[English] 日本語
Yorodumi
- PDB-8v8v: PI3Ka H1047R co-crystal structure with inhibitor in cryptic pocke... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8v8v
TitlePI3Ka H1047R co-crystal structure with inhibitor in cryptic pocket near H1047R (compound 7).
Components
  • Phosphatidylinositol 3-kinase regulatory subunit alpha
  • Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
KeywordsSIGNALING PROTEIN / H1047R / PI3K / PI3Ka
Function / homology
Function and homology information


perinuclear endoplasmic reticulum membrane / response to muscle inactivity / negative regulation of actin filament depolymerization / regulation of toll-like receptor 4 signaling pathway / response to L-leucine / phosphatidylinositol kinase activity / regulation of actin filament organization / phosphatidylinositol 3-kinase regulator activity / response to butyrate / positive regulation of focal adhesion disassembly ...perinuclear endoplasmic reticulum membrane / response to muscle inactivity / negative regulation of actin filament depolymerization / regulation of toll-like receptor 4 signaling pathway / response to L-leucine / phosphatidylinositol kinase activity / regulation of actin filament organization / phosphatidylinositol 3-kinase regulator activity / response to butyrate / positive regulation of focal adhesion disassembly / autosome genomic imprinting / IRS-mediated signalling / cellular response to hydrostatic pressure / phosphatidylinositol 3-kinase activator activity / interleukin-18-mediated signaling pathway / PI3K events in ERBB4 signaling / myeloid leukocyte migration / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / positive regulation of protein localization to membrane / cis-Golgi network / Activated NTRK3 signals through PI3K / ErbB-3 class receptor binding / negative regulation of fibroblast apoptotic process / RHOF GTPase cycle / kinase activator activity / cardiac muscle cell contraction / phosphatidylinositol 3-kinase complex, class IB / vasculature development / transmembrane receptor protein tyrosine kinase adaptor activity / RHOD GTPase cycle / Signaling by cytosolic FGFR1 fusion mutants / regulation of cellular respiration / positive regulation of endoplasmic reticulum unfolded protein response / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase complex, class IA / anoikis / phosphatidylinositol 3-kinase complex / Nephrin family interactions / RND1 GTPase cycle / Costimulation by the CD28 family / relaxation of cardiac muscle / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / RND2 GTPase cycle / MET activates PI3K/AKT signaling / PI3K/AKT activation / RND3 GTPase cycle / positive regulation of leukocyte migration / positive regulation of filopodium assembly / phosphatidylinositol-4,5-bisphosphate 3-kinase / vascular endothelial growth factor signaling pathway / negative regulation of stress fiber assembly / phosphatidylinositol 3-kinase / growth hormone receptor signaling pathway / insulin binding / phosphatidylinositol-3-phosphate biosynthetic process / RHOV GTPase cycle / negative regulation of macroautophagy / 1-phosphatidylinositol-3-kinase activity / RHOB GTPase cycle / negative regulation of cell-matrix adhesion / Signaling by ALK / GP1b-IX-V activation signalling / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / protein kinase activator activity / response to dexamethasone / PI-3K cascade:FGFR2 / RHOJ GTPase cycle / PI-3K cascade:FGFR4 / RHOC GTPase cycle / PI-3K cascade:FGFR1 / negative regulation of osteoclast differentiation / intracellular glucose homeostasis / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / CD28 dependent PI3K/Akt signaling / Synthesis of PIPs at the plasma membrane / CDC42 GTPase cycle / RHOU GTPase cycle / PI3K events in ERBB2 signaling / negative regulation of anoikis / RHOG GTPase cycle / intercalated disc / T cell differentiation / RET signaling / regulation of multicellular organism growth / extrinsic apoptotic signaling pathway via death domain receptors / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / RHOA GTPase cycle / positive regulation of TOR signaling / endothelial cell migration / RAC2 GTPase cycle / RAC3 GTPase cycle / Role of phospholipids in phagocytosis
Similarity search - Function
PI3Kalpha, catalytic domain / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Rho GTPase-activating protein domain ...PI3Kalpha, catalytic domain / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / Phosphoinositide 3-kinase C2 / Phosphoinositide 3-kinase, region postulated to contain C2 domain / C2 phosphatidylinositol 3-kinase-type domain / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Rho GTPase activation protein / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / C2 domain superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Armadillo-type fold / Ubiquitin-like domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-1LT / : / Phosphatidylinositol 3-kinase regulatory subunit alpha / Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsGunn, R.J. / Lawson, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Discovery of Pyridopyrimidinones that Selectively Inhibit the H1047R PI3K alpha Mutant Protein.
Authors: Ketcham, J.M. / Harwood, S.J. / Aranda, R. / Aloiau, A.N. / Bobek, B.M. / Briere, D.M. / Burns, A.C. / Caddell Haatveit, K. / Calinisan, A. / Clarine, J. / Elliott, A. / Engstrom, L.D. / ...Authors: Ketcham, J.M. / Harwood, S.J. / Aranda, R. / Aloiau, A.N. / Bobek, B.M. / Briere, D.M. / Burns, A.C. / Caddell Haatveit, K. / Calinisan, A. / Clarine, J. / Elliott, A. / Engstrom, L.D. / Gunn, R.J. / Ivetac, A. / Jones, B. / Kuehler, J. / Lawson, J.D. / Nguyen, N. / Parker, C. / Pearson, K.E. / Rahbaek, L. / Saechao, B. / Wang, X. / Waters, A. / Waters, L. / Watkins, A.H. / Olson, P. / Smith, C.R. / Christensen, J.G. / Marx, M.A.
History
DepositionDec 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 10, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
B: Phosphatidylinositol 3-kinase regulatory subunit alpha
C: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
D: Phosphatidylinositol 3-kinase regulatory subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,7678
Polymers317,0694
Non-polymers1,6984
Water1,982110
1
A: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
B: Phosphatidylinositol 3-kinase regulatory subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,3834
Polymers158,5342
Non-polymers8492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-20 kcal/mol
Surface area50210 Å2
MethodPISA
2
C: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
D: Phosphatidylinositol 3-kinase regulatory subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,3834
Polymers158,5342
Non-polymers8492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-21 kcal/mol
Surface area54990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.172, 121.137, 163.902
Angle α, β, γ (deg.)90.00, 92.04, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform / PI3-kinase subunit alpha / PI3K-alpha / PI3Kalpha / PtdIns-3-kinase subunit alpha / ...PI3-kinase subunit alpha / PI3K-alpha / PI3Kalpha / PtdIns-3-kinase subunit alpha / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase 110 kDa catalytic subunit alpha / PtdIns-3-kinase subunit p110-alpha / p110alpha / Phosphoinositide 3-kinase alpha / Phosphoinositide-3-kinase catalytic alpha polypeptide / Serine/threonine protein kinase PIK3CA


Mass: 124867.469 Da / Num. of mol.: 2 / Mutation: H1047R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3CA / Production host: Trichoplusia (butterflies/moths)
References: UniProt: P42336, phosphatidylinositol 3-kinase, phosphatidylinositol-4,5-bisphosphate 3-kinase, non-specific serine/threonine protein kinase
#2: Protein Phosphatidylinositol 3-kinase regulatory subunit alpha / PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit ...PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit alpha / PtdIns-3-kinase regulatory subunit p85-alpha


Mass: 33666.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R1, GRB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P27986
#3: Chemical ChemComp-YQ2 / 2-[[(1~{R})-1-(7-methyl-4-oxidanylidene-2-piperidin-1-yl-3~{H}-pyrido[1,2-a]pyrimidin-9-yl)ethyl]amino]benzoic acid


Mass: 407.485 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-1LT / (2S)-N~1~-{4-methyl-5-[2-(1,1,1-trifluoro-2-methylpropan-2-yl)pyridin-4-yl]-1,3-thiazol-2-yl}pyrrolidine-1,2-dicarboxamide / Alpelisib / Alpelisib


Mass: 441.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H22F3N5O2S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.6 M Sodium Formate, 0.1 M Citrate pH 5.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.61→73.77 Å / Num. obs: 79585 / % possible obs: 79.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 56.49 Å2 / Rpim(I) all: 0.093 / Net I/σ(I): 7.7
Reflection shellResolution: 2.61→2.7 Å / Num. unique obs: 5443 / Rpim(I) all: 0.45

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→73.77 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 41.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2879 1571 1.97 %
Rwork0.2372 --
obs0.2382 79571 79.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.61→73.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19904 0 120 112 20136
Refine LS restraintsType: f_plane_restr / Dev ideal: 0.005 / Number: 3539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.690.52960.544843X-RAY DIFFRACTION54
2.69-2.790.55441030.50785212X-RAY DIFFRACTION59
2.79-2.90.47571180.4545611X-RAY DIFFRACTION63
2.9-3.030.50081160.40485993X-RAY DIFFRACTION68
3.03-3.190.38911310.35546611X-RAY DIFFRACTION74
3.19-3.390.38841410.29457140X-RAY DIFFRACTION80
3.39-3.660.31911520.24867808X-RAY DIFFRACTION88
3.66-4.020.27141730.21548318X-RAY DIFFRACTION93
4.02-4.610.23441730.17548620X-RAY DIFFRACTION97
4.61-5.80.21351830.18278817X-RAY DIFFRACTION99
5.8-73.770.23181850.18299027X-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)
10.768-1.651.04843.5237-2.22971.40990.20910.87690.2917-0.9533-0.7768-0.2301-0.1255-0.94320.25561.75920.2141-0.09281.9978-0.00191.330636.7972-25.653-27.7533
20.98950.3821-2.11191.8395-0.24334.94670.43750.89660.7401-1.29930.3494-0.80340.0917-0.43770.23672.00070.08430.38261.17130.08731.56746.5359-25.0486-28.3121
32.97553.2929-0.7153.6809-0.50822.11960.53170.6586-0.1307-0.81450.8728-0.57850.0780.0834-0.63812.55030.06160.87251.29750.09381.578350.8178-34.2226-29.3069
40.87511.9294-0.56095.2686-1.10050.4498-0.47730.69371.52580.64580.2303-0.16330.0774-0.12890.29981.9123-0.0923-0.04851.30280.07641.538952.4927-31.4016-20.535
52.4821-1.3135-2.47610.89130.46686.5315-0.3899-0.0044-0.0914-0.4316-0.07420.0811-0.5739-1.3665-0.07151.78160.20170.04691.8368-0.08220.948733.2745-50.7317-17.596
60.62550.1994-0.69861.71271.35722.7823-0.2490.3156-0.20040.0381-0.06760.28780.22760.1440.06020.88260.17320.05010.6203-0.11980.521427.3075-24.741725.691
70.7528-0.1723-1.2041.65263.06926.4319-0.47290.2649-0.31490.2631-0.42030.4580.652-0.53380.41721.25420.12430.04060.6043-0.06770.518928.0525-29.399924.9247
82.34881.33311.70387.65060.16361.3308-0.05140.32870.5413-0.09660.22740.3159-0.0434-0.099-0.30451.3793-0.11380.03452.8665-0.03271.226416.0172-43.2204-16.7617
91.21010.00160.67661.25560.5951.71190.17510.2682-0.1102-0.1267-0.06120.0248-0.13660.4917-0.10120.904400.13220.3948-0.04330.428235.2224.866-88.4687
101.17420.76160.32961.85840.43860.9527-0.0473-0.1509-0.11670.09560.06740.166-0.0485-0.0619-0.05270.8833-0.04040.15090.3770.02540.445531.14610.1731-59.4217
111.57360.12570.77691.62070.68593.73740.1827-0.0493-0.15770.1677-0.08150.1625-0.1639-0.0088-0.04150.5261-0.06470.16350.21250.04830.396625.72628.5212-69.769
122.24640.03910.09410.7840.12442.44910.0629-0.43240.020.2982-0.12570.5433-0.295-0.4140.10770.67180.08070.19030.44820.0290.7061.964214.4838-65.6725
130.9261-0.0386-0.03651.26820.78322.9344-0.30620.46230.1496-0.0322-0.0213-0.0218-0.5286-0.06690.22111.1844-0.2541-0.02770.5567-0.04670.551940.923532.2014-88.0507
141.19731.19220.25841.19790.25980.05280.2067-0.6327-0.167-0.89370.1888-0.2074-0.7828-0.31730.15781.63170.07870.1122.8331-0.26711.7035.705545.1539-56.2552
151.2670.23020.7360.4607-0.06372.35170.08720.14260.19860.1410.02670.2366-0.2965-0.2811-0.09071.02920.1420.06050.50490.07580.401720.2718-3.840738.7817
161.1891-1.10380.12112.1354-0.32030.58890.06740.22770.191-0.2403-0.231-0.42320.09260.29280.09720.80750.07250.18970.57210.11530.540233.9967-1.43150.4714
172.2781-0.4771-0.87321.5696-0.31482.04310.08040.14370.2876-0.1397-0.1705-0.28520.15550.02720.11080.80130.10280.12480.40150.14970.472422.2496-3.20433.9001
183.59290.104-0.1481.0108-0.18591.73780.08261.2161-0.526-0.658-0.27260.0850.644-0.31250.09891.24960.08850.17970.96930.01820.46549.6594-13.9675-15.4009
194.26841.31822.36141.7612.5193.65290.5291.4237-1.52740.25-0.13780.5072-0.05710.11440.26221.7818-0.02150.23061.5925-0.2751.052139.2161-37.2353-28.1187
206.146-1.3125-2.88581.68821.74982.2656-0.7083-0.06530.61780.027-0.33550.1478-0.2432-0.48180.40921.26190.33220.10141.2914-0.35161.190740.3787-31.8329-12.4842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 355 through 367 )
2X-RAY DIFFRACTION2chain 'D' and (resid 368 through 400 )
3X-RAY DIFFRACTION3chain 'D' and (resid 401 through 410 )
4X-RAY DIFFRACTION4chain 'D' and (resid 411 through 430 )
5X-RAY DIFFRACTION5chain 'D' and (resid 431 through 441 )
6X-RAY DIFFRACTION6chain 'D' and (resid 442 through 514 )
7X-RAY DIFFRACTION7chain 'D' and (resid 515 through 587 )
8X-RAY DIFFRACTION8chain 'D' and (resid 588 through 600 )
9X-RAY DIFFRACTION9chain 'A' and (resid 2 through 198 )
10X-RAY DIFFRACTION10chain 'A' and (resid 199 through 553 )
11X-RAY DIFFRACTION11chain 'A' and (resid 554 through 784 )
12X-RAY DIFFRACTION12chain 'A' and (resid 785 through 1049 )
13X-RAY DIFFRACTION13chain 'B' and (resid 449 through 579 )
14X-RAY DIFFRACTION14chain 'B' and (resid 580 through 600 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 121 )
16X-RAY DIFFRACTION16chain 'C' and (resid 122 through 553 )
17X-RAY DIFFRACTION17chain 'C' and (resid 554 through 853 )
18X-RAY DIFFRACTION18chain 'C' and (resid 854 through 1047 )
19X-RAY DIFFRACTION19chain 'D' and (resid 326 through 340 )
20X-RAY DIFFRACTION20chain 'D' and (resid 341 through 354 )

+
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