[English] 日本語
Yorodumi
- PDB-6c9j: AMP-activated protein kinase bound to pharmacological activator R734 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6c9j
TitleAMP-activated protein kinase bound to pharmacological activator R734
Components
  • (5'-AMP-activated protein kinase subunit ...) x 2
  • 5'-AMP-activated protein kinase catalytic subunit alpha-1
KeywordsTRANSFERASE / AMPK / activator
Function / homology
Function and homology information


negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / [acetyl-CoA carboxylase] kinase activity / regulation of stress granule assembly / histone H2BS36 kinase activity / regulation of peptidyl-serine phosphorylation / cold acclimation ...negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / [acetyl-CoA carboxylase] kinase activity / regulation of stress granule assembly / histone H2BS36 kinase activity / regulation of peptidyl-serine phosphorylation / cold acclimation / positive regulation of peptidyl-lysine acetylation / lipid droplet disassembly / Lipophagy / regulation of bile acid secretion / import into nucleus / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / cAMP-dependent protein kinase regulator activity / regulation of vesicle-mediated transport / positive regulation of cholesterol biosynthetic process / cellular response to organonitrogen compound / protein kinase regulator activity / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of TOR signaling / negative regulation of hepatocyte apoptotic process / tau-protein kinase / bile acid and bile salt transport / nucleotide-activated protein kinase complex / cellular response to ethanol / protein localization to lipid droplet / bile acid signaling pathway / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to caffeine / motor behavior / positive regulation of protein targeting to mitochondrion / lipid biosynthetic process / regulation of glycolytic process / cAMP-dependent protein kinase activity / negative regulation of tubulin deacetylation / Macroautophagy / AMP-activated protein kinase activity / positive regulation of protein localization / tau-protein kinase activity / cholesterol biosynthetic process / AMP binding / fatty acid oxidation / cellular response to nutrient levels / fatty acid homeostasis / positive regulation of protein kinase activity / cellular response to glucose starvation / Activation of AMPK downstream of NMDARs / positive regulation of autophagy / negative regulation of lipid catabolic process / regulation of microtubule cytoskeleton organization / energy homeostasis / response to UV / negative regulation of insulin receptor signaling pathway / negative regulation of TORC1 signaling / positive regulation of adipose tissue development / cellular response to calcium ion / positive regulation of glycolytic process / response to activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / ADP binding / cellular response to glucose stimulus / response to gamma radiation / TP53 Regulates Metabolic Genes / tau protein binding / regulation of circadian rhythm / cellular response to hydrogen peroxide / Wnt signaling pathway / autophagy / neuron cellular homeostasis / cellular response to prostaglandin E stimulus / response to estrogen / fatty acid biosynthetic process / glucose metabolic process / rhythmic process / cellular response to xenobiotic stimulus / glucose homeostasis / cellular response to oxidative stress / positive regulation of cold-induced thermogenesis / cellular response to hypoxia / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / nuclear speck / apical plasma membrane / axon / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / neuronal cell body / chromatin binding / positive regulation of cell population proliferation
Similarity search - Function
PRKAA1, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase alpha 1 catalytic subunit, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / Association with the SNF1 complex (ASC) domain / ASC domain superfamily / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase ...PRKAA1, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase alpha 1 catalytic subunit, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / Association with the SNF1 complex (ASC) domain / ASC domain superfamily / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / KA1 domain/Ssp2, C-terminal / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Immunoglobulin E-set / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Chem-R34 / STAUROSPORINE / 5'-AMP-activated protein kinase subunit gamma-1 / 5'-AMP-activated protein kinase catalytic subunit alpha-1 / 5'-AMP-activated protein kinase subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsYan, Y. / Zhou, X.E. / Novick, S. / Shaw, S.J. / Li, Y. / Brunzelle, J.S. / Hitoshi, Y. / Griffin, P.R. / Xu, H.E. / Melcher, K.
Funding support United States, China, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM102545 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)DK071662 United States
National Natural Science Foundation of China (NSFC)31300245 China
Ministry of Science and Technology (MoST, China)2012ZX09301001 China
Ministry of Science and Technology (MoST, China)2012CB910403 China
Ministry of Science and Technology (MoST, China)2013CB910600 China
Ministry of Science and Technology (MoST, China)XDB08020303 China
Ministry of Science and Technology (MoST, China)2013ZX09507001 China
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Structures of AMP-activated protein kinase bound to novel pharmacological activators in phosphorylated, non-phosphorylated, and nucleotide-free states.
Authors: Yan, Y. / Zhou, X.E. / Novick, S.J. / Shaw, S.J. / Li, Y. / Brunzelle, J.S. / Hitoshi, Y. / Griffin, P.R. / Xu, H.E. / Melcher, K.
History
DepositionJan 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-AMP-activated protein kinase catalytic subunit alpha-1
B: 5'-AMP-activated protein kinase subunit beta-1
C: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,6056
Polymers117,3453
Non-polymers1,2613
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13240 Å2
ΔGint-73 kcal/mol
Surface area39930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.296, 123.296, 404.921
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein 5'-AMP-activated protein kinase catalytic subunit alpha-1 / AMPK subunit alpha-1 / Acetyl-CoA carboxylase kinase / ACACA kinase / Hydroxymethylglutaryl-CoA ...AMPK subunit alpha-1 / Acetyl-CoA carboxylase kinase / ACACA kinase / Hydroxymethylglutaryl-CoA reductase kinase / HMGCR kinase / Tau-protein kinase PRKAA1


Mass: 57245.625 Da / Num. of mol.: 1 / Mutation: S108D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAA1, AMPK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13131, non-specific serine/threonine protein kinase, [acetyl-CoA carboxylase] kinase, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase, tau-protein kinase

-
5'-AMP-activated protein kinase subunit ... , 2 types, 2 molecules BC

#2: Protein 5'-AMP-activated protein kinase subunit beta-1 / AMPKb


Mass: 23071.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAB1, AMPK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y478
#3: Protein 5'-AMP-activated protein kinase subunit gamma-1 / AMPKg


Mass: 37027.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P54619

-
Non-polymers , 3 types, 3 molecules

#4: Chemical ChemComp-R34 / 5-{[6-chloro-5-(1-methyl-1H-indol-5-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide


Mass: 446.886 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H19ClN4O3
#5: Chemical ChemComp-STU / STAUROSPORINE / Staurosporine


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M tri-ammonium citrate pH7, 12% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 32841 / % possible obs: 91.1 % / Redundancy: 34.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.807 / Net I/σ(I): 10
Reflection shellResolution: 3.05→3.22 Å / Rmerge(I) obs: 0.0897 / CC1/2: 0.722

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RER

4rer


Resolution: 3.05→49.646 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 2366 7.24 %
Rwork0.2144 --
obs0.2151 32702 91.34 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→49.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6944 0 90 0 7034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047211
X-RAY DIFFRACTIONf_angle_d0.7829796
X-RAY DIFFRACTIONf_dihedral_angle_d9.5314308
X-RAY DIFFRACTIONf_chiral_restr0.0531104
X-RAY DIFFRACTIONf_plane_restr0.0061218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0501-3.11230.3893920.36441048X-RAY DIFFRACTION55
3.1123-3.180.2641890.32661122X-RAY DIFFRACTION59
3.18-3.25390.29551040.31561265X-RAY DIFFRACTION66
3.2539-3.33530.3761940.28921457X-RAY DIFFRACTION75
3.3353-3.42550.24221250.27561835X-RAY DIFFRACTION95
3.4255-3.52620.27051460.25661912X-RAY DIFFRACTION100
3.5262-3.640.23271530.24111908X-RAY DIFFRACTION100
3.64-3.77010.24361370.24011922X-RAY DIFFRACTION100
3.7701-3.9210.22031390.21221940X-RAY DIFFRACTION100
3.921-4.09930.23071640.20651931X-RAY DIFFRACTION100
4.0993-4.31530.21821600.19141916X-RAY DIFFRACTION100
4.3153-4.58550.2131610.17991940X-RAY DIFFRACTION100
4.5855-4.93930.18251520.18581971X-RAY DIFFRACTION100
4.9393-5.43580.21651550.19021961X-RAY DIFFRACTION100
5.4358-6.22110.20911590.21561999X-RAY DIFFRACTION100
6.2211-7.83290.21541790.21232016X-RAY DIFFRACTION100
7.8329-49.65250.19681570.18462193X-RAY DIFFRACTION99
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)
13.40751.41531.36792.6043-0.03443.3250.02320.24480.129-0.10520.0877-0.0958-0.21110.1166-0.11090.5313-0.0018-0.00320.4342-0.11050.4644-9.408726.6555-32.2436
23.5482-0.91951.53760.6874-0.16742.3805-0.0054-0.08290.1498-0.04190.01560.1866-0.4875-0.3542-0.01020.6193-0.03390.02960.5275-0.04620.5061-23.126436.2116-30.5525
30.54810.1988-0.30990.7438-0.41520.9594-0.0125-0.01780.03620.0108-0.0036-0.0426-0.1251-0.03280.01610.4520.0315-0.03580.3911-0.11450.412-19.564325.0595-16.4564
41.07960.5547-0.13463.61021.17991.0679-0.03560.05940.1688-0.1362-0.00870.2391-0.2442-0.21110.04430.65930.0732-0.04420.6276-0.09930.5693-38.693730.7522-17.6189
50.8918-0.26520.21990.8845-0.01910.97830.0050.0212-0.1067-0.07820.00710.17310.0248-0.2524-0.01210.45210.0454-0.01890.4497-0.1090.4318-35.890114.8371-9.0951
60.8216-0.5539-0.68020.37340.45860.56320.0611-0.44010.52920.22040.0995-0.0326-0.3743-0.0883-0.16060.7240.0484-0.02420.6586-0.08880.678-32.215933.09365.2525
70.3768-0.30420.38090.31520.07992.5430.14070.28910.0841-0.4095-0.09990.0746-0.2087-0.0308-0.04081.30720.4285-0.03131.1343-0.16651.0946-52.489951.5232-15.9957
82.6995-0.3451-0.12051.9502-0.30433.1018-0.0189-0.13240.19650.1669-0.0626-0.0467-0.23780.03130.08150.5478-0.11350.00650.4651-0.10130.4566-10.976532.2015-52.1563
90000000.0478-0.05610.31080.07440.02530.2347-0.2198-0.2286-0.07311.00830.05210.00440.9866-0.05481.0523-30.755944.7066-35.7549
100000000.2109-0.54480.12020.7382-0.0158-0.38410.32260.1666-0.1951.15920.34930.1221.1807-0.17661.1278-43.460143.24114.5662
110.37310.2305-0.13731.98360.29931.87920.0073-0.07350.02060.0437-0.01310.0212-0.0643-0.050.00590.9340.32820.13360.9144-0.14990.88-44.835951.0542-3.126
121.63360.86330.35130.45620.18560.0755-0.0021-0.20450.15850.1968-0.0496-0.3844-0.28460.35530.05170.97570.11350.10851.0455-0.1011.1737-24.17759.91915.638
130.304-0.3161-0.82340.55880.8252.23430.01290.2138-0.0001-0.2352-0.0369-0.0628-0.0926-0.08050.02410.85430.22910.19180.7643-0.07330.9301-52.984367.76019.0558
144.9417-1.4233-1.82970.40990.5270.67750.0169-0.03660.6901-0.00860.2096-0.594-0.29860.3595-0.22661.19770.18340.1641.2983-0.15551.4145-43.06774.68013.517
150.8320.52440.84620.33050.53330.8606-0.0229-0.06680.24630.0839-0.005-0.343-0.22840.28050.02791.07450.1080.16611.2542-0.1781.4571-30.352170.08027.6699
162.6727-0.11322.09192.5088-0.80275.63620.10240.0481-0.02370.0867-0.1072-0.31560.310.42370.00480.91440.10530.20481.11-0.18991.3293-29.306959.78826.4643
17000000-0.03030.05270.0148-0.04610.0294-0.23180.05130.14640.00091.57310.09520.13011.762-0.20341.9939-13.999464.726422.9805
182.5609-0.37740.12061.29710.86870.63870.0422-0.21410.1190.2174-0.0373-0.4611-0.16850.4279-0.00490.85570.16240.070.9624-0.10061.0644-41.131673.026730.278
191.14070.07110.5061.4410.73512.45330.0728-0.1192-0.35290.154-0.0151-0.17290.30840.1174-0.05770.71510.19810.06850.7824-0.03130.8518-50.285562.764326.263
200.5452-0.23750.93740.1035-0.40841.61170.1473-0.1465-0.33710.07490.02820.00050.2025-0.2144-0.17551.58850.08230.09171.7172-0.23421.826-32.428259.451732.585
211.7118-0.2999-0.3390.9555-0.49740.83790.007-0.1104-0.03720.17950.0578-0.13050.18050.1754-0.06481.20620.05350.06691.333-0.23711.4721-28.118962.200329.1838
222.94320.96331.60242.96480.04980.9574-0.00420.45180.0391-0.35420.0766-0.2693-0.12830.0345-0.07241.18090.07070.06181.2919-0.2461.4525-25.435170.345921.503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 72 )
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 162 )
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 194 )
5X-RAY DIFFRACTION5chain 'A' and (resid 195 through 250 )
6X-RAY DIFFRACTION6chain 'A' and (resid 251 through 370 )
7X-RAY DIFFRACTION7chain 'A' and (resid 371 through 550 )
8X-RAY DIFFRACTION8chain 'B' and (resid 74 through 148 )
9X-RAY DIFFRACTION9chain 'B' and (resid 149 through 207 )
10X-RAY DIFFRACTION10chain 'B' and (resid 208 through 226 )
11X-RAY DIFFRACTION11chain 'B' and (resid 227 through 270 )
12X-RAY DIFFRACTION12chain 'C' and (resid 25 through 48 )
13X-RAY DIFFRACTION13chain 'C' and (resid 49 through 112 )
14X-RAY DIFFRACTION14chain 'C' and (resid 113 through 136 )
15X-RAY DIFFRACTION15chain 'C' and (resid 137 through 155 )
16X-RAY DIFFRACTION16chain 'C' and (resid 156 through 179 )
17X-RAY DIFFRACTION17chain 'C' and (resid 180 through 195 )
18X-RAY DIFFRACTION18chain 'C' and (resid 196 through 235 )
19X-RAY DIFFRACTION19chain 'C' and (resid 236 through 268 )
20X-RAY DIFFRACTION20chain 'C' and (resid 269 through 283 )
21X-RAY DIFFRACTION21chain 'C' and (resid 284 through 307 )
22X-RAY DIFFRACTION22chain 'C' and (resid 308 through 324 )

+
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