[English] 日本語
Yorodumi
- PDB-6hc9: STRUCTURE OF GLUA2 LIGAND-BINDING DOMAIN (S1S2J-L504Y-N775S) IN C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hc9
TitleSTRUCTURE OF GLUA2 LIGAND-BINDING DOMAIN (S1S2J-L504Y-N775S) IN COMPLEX WITH GLUTAMATE AND TDPAM02 AT 2.4 A RESOLUTION.
ComponentsGlutamate receptor 2,GRIA2
KeywordsMEMBRANE PROTEIN / ampa receptor / gluA2 / ligand-binding domain / glua2-S1S2J-L504Y-N775S / signaling protein / positive allosteric modulator
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 / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / dendritic shaft / 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 / scaffold protein binding / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / dendrite / synapse / glutamatergic 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 / : / 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
Chem-FXW / GLUTAMIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLaulumaa, S. / Hansen, K.V. / Frydenvang, K. / Kastrup, J.S.
CitationJournal: Acs Med.Chem.Lett. / Year: 2019
Title: Crystal Structures of Potent Dimeric Positive Allosteric Modulators at the Ligand-Binding Domain of the GluA2 Receptor.
Authors: Laulumaa, S. / Hansen, K.V. / Masternak, M. / Drapier, T. / Francotte, P. / Pirotte, B. / Frydenvang, K. / Kastrup, J.S.
History
DepositionAug 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
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)60,95025
Polymers58,6032
Non-polymers2,34623
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-153 kcal/mol
Surface area24220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.656, 121.942, 47.442
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 5:15 or (resid 16 and (name...
21(chain B and (resseq 5:15 or (resid 16 and (name...

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
11THRTHRPROPRO(chain A and (resseq 5:15 or (resid 16 and (name...AA5 - 155 - 15
12TYRTYRTYRTYR(chain A and (resseq 5:15 or (resid 16 and (name...AA1616
13GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
14GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
15GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
16GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
17GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
18GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
19GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
110GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
111GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
112GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
113GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
114GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
115GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
116GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
21THRTHRPROPRO(chain B and (resseq 5:15 or (resid 16 and (name...BB5 - 155 - 15
22TYRTYRTYRTYR(chain B and (resseq 5:15 or (resid 16 and (name...BB1616
23LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
24LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
25LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
26LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
27LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
28LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
29LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
210LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
211LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
212LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
213LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
214LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
215LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
216LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
217LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Glutamate receptor 2, / GRIA2 / 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: 29301.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NATIVE GLUA2 IS A MEMBRANE PROTEIN. THE CRYSTALLIZED PROTEIN IS A L540Y- N775S-MUTANT OF THE GLUA2 LIGAND-BINDING DOMAIN. TRANSMEMBRANE REGIONS ARE REPLACED WITH A GLY-THR LINKER (RESIDUES ...Details: NATIVE GLUA2 IS A MEMBRANE PROTEIN. THE CRYSTALLIZED PROTEIN IS A L540Y- N775S-MUTANT OF THE GLUA2 LIGAND-BINDING DOMAIN. TRANSMEMBRANE REGIONS ARE REPLACED WITH A GLY-THR LINKER (RESIDUES 118-119) AND GLY1 IS A CLONING REMNANT. THE SEQUENCE MATCHES DISCONTINUOUSLY WITH REFERENCE DATABASE (413-527, 653-797).
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 / References: UniProt: P19491

-
Non-polymers , 8 types, 235 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-FXW / 6,6'-(ETHANE-1,2-DIYL)BIS(4-CYCLOPROPYL-3,4-DIHYDRO-2H-1,2,4-BENZOTHIADIAZINE 1,1-DIOXIDE)


Mass: 474.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26N4O4S2 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG4000, 0.3 M lithium sulfate, 0.1 M phosphate citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.981 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 2.4→121.94 Å / Num. all: 22932 / Num. obs: 22932 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 28.14 Å2 / Rpim(I) all: 0.107 / Rrim(I) all: 0.295 / Rsym value: 0.275 / Net I/av σ(I): 2.3 / Net I/σ(I): 4.9 / Num. measured all: 172168
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.4-2.537.40.9160.832670.3590.9850.916100
2.53-2.687.50.719131020.2810.7730.719100
2.68-2.877.80.5741.329450.2190.6150.574100
2.87-3.17.70.4381.627450.1680.4690.438100
3.1-3.397.60.32.425480.1150.3220.3100
3.39-3.797.60.219322800.0840.2350.219100
3.79-4.387.40.173.620660.0660.1820.17100
4.38-5.377.50.1523.917570.0580.1630.152100
5.37-7.597.40.1623.813880.0630.1750.162100
7.59-76.2256.30.1174.28340.050.1280.11799.8

-
Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTJ

1ftj


Resolution: 2.4→76.225 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.13
RfactorNum. reflection% reflection
Rfree0.2391 1123 4.91 %
Rwork0.2081 --
obs0.2097 22873 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 150.15 Å2 / Biso mean: 34.0179 Å2 / Biso min: 0.78 Å2
Refinement stepCycle: final / Resolution: 2.4→76.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4072 0 227 214 4513
Biso mean--48.13 26.46 -
Num. residues----522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024285
X-RAY DIFFRACTIONf_angle_d0.5765764
X-RAY DIFFRACTIONf_chiral_restr0.041621
X-RAY DIFFRACTIONf_plane_restr0.002708
X-RAY DIFFRACTIONf_dihedral_angle_d17.1252578
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2714X-RAY DIFFRACTION7.308TORSIONAL
12B2714X-RAY DIFFRACTION7.308TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.50920.33671410.271426632804
2.5092-2.64150.26631280.252626932821
2.6415-2.8070.26221320.233826642796
2.807-3.02380.26341260.233727002826
3.0238-3.32810.28051560.21826762832
3.3281-3.80970.21471380.195627222860
3.8097-4.79970.20011590.159127492908
4.7997-76.26370.2211430.20728833026
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)
11.163-0.034-0.47640.5439-0.50512.26350.11290.01940.2133-0.11330.0030.019-0.21670.0164-0.10310.2250.0040.03220.18710.00480.260822.9125182.1565-32.6011
22.26390.80110.27152.35810.15051.4517-0.01340.1154-0.0880.0762-0.00640.27430.0852-0.21660.01360.210.00570.00850.24790.01240.25329.7592174.248-18.5312
30.99620.0508-0.92480.8620.60041.6518-0.0116-0.17160.05210.03740.0553-0.1724-0.20370.248-0.05640.22710.0226-0.0370.276-0.0160.327430.1358177.2026-25.5766
41.83250.210.22911.62790.35271.52290.0649-0.1095-0.2835-0.00730.02510.15050.2828-0.137-0.08990.3984-0.00850.04160.20770.01410.279629.9729143.0847-32.2511
52.48-0.35580.15052.0667-0.34071.7029-0.15860.1764-0.2641-0.41720.0356-0.25850.13350.25120.1650.35460.01750.01710.2902-0.04490.252438.4053148.6351-37.8604
61.55410.1105-0.13041.21480.43411.84430.09870.06290.102-0.0941-0.0231-0.18670.03270.2385-0.0740.26240.01780.0270.2591-0.0020.265940.2303158.0882-34.9876
72.45480.0443-0.17333.254-1.01592.7852-0.243-0.41440.1460.5122-0.1506-0.2429-0.37730.28290.38290.46-0.151-0.02710.72430.02760.421850.2765163.7908-8.4151
82.27610.4788-0.19351.6133-0.15131.6990.14450.17770.0535-0.1366-0.293-0.4151-0.00240.55180.14510.28630.05790.00280.42970.04660.439252.5484161.8899-23.3308
91.53460.8923-0.73611.9938-1.05521.871-0.0257-0.5047-0.36510.3821-0.133-0.19680.22590.19420.15840.39210.02740.01930.49050.04460.3742.2255153.7628-14.3092
101.6984-0.3171-0.21851.2970.03911.43530.05150.05390.046-0.29750.13670.18480.1637-0.0262-0.18810.29590.0325-0.00660.19930.01720.241827.114159.4829-37.9799
114.26030.55751.19073.7679-0.32383.8298-0.2404-0.3515-0.19520.4319-0.0387-0.55990.4181-0.63010.1840.4522-0.01220.08080.295-0.02160.283524.359151.3294-20.2349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 123 )A4 - 123
2X-RAY DIFFRACTION2chain 'A' and (resid 124 through 202 )A124 - 202
3X-RAY DIFFRACTION3chain 'A' and (resid 203 through 260 )A203 - 260
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 47 )B4 - 47
5X-RAY DIFFRACTION5chain 'B' and (resid 48 through 65 )B48 - 65
6X-RAY DIFFRACTION6chain 'B' and (resid 66 through 116 )B66 - 116
7X-RAY DIFFRACTION7chain 'B' and (resid 117 through 133 )B117 - 133
8X-RAY DIFFRACTION8chain 'B' and (resid 134 through 173 )B134 - 173
9X-RAY DIFFRACTION9chain 'B' and (resid 174 through 217 )B174 - 217
10X-RAY DIFFRACTION10chain 'B' and (resid 218 through 243 )B218 - 243
11X-RAY DIFFRACTION11chain 'B' and (resid 244 through 260 )B244 - 260

+
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