[English] 日本語
Yorodumi
- EMDB-45116: Composite map of mink RyR3 in closed conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45116
TitleComposite map of mink RyR3 in closed conformation
Map datacomposite map generated by combining four local refinement maps in UCSF ChimeraX
Sample
  • Complex: mink RyR3 + FKBP12.6
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
    • Protein or peptide: Ryanodine receptor 3
  • Ligand: ZINC ION
  • Ligand: CHLORIDE ION
KeywordsRyR3 / Ryanodine Receptor / calcium channel / ion channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of release of sequestered calcium ion into cytosol / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to redox state ...positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of release of sequestered calcium ion into cytosol / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to redox state / 'de novo' protein folding / negative regulation of heart rate / FK506 binding / positive regulation of axon regeneration / smooth muscle contraction / response to vitamin E / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / smooth endoplasmic reticulum / calcium channel inhibitor activity / striated muscle contraction / T cell proliferation / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / sarcoplasmic reticulum membrane / release of sequestered calcium ion into cytosol / calcium channel regulator activity / calcium channel complex / protein maturation / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / calcium-mediated signaling / sarcolemma / response to hydrogen peroxide / Stimuli-sensing channels / Z disc / intracellular calcium ion homeostasis / positive regulation of cytosolic calcium ion concentration / protein refolding / transmembrane transporter binding / calmodulin binding / signaling receptor binding / calcium ion binding / membrane / cytoplasm
Similarity search - Function
Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / 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, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / 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. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Ryanodine receptor 3 / Peptidyl-prolyl cis-trans isomerase FKBP1B
Similarity search - Component
Biological speciesNeogale vison (American mink) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsChen YS / Van Petegem F
Funding support Canada, 3 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-159601 Canada
Fonds de Recherche du Quebec - Sante (FRQS)BF7-310936 Canada
Other governmentRT-2023-3133
CitationJournal: Nat Commun / Year: 2024
Title: Cryo-EM investigation of ryanodine receptor type 3.
Authors: Yu Seby Chen / Maricela Garcia-Castañeda / Maria Charalambous / Daniela Rossi / Vincenzo Sorrentino / Filip Van Petegem /
Abstract: Ryanodine Receptor isoform 3 (RyR3) is a large ion channel found in the endoplasmic reticulum membrane of many different cell types. Within the hippocampal region of the brain, it is found in ...Ryanodine Receptor isoform 3 (RyR3) is a large ion channel found in the endoplasmic reticulum membrane of many different cell types. Within the hippocampal region of the brain, it is found in dendritic spines and regulates synaptic plasticity. It controls myogenic tone in arteries and is upregulated in skeletal muscle in early development. RyR3 has a unique functional profile with a very high sensitivity to activating ligands, enabling high gain in Ca-induced Ca release. Here we solve high-resolution cryo-EM structures of RyR3 in non-activating and activating conditions, revealing structural transitions that occur during channel opening. Addition of activating ligands yields only open channels, indicating an intrinsically high open probability under these conditions. RyR3 has reduced binding affinity to the auxiliary protein FKBP12.6 due to several sequence variations in the binding interface. We map disease-associated sequence variants and binding sites for known pharmacological agents. The N-terminal region contains ligand binding sites for a putative chloride anion and ATP, both of which are targeted by sequence variants linked to epileptic encephalopathy.
History
DepositionMay 29, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45116.png

Downloads & links

-
Map

FileDownload / File: emd_45116.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map generated by combining four local refinement maps in UCSF ChimeraX
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 512 pix.
= 478.72 Å		0.94 Å/pix.
x 512 pix.
= 478.72 Å		0.94 Å/pix.
x 512 pix.
= 478.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.935 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.068
Minimum - Maximum0.0 - 0.6177594
Average (Standard dev.)0.001696638 (±0.014113377)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 478.72 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : mink RyR3 + FKBP12.6

EntireName: mink RyR3 + FKBP12.6
Components
  • Complex: mink RyR3 + FKBP12.6
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
    • Protein or peptide: Ryanodine receptor 3
  • Ligand: ZINC ION
  • Ligand: CHLORIDE ION

-
Supramolecule #1: mink RyR3 + FKBP12.6

SupramoleculeName: mink RyR3 + FKBP12.6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Neogale vison (American mink)
Molecular weightTheoretical: 2.25 MDa

-
Macromolecule #1: Peptidyl-prolyl cis-trans isomerase FKBP1B

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase FKBP1B / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.939562 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SNAGVEIETI SPGDGRTFPK KGQTCVVHYT GMLQNGKKFD SSRDRNKPFK FRIGKQEVIK GFEEGAAQMS LGQRAKLTCT PDVAYGATG HPGVIPPNAT LIFDVELLNL E

UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP1B

-
Macromolecule #2: Ryanodine receptor 3

MacromoleculeName: Ryanodine receptor 3 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Neogale vison (American mink)
Molecular weightTheoretical: 551.217375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAEGGEGGED EIQFLRTEDE VVLQCIANIH KEQRKFCLAA EGLGNRLCFL EPTSEAKYVP PDLCVCNFVL EQSLSVRALQ EMLANTGEN GGEGAAQGGG HRTLLYGHAI LLRHSFSGMY LTCLTTSRSQ TDKLAFDVGL RENATGEACW WTIHPASKQR S EGEKVRIG ...String:
MAEGGEGGED EIQFLRTEDE VVLQCIANIH KEQRKFCLAA EGLGNRLCFL EPTSEAKYVP PDLCVCNFVL EQSLSVRALQ EMLANTGEN GGEGAAQGGG HRTLLYGHAI LLRHSFSGMY LTCLTTSRSQ TDKLAFDVGL RENATGEACW WTIHPASKQR S EGEKVRIG DDLILVSVSS ERYLHLSVSN GNVQVDASFM QTLWNVHPTC SGSSIEEGYL LGGHVVRLFH GHDECLTIPS TD QNDAQHR RIFYEAGGAG TRARSLWRVE PLRISWSGSN IRWGQAFRLR HITTGHYLAL TEDQGLLLQD RAKSDTKSTA FSF RASKEI KEKLDSSHKR DIEGMGVPEI KYGDSVCFVQ HIASGLWVTY KAQDAKTSRL GPLKRKVILH QEGHMDDGLT LQRC QREES QAARIIRNTT ALFSQFVSGN NRAAAPVTLP IQEVLQTLQD LIAYFQPPEE EMQHEDKQNK LRSLKNRQNL FKEEG MLAL VLNCIDRLNI YNSVAHFAGI AREESGMAWK EILNLLYKLL AALIRGNRNN CAQFSNNLDW LISKLDRLES SSGILE VLH CILIESPEAL NLIAEGHIKS IISLLDKHGR NHKVLDVLCS LCLCNGVAVR ANQNLICDNL LPRRNLLLQT RLINDVT SI RPNIFLGVAE GSAQYKKWYF ELIIDQVDPF LTAEPTHLRV GWASSSGYAP YPGGGEGWGG NGVGDDLYSY GFDGLHLW S GRIPRAVASI NLHLLRSDDV VSCCLDLGVP SISFRINGQP VQGMFENFNT DGLFFPVVSF SAGVKVRFLT GGRHGEFKF LPPSGYAPCY EALLPKEKMR LEPVKEYKRD AEGIRDLLGT TQSLSQASFI PCPIDTSQVV LPPHLEKIRD RLAENIHELW GMNKIELGW TFGKIRDDNK RQHPCLVEFS KLPETEKNYN LQMSTETLKT LLALGCHIAH VNPAAEEDLK KVKLPKNYMM S NGYKPAPL DLSDVKLLPP QEVLVDKLAE NAHNVWAKDR IKQGWTYGIQ QDLKNKRNPR LVPYALLDER TKKSNRDSLR EA VRTFVGY GYNIEPSDQE LADPAVEKVS IDKIRFFRVE WSYAVRSGKW YFEFEVVTGG DMRVGWARPG CRPDIELGAD DQA FVFEGS RGQRWHQGSG YFGRTWQPGD VVGCMINLDD ASMIFTLNGE LLITNKGSEL AFADYEIENG FVPICSLGLS QIGR MNLGM DASTFKFYTM CGLQEGFEPF AVNMNRDVAM WFSKRLPTFV NVPKDHPHIE VVRIDGTMDS PPCLKVTHKT FGTQN SNAS MIYCRLSMPV ECHSSFSHSP CLDSEAFQKR KQMQEILSHT TTQCYYAIRI FAGQDPSCVW VGWVTPDYHL YSEKFD LNK NCTVTVTLGD ERGRVHESVK RSNCYMVWGG DIVATSQRSS RSNVDLEIGC LVDLAMGMLS FSANGRELGT CYQVEPN TK VFPAVFLQPT STALFQFELG KLKNAMPLSA AIFKSEEKNP VPQCPPRLDV QTIQPVLWSR MPSSFLKVET ERVSERHG W AVQCLEPLQM MALHIPEENR CVDILELCEQ EDLMQFHYHT LRLYSAVCAL GNSRVAYALC GHVDLSQLFY AIDNKYLPG LLRSGFYDLL ISIHLANAKE RKLMMKNEYI IPITSATRKI RLYPDESKRH GLPGVGLRTC LKPGFRFSTP CFVVTGEEHQ KQSPEIPLE ILKTKALSML TEAVQHSGAH IRDPVGGSVE FQFVPVLKLI GTLLVMGVFD DDDIRQILLL IDPSVFGEHS V ETEDGAEK EEVTQVEEKA VEAGEKAGKE APVKGLLQTR LPESVKLQMC ELLSYLCDCE LQHRVEAIVA FGDIYVSKLQ AN QKSRYNE LMQALNMSAA LTARKTREFR SPPQEQINML LNFQLGENCP CPEEIREELY DFHEDLLIHC GVPLEEEEEE EED TSWAGK LRALVYKIKG PPKPEKEQPT EEEERCPTTL KELISQTMIR WAQEDQIQDA ELVRMMFSLL QRQYDSIGEL LQAL RKTYT ISQASVSDTI NLLAALGQIR CLLSVRMGKE EELLMINGLG DIMNNKVFYQ HPNLMRVLGM HETVMEVMVD VLGAE KSQI AFPKMVASCC RFLCYFCRIS RQNQKAMFEH LSYLLENSSV GLASPSMRGS TPLDVAASSV MDNNELALGL EEPDLE KVV TYLAGCGLQS CPMLLAKGYP DVGWNPIEGE RYLSFLRFAV FVNSESVEEN ASVVVKLLIR RPECFGPALR GEGGNGL LA AMQGAIKISE NPALDLPSQG YKREVMEDGE DEEIVHMGNA IMSFYSALID LLGRCAPEMH LIQTGKGEAI RIRSILRS L VPTEDLVGII SIPLKLPSLN KDGSISEPDM AANFCPDHKA PMVLFLDRVY GIKDQTFLLH LLEVGFLPDL RASASLDTV SLSTTEAALA LNRYLCSAVL PLLTRCAPLF AGTEHYTSLI DSTLQTIYRL SKGRSLTKAQ RDTIEECLLA ICNHLRPSML QQLLRRLVF DVPQLNEYCK MPLKLLTNHY EQCWKYYCLP SGWGSYGLAV EEELHLTEKL FWGIFDSLSH KKYDPDLFRM A LPCLSAIA GALPPDYLDT RISATLEKQI SVDADGNFDP KPINTMNFSL PEKWEYIVTK YAEHSHDKWA CDKSQNGWKY GI SLDENVK THPLIRPFKT LTEKEKEIYR WPARESLKTM LAVGWSVERT KEGEALVQQR ENEKLRSVSQ ASQGNSYSPA PLD LSNVVL SRELQGMVEV VAENYHNIWA KKKKLELESK GGGSHPLLVP YDTLTAKEKF RDREKAQDLF KFLQVNGIVV SRGV KDMEL DASSMEKRFA YKFLKKILKY VDSAQEFIAH LEAIVSSGKT EKSPHDQEIK FFAKVLLPLV DQYFTNHHLY FLSSP LKPL SSSGYASHKE KEMVASLFCK LAALVRHRIS LFGSDSTTMV SCLHILAQTL DTRTVMKSGS ELVKAGLRAF FENAAE DLE KTSENLKLGK FTHSRTQIKG VSQNINYTTV ALLPILTSIF EHVAQHQFGV DLLLGDVQIS CYHILCSLYS LGTGKNI YV ERQRPALGEC LASLAAAIPV AFLEPTLNRY NPLSVFNTKT PRERSILGMP DTVEEMCPDI PQLEGLMKEI SDLAESGA R YTEMPHVIEV ILPMLCNYLS YWWERGPEHL PPSTGPWCTK VTSEHLSVIL GNILKIINNN LGIDEASWMK RIAVYAQPI ISKARPDLLK SHFIPTLEKL KKKAVKTVQE EEQLKADTKG DTQEAELLIL DEFAVLCRDL YAFYPMLIRY VDNNRSNWLK SPSADSDQL FRMVAEVFIL WCKSHNFKRE EQNFVIQNEI NNLAFLTGDS KSKMSKSGGQ DQERKKTKRR GDLYSIQTSL I VAALKKML PIGLNMCTPG DQELISLAKS RYSYRDTDEE VKEHLRNNLH LQEKSDDPAV KWQLNLYKDV LKSEEPFNAE KT IERVQRI SAAVFHLEQV EQPLRSKKAV WHKLLSKQRK RAVVACFRMA PLYNLPRHKI NNFFLSTFQR VWLEKVNEKT QYD RLIPIL MKSPKVEEEE EEEMEKQPDP LHQIILHFSR NALTERSKLE DDPLYTSYSS MMAKSCQSGE DEEEEEDKEK TFEE KEMEK QKTLYQQARL HERGAAEMVL QMISASKGEM SPMVVETLKL GIAILNGGNA GVQQKMLDYL KEKKDAGFFQ SLSGL MQSC SVLDLNAFER QNKAEGLGMV TEEGTREKVL QNDEFTRDLF RFLQLLCEGH NSDFQNFLRT QMGNTTTINV IISTVD YLL RLQESISDFY WYYSGKDIID ESGQHNFSKA LAVTKQIFNS LTEYIQGPCI GNQQSLAHSR LWDAVVGFLH VFANMQM KL SQDSSQIELL KELLDLLQDM VVMLLSLLEG NVVNGTIGKQ MVDTLVESST NVEMILKFFD MFLKLKDLTS SDTFKEYD P DGKGIISKKE FQKAMEGQKQ YTQSEIDFLL SCAEADENDM FNYVDFVDRF HEPAKDIGFN VAVLLTNLSE HMPNDSRLK CLLDPAGSVL NYFEPYLGRI EIMGGAKKIE RVYFEISESS RTQWEKPQVK ESKRQFIFDV VNEGGEQEKM ELFVNFCEDT IFEMQLASQ ISETDSAERP DEEEEEDEDS SYVLEIEGEE EDDKSFESAS AFAMACASVK RNVANFLKKA TLKNLRKQYR K VKKMTVKE LVKVFFSFFW MLFVGLFRLF FTILGGIFQI LWNTVFGGGL VEGAKNIRVT KILGDMPDPT QFGIHDDALD AE RAEVTEP GVPPELIHFV KGEKGDADIM SDLFGFHPKK EGGLKHGPEG GLGDLSEIIG KDEPPTLEST VRKKRKAQAA EMK AAHEAE GKVEPEKTDL EDGEKEDTAK EEEQAEALWA DVTKKKKRRR GQKVEKPEAF MANFFKGLEI YQTKLLHYLA RNFY NLRFL ALFVAFAINF ILLFYKVTEE PVEEETEDVA NLWNSFTDEE EEEAMVFFVL QESTGYMAPA LRALAIIHTV ISLVC VVGY YCLKVPLVVF KREKEIARKL EFDGLYITEQ PSEDDIKGQW DRLVINTPSF PNNYWDKFVK RKVINKYGDL YGAERI AEL LGLDKNALDF SPVEASKAEA ASLVSWLSSI DMKYHIWKLG VVFTDNSFLY LAWYTTMSVL GHYNNFFFAA HLLDIAM GF KTLRTILSSV THNGKQLVLT VGLLAVVVYL YTVVAFNFFR KFYNKSEDDD EPDMKCDDMM TCYLFHMYVG VRAGGGIG D EIEDPAGDPY EMYRIVFDIT FFFFVIVILL AIIQGLIIDA FGELRDQQEQ VREDMETKCF ICGIGNDYFD TTPHGFETH TLQEHNLANY LFFLMYLINK DETEHTGQES YVWKMYQERC WDFFPAGDCF RKQYEDQLG

UniProtKB: Ryanodine receptor 3

-
Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #4: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 7.5
Details: 20 mM HEPES pH 7.5, 250 mM NaCl, 2 mM DTT, 0.02% GDN, 5 mM EGTA, 1:1000 diluted protease inhibitor cocktail
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: blotted for 3 s (blot force of 7 to 10) using ashless blotting paper (Whatman).

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 10545 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 201998
Startup modelType of model: INSILICO MODEL
In silico model: Generated by stochastic gradient descent using ab initio reconstruction job type in cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 109618
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.0)

-
Atomic model buiding 1

Initial modelPDB ID:

5413


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation coefficient
Output model

PDB-9c1e:
Mink RyR3 in closed conformation

+
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