05230.02970.0678-0.0859-0.00110.1385-0.07540.13810.0056-0.01460.1361-0.00530.157727.884955.6825-22.939
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 79 )A48 - 79
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 123 )A80 - 123
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 202 )A124 - 202
5X-RAY DIFFRACTION5chain 'A' and (resid 203 through 217 )A203 - 217
6X-RAY DIFFRACTION6chain 'A' and (resid 218 through 243 )A218 - 243
7X-RAY DIFFRACTION7chain 'A' and (resid 244 through 264 )A244 - 264
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 47 )B1 - 47
9X-RAY DIFFRACTION9chain 'B' and (resid 48 through 79 )B48 - 79
10X-RAY DIFFRACTION10chain 'B' and (resid 80 through 123 )B80 - 123
11X-RAY DIFFRACTION11chain 'B' and (resid 124 through 152 )B124 - 152
12X-RAY DIFFRACTION12chain 'B' and (resid 153 through 173 )B153 - 173
13X-RAY DIFFRACTION13chain 'B' and (resid 174 through 187 )B174 - 187
14X-RAY DIFFRACTION14chain 'B' and (resid 188 through 263 )B188 - 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