[English] 日本語
Yorodumi
- PDB-7pg6: Crystal Structure of PI3Kalpha in complex with the inhibitor NVP-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pg6
TitleCrystal Structure of PI3Kalpha in complex with the inhibitor NVP-BYL719
Components
  • Phosphatidylinositol 3-kinase regulatory subunit alpha
  • Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
KeywordsTRANSFERASE / PI3K / PIK3CA / PIK3R1 / p110 / p85 / NVP-BYL719
Function / homology
Function and homology information


perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / response to muscle inactivity / phosphatidylinositol kinase activity / regulation of actin filament organization / negative regulation of actin filament depolymerization / response to butyrate / phosphatidylinositol 3-kinase regulator activity / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response ...perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / response to muscle inactivity / phosphatidylinositol kinase activity / regulation of actin filament organization / negative regulation of actin filament depolymerization / response to butyrate / phosphatidylinositol 3-kinase regulator activity / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response / response to L-leucine / IRS-mediated signalling / phosphatidylinositol 3-kinase activator activity / T follicular helper cell differentiation / interleukin-18-mediated signaling pathway / PI3K events in ERBB4 signaling / phosphatidylinositol 3-kinase regulatory subunit binding / myeloid leukocyte migration / neurotrophin TRKA receptor binding / cellular response to hydrostatic pressure / positive regulation of focal adhesion disassembly / autosome genomic imprinting / Activated NTRK2 signals through PI3K / cis-Golgi network / negative regulation of fibroblast apoptotic process / TORC2 signaling / transmembrane receptor protein tyrosine kinase adaptor activity / Activated NTRK3 signals through PI3K / phosphatidylinositol 3-kinase complex, class IB / ErbB-3 class receptor binding / phosphatidylinositol 3-kinase complex / negative regulation of stress fiber assembly / positive regulation of protein localization to membrane / Signaling by cytosolic FGFR1 fusion mutants / Co-stimulation by ICOS / vasculature development / RHOD GTPase cycle / regulation of cellular respiration / Nephrin family interactions / anoikis / 1-phosphatidylinositol-4-phosphate 3-kinase activity / Signaling by LTK in cancer / RHOF GTPase cycle / Signaling by LTK / kinase activator activity / positive regulation of leukocyte migration / relaxation of cardiac muscle / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / MET activates PI3K/AKT signaling / RND1 GTPase cycle / PI3K/AKT activation / phosphatidylinositol 3-kinase complex, class IA / RND2 GTPase cycle / phosphatidylinositol-4,5-bisphosphate 3-kinase / RND3 GTPase cycle / positive regulation of filopodium assembly / cardiac muscle cell contraction / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / growth hormone receptor signaling pathway / insulin binding / Signaling by ALK / 1-phosphatidylinositol-3-kinase activity / RHOV GTPase cycle / vascular endothelial growth factor signaling pathway / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / PI-3K cascade:FGFR3 / RHOB GTPase cycle / natural killer cell mediated cytotoxicity / GP1b-IX-V activation signalling / response to dexamethasone / negative regulation of macroautophagy / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / RHOC GTPase cycle / RHOJ GTPase cycle / negative regulation of osteoclast differentiation / phosphatidylinositol phosphate biosynthetic process / phosphatidylinositol-mediated signaling / Synthesis of PIPs at the plasma membrane / intracellular glucose homeostasis / RHOU GTPase cycle / CDC42 GTPase cycle / RET signaling / negative regulation of anoikis / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / intercalated disc / PI3K Cascade / PI3K events in ERBB2 signaling / T cell differentiation / RHOG GTPase cycle / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of cell-matrix adhesion / CD28 dependent PI3K/Akt signaling / regulation of multicellular organism growth / Role of LAT2/NTAL/LAB on calcium mobilization / RHOA GTPase cycle / RAC2 GTPase cycle
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 / Phosphatidylinositol 3-kinase, accessory domain (PIK) ...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 / Phosphatidylinositol 3-kinase, accessory domain (PIK) / 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. / Rho GTPase activation protein / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / C2 domain / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Ubiquitin-like domain superfamily / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
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: 2.49943744477 Å
AuthorsGong, G. / Pinotsis, N. / Williams, R.L. / Vanhaesebroeck, B.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission United Kingdom
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Nature / Year: 2023
Title: A small-molecule PI3K alpha activator for cardioprotection and neuroregeneration.
Authors: Gong, G.Q. / Bilanges, B. / Allsop, B. / Masson, G.R. / Roberton, V. / Askwith, T. / Oxenford, S. / Madsen, R.R. / Conduit, S.E. / Bellini, D. / Fitzek, M. / Collier, M. / Najam, O. / He, Z. ...Authors: Gong, G.Q. / Bilanges, B. / Allsop, B. / Masson, G.R. / Roberton, V. / Askwith, T. / Oxenford, S. / Madsen, R.R. / Conduit, S.E. / Bellini, D. / Fitzek, M. / Collier, M. / Najam, O. / He, Z. / Wahab, B. / McLaughlin, S.H. / Chan, A.W.E. / Feierberg, I. / Madin, A. / Morelli, D. / Bhamra, A. / Vinciauskaite, V. / Anderson, K.E. / Surinova, S. / Pinotsis, N. / Lopez-Guadamillas, E. / Wilcox, M. / Hooper, A. / Patel, C. / Whitehead, M.A. / Bunney, T.D. / Stephens, L.R. / Hawkins, P.T. / Katan, M. / Yellon, D.M. / Davidson, S.M. / Smith, D.M. / Phillips, J.B. / Angell, R. / Williams, R.L. / Vanhaesebroeck, B.
History
DepositionAug 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.2Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,2784
Polymers158,8142
Non-polymers4642
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-24 kcal/mol
Surface area57940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.87, 105.19, 135.74
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
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: 124458.984 Da / Num. of mol.: 1 / Mutation: M232K, L233K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3CA / Production host: Spodoptera frugiperda (fall armyworm)
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 / PI3-kinase regulatory subunit alpha / PI3K regulatory subunit alpha / PtdIns-3-kinase regulatory ...PI3-kinase regulatory subunit alpha / PI3K regulatory subunit alpha / PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit alpha / PI3-kinase subunit p85-alpha / PtdIns-3-kinase regulatory subunit p85-alpha


Mass: 34354.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R1, GRB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27986
#3: 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


Mass: 441.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22F3N5O2S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 5000, 160 mM KSCN and 100 mM sodium cacodylate pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2019 / Details: KB-mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.499→50 Å / Num. obs: 52624 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 58.5772677043 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.217 / Net I/σ(I): 13.48
Reflection shellResolution: 2.499→2.65 Å / Redundancy: 13.7 % / Num. unique obs: 8343 / CC1/2: 0.469 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PG5

7pg5


Resolution: 2.49943744477→49.0422761719 Å / SU ML: 0.399134624379 / Cross valid method: FREE R-VALUE / σ(F): 1.33676695759 / Phase error: 28.413771157
RfactorNum. reflection% reflection
Rfree0.240324192397 2627 4.99809741248 %
Rwork0.187252392396 49933 -
obs0.189921800655 52560 99.7968367289 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70 Å2
Refinement stepCycle: LAST / Resolution: 2.49943744477→49.0422761719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10585 0 31 59 10675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086023223474710901
X-RAY DIFFRACTIONf_angle_d1.2608516953214728
X-RAY DIFFRACTIONf_chiral_restr0.0479668767531592
X-RAY DIFFRACTIONf_plane_restr0.005806433555021898
X-RAY DIFFRACTIONf_dihedral_angle_d16.2995667224168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4995-2.54490.3803058046361300.3398605861582514X-RAY DIFFRACTION96.5668371074
2.5449-2.59380.3670723093661360.3179933572482575X-RAY DIFFRACTION100
2.5938-2.64680.3625898996731380.3090814044772631X-RAY DIFFRACTION99.9278238903
2.6468-2.70430.3659111097411360.3089586542562575X-RAY DIFFRACTION99.9631268437
2.7043-2.76720.3229649621661390.2860217181062637X-RAY DIFFRACTION99.9280057595
2.7672-2.83640.3758241992371360.2683324346632581X-RAY DIFFRACTION100
2.8364-2.91310.2924112346121390.2538229205732642X-RAY DIFFRACTION99.928135106
2.9131-2.99880.342176107831350.2351366570962566X-RAY DIFFRACTION100
2.9988-3.09560.3027719952331390.2355147200142640X-RAY DIFFRACTION100
3.0956-3.20620.322836253191350.2231481994682566X-RAY DIFFRACTION99.9629903775
3.2062-3.33450.2713053405381370.2038849109242606X-RAY DIFFRACTION100
3.3345-3.48630.2864190409031400.1977603560042648X-RAY DIFFRACTION100
3.4863-3.670.2436679125231380.187614867182631X-RAY DIFFRACTION100
3.67-3.89990.2116593053611390.1699631721772645X-RAY DIFFRACTION100
3.8999-4.20080.2109594736021390.1616908424912637X-RAY DIFFRACTION100
4.2008-4.62330.2078517790471390.1422646521792646X-RAY DIFFRACTION100
4.6233-5.29160.202474311861410.1413329711482677X-RAY DIFFRACTION100
5.2916-6.66420.1961752500491420.1786334688392690X-RAY DIFFRACTION100
6.6642-100.1725354911611490.1465986038282826X-RAY DIFFRACTION99.8322147651
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)
11.131678700880.2881056567880.1475230920010.5554027917170.03515499827150.615106046623-0.07281720386820.0374931441312-0.02124656848440.09601255445260.05715516412950.007225632486870.06871971755950.1823801946710.0406459590880.4913613122240.0520105267773-0.01063952799670.388419741358-0.01548276885920.42586877132817.9431532056-36.44076427138.1982047421
22.62325060585-0.24142610872-0.5660427565812.62796707578-1.873533327191.47997910297-0.1280385593031.04070372738-0.47393031939-0.675635946475-0.0475815016319-0.002293330619530.522507851-0.1928315542030.1356175532710.448781811011-0.04092858647320.01731239294990.540935200016-0.1608276050860.335020766552-4.66851366168-38.56497068871.74142096353
30.743513251589-0.103459572121-0.2002456280110.893079369556-0.2063318489130.997683657265-0.05694017368020.04300967066880.0154999118659-0.02937021156790.04329777190780.1478244886840.00336579722694-0.193923282701-0.003728006894630.352778880538-0.00844257973854-0.007914963963250.343123401851-0.02358484709130.36928351452-16.7989251509-22.091972312630.1610426462
40.458990431265-0.555718545309-0.00675459154830.933178055308-0.1664381658141.069542204220.0777177307837-0.09628789727160.07832440546990.2609507879840.02128402936640.925683569971-0.210905195246-0.491974121968-0.03622228892380.8296164948380.2421403505820.1416456284720.884961831832-0.06446673114840.98672221768-46.4727060259-13.605606481744.5003667762
51.1656838445-0.55066520463-0.154404263630.93847684431-0.005650697616320.760115923363-0.0605049583727-0.2051287572680.1364978827120.1607266010860.195593548373-0.0923424760328-0.01933966840690.0235470656806-0.1404530966280.618018520723-0.003591779342120.003597484413660.504089211176-0.02294840105770.5023760414864.93324988735-16.225622240351.5396917798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 3:160))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 161:313))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 323:1065))
4X-RAY DIFFRACTION4chain 'B' and ((resseq 326:439))
5X-RAY DIFFRACTION5chain 'B' and ((resseq 440:591))

+
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