[English] 日本語
Yorodumi
- EMDB-25833: Rabbit RyR1 with AMP-PCP and high Ca2+ embedded in nanodisc in in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25833
TitleRabbit RyR1 with AMP-PCP and high Ca2+ embedded in nanodisc in inactivated conformation (Dataset-B)
Map dataRabbit RyR1 with AMP-PCP and high Ca2+ embedded in nanodisc in inactivated conformation (Dataset-B)
Sample
  • Complex: Rabbit RyR1 with AMP-PCP and high Ca2+ in nanodisc
    • Protein or peptide: RyR1Ryanodine receptor 1
KeywordsRyanodine Receptor / RyR1 / Intracellular Calcium channel / Ca2+ / Inactivation / Excitation-Contraction coupling / TRANSPORT PROTEIN
Function / homology
Function and homology information


ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / cellular response to caffeine / intracellularly gated calcium channel activity / outflow tract morphogenesis ...ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / cellular response to caffeine / intracellularly gated calcium channel activity / outflow tract morphogenesis / organelle membrane / toxic substance binding / voltage-gated calcium channel activity / skeletal muscle fiber development / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / muscle contraction / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / calcium ion binding / ATP binding / membrane / identical protein binding
Similarity search - Function
: / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain ...: / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain / RyR/IP3 receptor binding core, RIH domain superfamily / : / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Ryanodine receptor 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsNayak AR / Samso M
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01 AR068431 United States
Other privateMDA 352845 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)HSSN261200800001E United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM116789 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM116790 United States
CitationJournal: Elife / Year: 2022
Title: Ca inactivation of the mammalian ryanodine receptor type 1 in a lipidic environment revealed by cryo-EM.
Authors: Ashok R Nayak / Montserrat Samsó /
Abstract: Activation of the intracellular Ca channel ryanodine receptor (RyR) triggers a cytosolic Ca surge, while elevated cytosolic Ca inhibits the channel in a negative feedback mechanism. Cryogenic ...Activation of the intracellular Ca channel ryanodine receptor (RyR) triggers a cytosolic Ca surge, while elevated cytosolic Ca inhibits the channel in a negative feedback mechanism. Cryogenic electron microscopy of rabbit RyR1 embedded in nanodiscs under partially inactivating Ca conditions revealed an open and a closed-inactivated conformation. Ca binding to the high-affinity site engages the central and C-terminal domains into a block, which pries the S6 four-helix bundle open. Further rotation of this block pushes S6 toward the central axis, closing (inactivating) the channel. Main characteristics of the Ca-inactivated conformation are downward conformation of the cytoplasmic assembly and tightly knit subunit interface contributed by a fully occupied Ca activation site, two inter-subunit resolved lipids, and two salt bridges between the EF hand domain and the S2-S3 loop validated by disease-causing mutations. The structural insight illustrates the prior Ca activation prerequisite for Ca inactivation and provides for a seamless transition from inactivated to closed conformations.
History
DepositionDec 31, 2021-
Header (metadata) releaseMar 9, 2022-
Map releaseMar 9, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25833.png

Downloads & links

-
Map

FileDownload / File: emd_25833.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRabbit RyR1 with AMP-PCP and high Ca2+ embedded in nanodisc in inactivated conformation (Dataset-B)
Voxel sizeX=Y=Z: 1.075 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.07143278 - 0.1464874
Average (Standard dev.)0.001049067 (±0.0059402306)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 464.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0751.0751.075
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z464.400464.400464.400
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.0710.1460.001

-
Supplemental data

-
Half map: Half Map 1

Fileemd_25833_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map 2

Fileemd_25833_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Rabbit RyR1 with AMP-PCP and high Ca2+ in nanodisc

EntireName: Rabbit RyR1 with AMP-PCP and high Ca2+ in nanodisc
Components
  • Complex: Rabbit RyR1 with AMP-PCP and high Ca2+ in nanodisc
    • Protein or peptide: RyR1Ryanodine receptor 1

-
Supramolecule #1: Rabbit RyR1 with AMP-PCP and high Ca2+ in nanodisc

SupramoleculeName: Rabbit RyR1 with AMP-PCP and high Ca2+ in nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Purified RyR1 was reconstituted with membrane scaffold protein MSP1E3D1 and POPC.
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Strain: New Zealand White / Organ: Skeletal Muscle / Organelle: Sarcoplasmic Reticulum / Location in cell: Sarcoplasmic Reticulum membrane
Molecular weightTheoretical: 2.26 MDa

-
Macromolecule #1: RyR1

MacromoleculeName: RyR1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
SequenceString: MGDGGEGEDE VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFTL EQSLSVRALQ EMLANTVEAG VESSQGGGHR TLLYGHAILL RHAHSRMYLS C LTTSRSMT DKLAFDVGLQ EDATGEACWW TMHPASKQRS EGEKVRVGDD ...String:
MGDGGEGEDE VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFTL EQSLSVRALQ EMLANTVEAG VESSQGGGHR TLLYGHAILL RHAHSRMYLS C LTTSRSMT DKLAFDVGLQ EDATGEACWW TMHPASKQRS EGEKVRVGDD LILVSVSSER YL HLSTASG ELQVDASFMQ TLWNMNPICS CCEEGYVTGG HVLRLFHGHM DECLTISAAD SDD QRRLVY YEGGAVCTHA RSLWRLEPLR ISWSGSHLRW GQPLRIRHVT TGRYLALTED QGLV VVDAC KAHTKATSFC FRVSKEKLDT APKRDVEGMG PPEIKYGESL CFVQHVASGL WLTYA APDP KALRLGVLKK KAILHQEGHM DDALFLTRCQ QEESQAARMI HSTAGLYNQF IKGLDS FSG KPRGSGPPAG PALPIEAVIL SLQDLIGYFE PPSEELQHEE KQSKLRSLRN RQSLFQE EG MLSLVLNCID RLNVYTTAAH FAEYAGEEAA ESWKEIVNLL YELLASLIRG NRANCALF S TNLDWVVSKL DRLEASSGIL EVLYCVLIES PEVLNIIQEN HIKSIISLLD KHGRNHKVL DVLCSLCVCN GVAVRSNQDL ITENLLPGRE LLLQTNLINY VTSIRPNIFV GRAEGSTQYG KWYFEVMVD EVVPFLTAQA THLRVGWALT EGYSPYPGGG EGWGGNGVGD DLYSYGFDGL H LWTGHVAR PVTSPGQHLL APEDVVSCCL DLSVPSISFR INGCPVQGVF EAFNLDGLFF PV VSFSAGV KVRFLLGGRH GEFKFLPPPG YAPCHEAVLP RERLRLEPIK EYRREGPRGP HLV GPSRCL SHTDFVPCPV DTVQIVLPPH LERIREKLAE NIHELWALTR IEQGWTYGPV RDDN KRLHP CLVNFHSLPE PERNYNLQMS GETLKTLLAL GCHVGMADEK AEDNLKKTKL PKTYM MSNG YKPAPLDLSH VRLTPAQTTL VDRLAENGHN VWARDRVAQG WSYSAVQDIP ARRNPR LVP YRLLDEATKR SNRDSLCQAV RTLLGYGYNI EPPDQEPSQV ENQSRWDRVR IFRAEKS YT VQSGRWYFEF EAVTTGEMRV GWARPELRPD VELGADELAY VFNGHRGQRW HLGSEPFG R PWQSGDVVGC MIDLTENTII FTLNGEVLMS DSGSETAFRE IEIGDGFLPV CSLGPGQVG HLNLGQDVSS LRFFAICGLQ EGFEPFAINM QRPVTTWFSK SLPQFEPVPP EHPHYEVARM DGTVDTPPC LRLAHRTWGS QNSLVEMLFL RLSLPVQFHQ HFRCTAGATP LAPPGLQPPA E DEARAAEP DPDYENLRRS AGGWGEAEGG KEGTAKEGTP GGTPQPGVEA QPVRAENEKD AT TEKNKKR GFLFKAKKAA MMTQPPATPA LPRLPHDVVP ADNRDDPEII LNTTTYYYSV RVF AGQEPS CVWVGWVTPD YHQHDMNFDL SKVRAVTVTM GDEQGNVHSS LKCSNCYMVW GGDF VSPGQ QGRISHTDLV IGCLVDLATG LMTFTANGKE SNTFFQVEPN TKLFPAVFVL PTHQN VIQF ELGKQKNIMP LSAAMFLSER KNPAPQCPPR LEVQMLMPVS WSRMPNHFLQ VETRRA GER LGWAVQCQDP LTMMALHIPE ENRCMDILEL SERLDLQRFH SHTLRLYRAV CALGNNR VA HALCSHVDQA QLLHALEDAH LPGPLRAGYY DLLISIHLES ACRSRRSMLS EYIVPLTP E TRAITLFPPG RKGGNARRHG LPGVGVTTSL RPPHHFSPPC FVAALPAAGV AEAPARLSP AIPLEALRDK ALRMLGEAVR DGGQHARDPV GGSVEFQFVP VLKLVSTLLV MGIFGDEDVK QILKMIEPE VFTEEEEEEE EEEEEEEEEE EDEEEKEEDE EEEEKEDAEK EEEEAPEGEK E DLEEGLLQ MKLPESVKLQ MCNLLEYFCD QELQHRVESL AAFAERYVDK LQANQRSRYA LL MRAFTMS AAETARRTRE FRSPPQEQIN MLLHFKDEAD EEDCPLPEDI RQDLQDFHQD LLA HCGIQL EGEEEEPEEE TSLSSRLRSL LETVRLVKKK EEKPEEELPA EEKKPQSLQE LVSH MVVRW AQEDYVQSPE LVRAMFSLLH RQYDGLGELL RALPRAYTIS PSSVEDTMSL LECLG QIRS LLIVQMGPQE ENLMIQSIGN IMNNKVFYQH PNLMRALGMH ETVMEVMVNV LGGGET KEI RFPKMVTSCC RFLCYFCRIS RQNQRSMFDH LSYLLENSGI GLGMQGSTPL DVAAASV ID NNELALALQE QDLEKVVSYL AGCGLQSCPM LLAKGYPDIG WNPCGGERYL DFLRFAVF V NGESVEENAN VVVRLLIRKP ECFGPALRGE GGSGLLAAIE EAIRISEDPA RDGPGVRRD RRREHFGEEP PEENRVHLGH AIMSFYAALI DLLGRCAPEM HLIQAGKGEA LRIRAILRSL VPLDDLVGI ISLPLQIPTL GKDGALVQPK MSASFVPDHK ASMVLFLDRV YGIENQDFLL H VLDVGFLP DMRAAASLDT ATFSTTEMAL ALNRYLCLAV LPLITKCAPL FAGTEHRAIM VD SMLHTVY RLSRGRSLTK AQRDVIEDCL MALCRYIRPS MLQHLLRRLV FDVPILNEFA KMP LKLLTN HYERCWKYYC LPTGWANFGV TSEEELHLTR KLFWGIFDSL AHKKYDQELY RMAM PCLCA IAGALPPDYV DASYSSKAEK KATVDAEGNF DPRPVETLNV IIPEKLDSFI NKFAE YTHE KWAFDKIQNN WSYGENVDEE LKTHPMLRPY KTFSEKDKEI YRWPIKESLK AMIAWE WTI EKAREGEEER TEKKKTRKIS QTAQTYDPRE GYNPQPPDLS GVTLSRELQA MAEQLAE NY HNTWGRKKKQ ELEAKGGGTH PLLVPYDTLT AKEKARDREK AQELLKFLQM NGYAVTRG L KDMELDTSSI EKRFAFGFLQ QLLRWMDISQ EFIAHLEAVV SSGRVEKSPH EQEIKFFAK ILLPLINQYF TNHCLYFLST PAKVLGSGGH ASNKEKEMIT SLFCKLAALV RHRVSLFGTD APAVVNCLH ILARSLDART VMKSGPEIVK AGLRSFFESA SEDIEKMVEN LRLGKVSQAR T QVKGVGQN LTYTTVALLP VLTTLFQHIA QHQFGDDVIL DDVQVSCYRT LCSIYSLGTT KN TYVEKLR PALGECLARL AAAMPVAFLE PQLNEYNACS VYTTKSPRER AILGLPNSVE EMC PDIPVL DRLMADIGGL AESGARYTEM PHVIEITLPM LCSYLPRWWE RGPEAPPPAL PAGA PPPCT AVTSDHLNSL LGNILRIIVN NLGIDEATWM KRLAVFAQPI VSRARPELLH SHFIP TIGR LRKRAGKVVA EEEQLRLEAK AEAEEGELLV RDEFSVLCRD LYALYPLLIR YVDNNR AHW LTEPNANAEE LFRMVGEIFI YWSKSHNFKR EEQNFVVQNE INNMSFLTAD SKSKMAK AG DAQSGGSDQE RTKKKRRGDR YSVQTSLIVA TLKKMLPIGL NMCAPTDQDL IMLAKTRY A LKDTDEEVRE FLQNNLHLQG KVEGSPSLRW QMALYRGLPG REEDADDPEK IVRRVQEVS AVLYHLEQTE HPYKSKKAVW HKLLSKQRRR AVVACFRMTP LYNLPTHRAC NMFLESYKAA WILTEDHSF EDRMIDDLSK AGEQEEEEEE VEEKKPDPLH QLVLHFSRTA LTEKSKLDED Y LYMAYADI MAKSCHLEEG GENGEAEEEE VEVSFEEKEM EKQRLLYQQS RLHTRGAAEM VL QMISACK GETGAMVSST LKLGISILNG GNAEVQQKML DYLKDKKEVG FFQSIQALMQ TCS VLDLNA FERQNKAEGL GMVNEDGTVI NRQNGEKVMA DDEFTQDLFR FLQLLCEGHN NDFQ NYLRT QTGNTTTINI IICTVDYLLR LQESISDFYW YYSGKDVIEE QGKRNFSKAM SVAKQ VFNS LTEYIQGPCT GNQQSLAHSR LWDAVVGFLH VFAHMMMKLA QDSSQIELLK ELLDLQ KDM VVMLLSLLEG NVVNGMIARQ MVDMLVESSS NVEMILKFFD MFLKLKDIVG SEAFQDY VT DPRGLISKKD FQKAMDSQKQ FTGPEIQFLL SCSEADENEM INFEEFANRF QEPARDIG F NVAVLLTNLS EHVPHDPRLR NFLELAESIL EYFRPYLGRI EIMGASRRIE RIYFEISET NRAQWEMPQV KESKRQFIFD VVNEGGEAEK MELFVSFCED TIFEMQIAAQ ISEPEGEPEA DEDEGMGEA AAEGAEEGAA GAEGAAGTVA AGATARLAAA AARALRGLSY RSLRRRVRRL R RLTAREAA TALAALLWAV VARAGAAGAG AAAGALRLLW GSLFGGGLVE GAKKVTVTEL LA GMPDPTS DEVHGEQPAG PGGDADGAGE GEGEGDAAEG DGDEEVAGHE AGPGGAEGVV AVA DGGPFR PEGAGGLGDM GDTTPAEPPT PEGSPILKRK LGVDGEEEEL VPEPEPEPEP EPEK ADEEN GEKEEVPEAP PEPPKKAPPS PPAKKEEAGG AGMEFWGELE VQRVKFLNYL SRNFY TLRF LALFLAFAIN FILLFYKVSD SPPGEDDMEG SAAGDLAGAG SGGGSGWGSG AGEEAE GDE DENMVYYFLE ESTGYMEPAL WCLSLLHTLV AFLCIIGYNC LKVPLVIFKR EKELARK LE FDGLYITEQP GDDDVKGQWD RLVLNTPSFP SNYWDKFVKR KVLDKHGDIF GRERIAEL L GMDLASLEIT AHNERKPDPP PGLLTWLMSI DVKYQIWKFG VIFTDNSFLY LGWYMVMSL LGHYNNFFFA AHLLDIAMGV KTLRTILSSV THNGKQLVMT VGLLAVVVYL YTVVAFNFFR KFYNKSEDE DEPDMKCDDM MTCYLFHMYV GVRAGGGIGD EIEDPAGDEY ELYRVVFDIT F FFFVIVIL LAIIQGLIID AFGELRDQQE QVKEDMETKC FICGIGSDYF DTTPHGFETH TL EEHNLAN YMFFLMYLIN KDETEHTGQE SYVWKMYQER CWDFFPAGDC FRKQYEDQLS

UniProtKB: Ryanodine receptor 1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4.35 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMMOPS (pH7.4)
635.0 mMPotassium ChlorideKCL
2.0 mMDithiothreitol
2.0 mMAMP-PCP
3.7 mMCalcium ChlorideCaCl2
GridModel: Quantifoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Sample was blotted for 1 second on both sides with Whatman hardened ashless filter paper with blot force 2..
DetailsPurified RyR1 was reconstituted with membrane scaffold protein MSP1E3D1 and POPC at a 1:2:50 molar ratio.

-
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: 2.5 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 1346 / Average exposure time: 14.0 sec. / Average electron dose: 70.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 35554
Startup modelType of model: EMDB MAP
EMDB ID:

22616

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 1 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 14669
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

+
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