[English] 日本語
Yorodumi
- EMDB-40655: Phosphoinositide phosphate 3 kinase gamma bound with ADP and two ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40655
TitlePhosphoinositide phosphate 3 kinase gamma bound with ADP and two Gbetagamma subunits in State 2
Map data
Sample
  • Complex: PI3K-gamma-ADP bound with two Gbetagamma subunits in State 2
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: phosphatidylinositol-4,5-bisphosphate 3-kinase
    • Protein or peptide: Phosphoinositide 3-kinase regulatory subunit 5
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsPhosphoinositide 3-Kinase / Chemotaxis / Cancer / SIGNALING PROTEIN
Function / homology
Function and homology information


Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Activation of the phototransduction cascade / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase complex, class IB / phosphatidylinositol-mediated signaling / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma ...Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Activation of the phototransduction cascade / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase complex, class IB / phosphatidylinositol-mediated signaling / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / phosphatidylinositol-4,5-bisphosphate 3-kinase / G alpha (q) signalling events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / phosphatidylinositol phosphate biosynthetic process / photoreceptor disc membrane / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / sensory perception of taste / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / retina development in camera-type eye / GTPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / kinase activity / cell population proliferation / G protein-coupled receptor signaling pathway / phosphorylation / GTPase activity / protein-containing complex binding / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Phosphoinositide 3-kinase regulatory subunit 5/6 / Phosphoinositide 3-kinase gamma adapter protein p101 subunit / PIK3 catalytic subunit gamma, adaptor-binding domain / PIK3 catalytic subunit gamma adaptor-binding domain / 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 regulatory subunit 5/6 / Phosphoinositide 3-kinase gamma adapter protein p101 subunit / PIK3 catalytic subunit gamma, adaptor-binding domain / PIK3 catalytic subunit gamma adaptor-binding domain / 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) / 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 / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / Armadillo-type fold / G-protein beta WD-40 repeat / Ubiquitin-like domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Phosphoinositide 3-kinase regulatory subunit 5 / phosphatidylinositol-4,5-bisphosphate 3-kinase / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesSus scrofa (pig) / Bos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsChen C-L / Tesmer JJG / Bandekar SJ / Cash J
Funding support United States, 1 items
OrganizationGrant numberCountry
American Heart Association834497 United States
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Molecular basis for Gβγ-mediated activation of phosphoinositide 3-kinase γ.
Authors: Chun-Liang Chen / Ramizah Syahirah / Sandeep K Ravala / Yu-Chen Yen / Thomas Klose / Qing Deng / John J G Tesmer /
Abstract: The conversion of phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 3,4,5-triphosphate by phosphoinositide 3-kinase γ (PI3Kγ) is critical for neutrophil chemotaxis and cancer metastasis. ...The conversion of phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 3,4,5-triphosphate by phosphoinositide 3-kinase γ (PI3Kγ) is critical for neutrophil chemotaxis and cancer metastasis. PI3Kγ is activated by Gβγ heterodimers released from G protein-coupled receptors responding to extracellular signals. Here we determined cryo-electron microscopy structures of Sus scrofa PI3Kγ-human Gβγ complexes in the presence of substrates/analogs, revealing two Gβγ binding sites: one on the p110γ helical domain and another on the p101 C-terminal domain. Comparison with PI3Kγ alone reveals conformational changes in the kinase domain upon Gβγ binding that are similar to Ras·GTP-induced changes. Assays of variants perturbing the Gβγ binding sites and interdomain contacts altered by Gβγ binding suggest that Gβγ recruits the enzyme to membranes and allosterically regulates activity via both sites. Studies of zebrafish neutrophil migration align with these findings, paving the way for in-depth investigation of Gβγ-mediated activation mechanisms in this enzyme family and drug development for PI3Kγ.
History
DepositionApr 28, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40655.png

Downloads & links

-
Map

FileDownload / File: emd_40655.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 3.2
Minimum - Maximum-27.435865 - 53.777687
Average (Standard dev.)0.0039015424 (±0.99908423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_40655_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_40655_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : PI3K-gamma-ADP bound with two Gbetagamma subunits in State 2

EntireName: PI3K-gamma-ADP bound with two Gbetagamma subunits in State 2
Components
  • Complex: PI3K-gamma-ADP bound with two Gbetagamma subunits in State 2
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: phosphatidylinositol-4,5-bisphosphate 3-kinase
    • Protein or peptide: Phosphoinositide 3-kinase regulatory subunit 5
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

-
Supramolecule #1: PI3K-gamma-ADP bound with two Gbetagamma subunits in State 2

SupramoleculeName: PI3K-gamma-ADP bound with two Gbetagamma subunits in State 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 210 kDa/nm

-
Macromolecule #1: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 37.41693 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String:
MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD INAICFFPNG NA FATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGV TDDGMA VATGSWDSFL KIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

-
Macromolecule #2: phosphatidylinositol-4,5-bisphosphate 3-kinase

MacromoleculeName: phosphatidylinositol-4,5-bisphosphate 3-kinase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 127.573531 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHELE NYEQPVVLRE DNRRRRRRMK PRSTAASLSS MELIPIEFVL PTSQRNTKTP ETALLHVAGH GNVEQMKAQV WLRALETSV SADFYHRLGP DHFLLLYQKK GQWYEIYDKY QVVQTLDCLR YWKVLHRSPG QIHVVQRHAP SEETLAFQRQ L NALIGYDV ...String:
MHHHHHHELE NYEQPVVLRE DNRRRRRRMK PRSTAASLSS MELIPIEFVL PTSQRNTKTP ETALLHVAGH GNVEQMKAQV WLRALETSV SADFYHRLGP DHFLLLYQKK GQWYEIYDKY QVVQTLDCLR YWKVLHRSPG QIHVVQRHAP SEETLAFQRQ L NALIGYDV TDVSNVHDDE LEFTRRRLVT PRMAEVAGRD PKLYAMHPWV TSKPLPEYLL KKITNNCVFI VIHRSTTSQT IK VSADDTP GTILQSFFTK MAKKKSLMDI PESQNERDFV LRVCGRDEYL VGETPIKNFQ WVRQCLKNGE EIHLVLDTPP DPA LDEVRK EEWPLVDDCT GVTGYHEQLT IHGKDHESVF TVSLWDCDRK FRVKIRGIDI PVLPRTADLT VFVEANIQYG QQVL CQRRT SPKPFTEEVL WNVWLEFSIK IKDLPKGALL NLQIYCGKAP ALSGKTSAEM PSPESKGKAQ LLYYVNLLLI DHRFL LRHG EYVLHMWQLS GKGEDQGSFN ADKLTSATNP DKENSMSISI LLDNYCHPIA LPKHRPTPDP EGDRVRAEMP NQLRKQ LEA IIATDPLNPL TAEDKELLWH FRYESLKDPK AYPKLFSSVK WGQQEIVAKT YQLLAKREVW DQSALDVGLT MQLLDCN FS DENVRAIAVQ KLESLEDDDV LHYLLQLVQA VKFEPYHDSA LARFLLKRGL RNKRIGHFLF WFLRSEIAQS RHYQQRFA V ILEAYLRGCG TAMLHDFTQQ VQVIDMLQKV TIDIKSLSAE KYDVSSQVIS QLKQKLENLQ NLNLPQSFRV PYDPGLKAG ALVIEKCKVM ASKKKPLWLE FKCADPTALS NETIGIIFKH GDDLRQDMLI LQILRIMESI WETESLDLCL LPYGCISTGD KIGMIEIVK DATTIAKIQQ STVGNTGAFK DEVLSHWLKE KCPIEEKFQA AVERFVYSCA GYCVATFVLG IGDRHNDNIM I SETGNLFH IDFGHILGNY KSFLGINKER VPFVLTPDFL FVMGTSGKKT SLHFQKFQDV CVKAYLALRH HTNLLIILFS MM LMTGMPQ LTSKEDIEYI RDALTVGKSE EDAKKYFLDQ IEVCRDKGWT VQFNWFLHLV LGIKQGEKHS A

UniProtKB: phosphatidylinositol-4,5-bisphosphate 3-kinase

-
Macromolecule #3: Phosphoinositide 3-kinase regulatory subunit 5

MacromoleculeName: Phosphoinositide 3-kinase regulatory subunit 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 98.497773 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MQPGATTCTE DRIQHALERC LHGLSLSRRS TSWSAGLCLN CWSLQELVSR DPGHFLILLE QILQKTREVQ EKGTYDLLAP LALLFYSTV LCTPHFPPDS DLLLKAARTY HRFLTWPVPY CSICQELLTF IDAELKAPGI SYQRLVRAEQ GLSTRSHRSS T VTVLLLNP ...String:
MQPGATTCTE DRIQHALERC LHGLSLSRRS TSWSAGLCLN CWSLQELVSR DPGHFLILLE QILQKTREVQ EKGTYDLLAP LALLFYSTV LCTPHFPPDS DLLLKAARTY HRFLTWPVPY CSICQELLTF IDAELKAPGI SYQRLVRAEQ GLSTRSHRSS T VTVLLLNP VEVQAEFLDV ADKLSTPGPS PHSAYITLLL HAFQATFGAH CDLSGLHRRL QSKTLAELEA IFTETAEAQE LA SGIGDAA EARQWLRTKL QAVGEKAGFP GVLDTAKPGK LRTIPIPVAR CYTYSWNQDS FDILQEILLK EQELLQPEIL DDE EDEDEE DEEEDLDADG HCAERDSVLS TGSAASHAST LSLASSQASG PTLSRQLLTS FVSGLSDGVD SGYMEDIEES AYER PRRPG GHERRGHRRP GQKFNRIYKL FKSTSQMVLR RDSRSLEGSP DSGPPLRRAG SLCSPLDSPT LPPSRAQRSR SLPQP KLSP QLPGWLLAPA SRHQRRRPFL SGDEDPKAST LRVVVFGSDR ISGKVARAYS NLRRLENNRP LLTRFFKLQF FYVPVK RSR GTGTPTSPAP RSQTPPLPTD APRHPGPAEL GAAPWEESTN DISHYLGMLD PWYERNVLGL MHLPPEVLCQ SLKAEPR PL EGSPAQLPIL ADMLLYYCRF AARPVLLQVY QTELTFITGE KTTEIFIHSL ELGHSAATRA IKASGPGSKR LGIDGDRE A VPLTLQIIYS KGAISGRSRW SNMEKLCTSV NLSKACRQQE ELDSSTEALT LNLTEVVKRQ TPKSKKGFNQ ISTSQIKVD KVQIIGSNSC PFAVCLDQDE RKILQSVIRC EVSPCYKPEK SSLCPPPQRP SYPPAPATPD LCSLLCLPIM TFSGALPGGG GSDYKDDDD K

UniProtKB: Phosphoinositide 3-kinase regulatory subunit 5

-
Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 8.673959 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
HHHHHHMASN NTASIAQARK LVEQLKMEAN IDRIKVSKAA ADLMAYCEAH AKEDPLLTPV PASENPFREK KFFSAIL

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

-
Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4S(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)
200.0 mMNaClSodium chlorideSodium Chloride
10.0 mMMgCl2Magnesium Chloride
1.0 mMC10H16N5O10P2ADPAdenosine diphosphate
5.0 mMBeF3Beryllium Fluoride
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 2.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Specialist opticsEnergy filter - Name: GIF Quantum ER / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Alignment procedureComa free - Residual tilt: 0.01 mrad
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Average exposure time: 3.12 sec. / Average electron dose: 55.0 e/Å2
Details: Images were collected in movie-mode at 40 frames per second
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE / Details: Ab-initio model generated from cryoSPARC
Initial angle assignmentType: COMMON LINE / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: COMMON LINE / Software - Name: cryoSPARC (ver. 3.3.1)
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 181939
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

1e8x

chain_id: A, source_name: SwissModel, initial_model_type: in silico model
chain_id: B, source_name: AlphaFold, initial_model_type: in silico model

6c2y

chain_id: B, source_name: PDB, initial_model_type: experimental model

6c2y

chain_id: G, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: correlation coefficient
Output model

PDB-8soe:
Phosphoinositide phosphate 3 kinase gamma bound with ADP and two Gbetagamma subunits in State 2

+
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