[English] 日本語
Yorodumi
- EMDB-25361: Composite map of ciliary C2 central pair apparatus isolated from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25361
TitleComposite map of ciliary C2 central pair apparatus isolated from Chlamydomonas reinhardtii
Map dataCiliary C2 central pair apparatus isolated from Chlamydomonas reinhardtii
Sample
  • Complex: C2 central pair apparatus complex
    • Protein or peptide: x 18 types
  • Ligand: x 3 types
Keywordscilia / microtubule / STRUCTURAL PROTEIN
Function / homology
Function and homology information


axonemal central pair / axonemal outer doublet / positive regulation of cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / establishment of protein localization to organelle / cilium movement / axoneme assembly / axonemal microtubule / motile cilium / microtubule associated complex ...axonemal central pair / axonemal outer doublet / positive regulation of cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / establishment of protein localization to organelle / cilium movement / axoneme assembly / axonemal microtubule / motile cilium / microtubule associated complex / regulation of cytoskeleton organization / axoneme / cilium assembly / ciliary basal body / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule binding / microtubule / transcription coactivator activity / hydrolase activity / GTPase activity / calcium ion binding / regulation of DNA-templated transcription / GTP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
MYCBP-associated protein / Protein FAM228 / MYCBP-associated protein family / Associate of Myc 1 / Flagellar-associated PapD-like / CH-like domain in sperm protein / CH-like domain in sperm protein / CFA20 domain / Cilia- and flagella-associated protein 20/CFAP20DC / CFA20 domain ...MYCBP-associated protein / Protein FAM228 / MYCBP-associated protein family / Associate of Myc 1 / Flagellar-associated PapD-like / CH-like domain in sperm protein / CH-like domain in sperm protein / CFA20 domain / Cilia- and flagella-associated protein 20/CFAP20DC / CFA20 domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Quinoprotein alcohol dehydrogenase-like superfamily / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Tetratricopeptide-like helical domain superfamily / G-protein beta WD-40 repeat / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein / Calponin-homology (CH) domain-containing protein / Cilia- and flagella-associated protein 70 / Abnormal spindle-like microcephaly-associated protein ASH domain-containing protein / Flagellar associated protein / Flagellar associated protein / EF-hand domain-containing protein / Predicted protein / Flagellar associated protein 174 ...Uncharacterized protein / Uncharacterized protein / Calponin-homology (CH) domain-containing protein / Cilia- and flagella-associated protein 70 / Abnormal spindle-like microcephaly-associated protein ASH domain-containing protein / Flagellar associated protein / Flagellar associated protein / EF-hand domain-containing protein / Predicted protein / Flagellar associated protein 174 / Cilia- and flagella-associated protein 20 / Flagellar associated protein / Tubulin beta-1/beta-2 chain / Tubulin alpha-1 chain / Flagellar WD repeat-containing protein Pf20
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGui M / Wang X / Dutcher SK / Brown A / Zhang R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Ciliary central apparatus structure reveals mechanisms of microtubule patterning.
Authors: Miao Gui / Xiangli Wang / Susan K Dutcher / Alan Brown / Rui Zhang /
Abstract: A pair of extensively modified microtubules form the central apparatus (CA) of the axoneme of most motile cilia, where they regulate ciliary motility. The external surfaces of both CA microtubules ...A pair of extensively modified microtubules form the central apparatus (CA) of the axoneme of most motile cilia, where they regulate ciliary motility. The external surfaces of both CA microtubules are patterned asymmetrically with large protein complexes that repeat every 16 or 32 nm. The composition of these projections and the mechanisms that establish asymmetry and longitudinal periodicity are unknown. Here, by determining cryo-EM structures of the CA microtubules, we identify 48 different CA-associated proteins, which in turn reveal mechanisms for asymmetric and periodic protein binding to microtubules. We identify arc-MIPs, a novel class of microtubule inner protein, that bind laterally across protofilaments and remodel tubulin structure and lattice contacts. The binding mechanisms utilized by CA proteins may be generalizable to other microtubule-associated proteins. These structures establish a foundation to elucidate the contributions of individual CA proteins to ciliary motility and ciliopathies.
History
DepositionNov 1, 2021-
Header (metadata) releaseApr 13, 2022-
Map releaseApr 13, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_25361.png

Downloads & links

-
Map

FileDownload / File: emd_25361.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCiliary C2 central pair apparatus isolated from Chlamydomonas reinhardtii
Voxel sizeX=Y=Z: 1.39 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum0.0 - 1.9984493
Average (Standard dev.)0.00584893 (±0.04987752)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 711.68 Å
α=β=γ: 90.0 °

-
Supplemental data

+
Mask #1

Fileemd_25361_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Additional map 1

Fileemd_25361_additional_1.map
AnnotationAdditional map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Additional map 2

Fileemd_25361_additional_2.map
AnnotationAdditional map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Additional map 3

Fileemd_25361_additional_3.map
AnnotationAdditional map 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Additional map 4

Fileemd_25361_additional_4.map
AnnotationAdditional map 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: consensus refinement

Fileemd_25361_additional_5.map
Annotationconsensus refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: mask for fsc curve

Fileemd_25361_additional_6.map
Annotationmask for fsc curve
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Additional map 7

Fileemd_25361_additional_7.map
AnnotationAdditional map 7
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Additional map 8

Fileemd_25361_additional_8.map
AnnotationAdditional map 8
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Additional map 9

Fileemd_25361_additional_9.map
AnnotationAdditional map 9
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : C2 central pair apparatus complex

EntireName: C2 central pair apparatus complex
Components
  • Complex: C2 central pair apparatus complex
    • Protein or peptide: Tubulin beta
    • Protein or peptide: Tubulin alpha
    • Protein or peptide: FAP196
    • Protein or peptide: FAP213
    • Protein or peptide: FAP225
    • Protein or peptide: FAP239
    • Protein or peptide: FAP388
    • Protein or peptide: FAP424
    • Protein or peptide: Cilia- and flagella-associated protein 20
    • Protein or peptide: Flagellar WD repeat-containing protein Pf20
    • Protein or peptide: Flagellar associated protein
    • Protein or peptide: FAP65
    • Protein or peptide: FAP70
    • Protein or peptide: FAP147
    • Protein or peptide: FAP178
    • Protein or peptide: Unknown protein
    • Protein or peptide: Unknown protein
    • Protein or peptide: Unknown protein
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: C2 central pair apparatus complex

SupramoleculeName: C2 central pair apparatus complex / type: complex / ID: 1 / Parent: 0
Macromolecule list: #1-#2, #13-#18, #3, #11-#12, #7-#10, #4-#6
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

+
Macromolecule #1: Tubulin beta

MacromoleculeName: Tubulin beta / type: protein_or_peptide / ID: 1 / Number of copies: 74 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 49.665809 KDa
SequenceString: MREIVHIQGG QCGNQIGAKF WEVVSDEHGI DPTGTYHGDS DLQLERINVY FNEATGGRYV PRAILMDLEP GTMDSVRSGP YGQIFRPDN FVFGQTGAGN NWAKGHYTEG AELIDSVLDV VRKEAESCDC LQGFQVCHSL GGGTGSGMGT LLISKIREEY P DRMMLTFS ...String:
MREIVHIQGG QCGNQIGAKF WEVVSDEHGI DPTGTYHGDS DLQLERINVY FNEATGGRYV PRAILMDLEP GTMDSVRSGP YGQIFRPDN FVFGQTGAGN NWAKGHYTEG AELIDSVLDV VRKEAESCDC LQGFQVCHSL GGGTGSGMGT LLISKIREEY P DRMMLTFS VVPSPKVSDT VVEPYNATLS VHQLVENADE CMVLDNEALY DICFRTLKLT TPTFGDLNHL ISAVMSGITC CL RFPGQLN ADLRKLAVNL IPFPRLHFFM VGFTPLTSRG SQQYRALTVP ELTQQMWDAK NMMCAADPRH GRYLTASALF RGR MSTKEV DEQMLNVQNK NSSYFVEWIP NNVKSSVCDI PPKGLKMSAT FIGNSTAIQE MFKRVSEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDASAEEEGE FEGEEEEA

UniProtKB: Tubulin beta-1/beta-2 chain

+
Macromolecule #2: Tubulin alpha

MacromoleculeName: Tubulin alpha / type: protein_or_peptide / ID: 2 / Number of copies: 74 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 49.638008 KDa
SequenceString: MREVISIHIG QAGIQVGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDAFN TFFSETGAGK HVPRCIFLDL EPTVVDEVRT GTYRQLFHP EQLISGKEDA ANNFARGHYT IGKEIVDLAL DRIRKLADNC TGLQGFLVFN AVGGGTGSGL GSLLLERLSV D YGKKSKLG ...String:
MREVISIHIG QAGIQVGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDAFN TFFSETGAGK HVPRCIFLDL EPTVVDEVRT GTYRQLFHP EQLISGKEDA ANNFARGHYT IGKEIVDLAL DRIRKLADNC TGLQGFLVFN AVGGGTGSGL GSLLLERLSV D YGKKSKLG FTVYPSPQVS TAVVEPYNSV LSTHSLLEHT DVAVMLDNEA IYDICRRSLD IERPTYTNLN RLIAQVISSL TA SLRFDGA LNVDITEFQT NLVPYPRIHF MLSSYAPIIS AEKAYHEQLS VAEITNAAFE PASMMVKCDP RHGKYMACCL MYR GDVVPK DVNASVATIK TKRTIQFVDW CPTGFKCGIN YQPPTVVPGG DLAKVQRAVC MISNSTAIGE IFSRLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDL AALEKDFEEV GAESAEGAGE GEGEEY

UniProtKB: Tubulin alpha-1 chain

+
Macromolecule #3: Cilia- and flagella-associated protein 20

MacromoleculeName: Cilia- and flagella-associated protein 20 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 64.880324 KDa
SequenceString: MPLVLRHIAG LNGQMFGAMR SIPNSRGPYN IAQISGVSVI LGNENNLAPQ FTLRGHDDVI TAFAMSHGGS MLATGQKGSN SDVIVWDVA ACAPKYKFQE HDVEVATVSF SADDRLLLSA SCFTDAKLYV WDMATGKIVA KHGLEPGKRI TCSAWSPALA N GRAYTCAT ...String:
MPLVLRHIAG LNGQMFGAMR SIPNSRGPYN IAQISGVSVI LGNENNLAPQ FTLRGHDDVI TAFAMSHGGS MLATGQKGSN SDVIVWDVA ACAPKYKFQE HDVEVATVSF SADDRLLLSA SCFTDAKLYV WDMATGKIVA KHGLEPGKRI TCSAWSPALA N GRAYTCAT AAGEELALWT VDPFTGMVSG QKVVLGTVRR EYTSLAFSAD GAWLYGGTTS ADVVTVNVQR ASVQMTHPVC SG GVGALLL SPDGGGACLV GGRDGSLSTF NAAGGAWREL RPFAKVPGCV TSLSLSADGG AFLVGTAQGG VYRLDRTSLQ LHT ISQAQQ GQLTAVAFAP GQPEAVATSS TDGSIYVWST ADYTLQCRVQ EPTQAGGALC CVLTRDAVIS GWGDGNIRCH ARAA GGATC AQMWMIPGAH ALAHSVGVTA LRLSNGGAFL LSGGMGGELR VWDLRSREMA AHMKMHNSRI VGAAVMADDK HVAAA SEDR TWSLWDVGSE RVRTTWRGQS MFRGMAVSAD KVSVVTVTLD RKIQMWDVRG PDPRWTKVEA HGKEVGCVAS DHRGAA FAT GGADQAVRVW DWRNGGEVGG AACHSAPVAA MAFSPDDAGL VSVALDGSTC FWQLT

UniProtKB: Cilia- and flagella-associated protein 20

+
Macromolecule #4: Unknown protein

MacromoleculeName: Unknown protein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 22.262674 KDa
SequenceString: MEGAAGPSGF RNVEPLSRQE RAAARDKDLL EKSRLQARNR GGPLKQPENV VGNPVMPARN APAFCDEYDR FNRDVAGEMN AKKQQNLQK KEEVYAVKRA EQYHRERSNW ETQAQAAARE AARLEASRTT GTGAKRNQGS ESYNIISLNY NNSSGGQQLA A KDTAVKEA ...String:
MEGAAGPSGF RNVEPLSRQE RAAARDKDLL EKSRLQARNR GGPLKQPENV VGNPVMPARN APAFCDEYDR FNRDVAGEMN AKKQQNLQK KEEVYAVKRA EQYHRERSNW ETQAQAAARE AARLEASRTT GTGAKRNQGS ESYNIISLNY NNSSGGQQLA A KDTAVKEA RQARAVNLYS KSHSVSHNII TGEPIKFPTA GKE

+
Macromolecule #5: Unknown protein

MacromoleculeName: Unknown protein / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 81.430711 KDa
SequenceString: MATYEPPRSP GSRRVRRHAM GVSNASSIDE CEASSSARST VTLIQSGRLV RLQPHERPTD SVARETRTED RPIVDKVHDK LFKAHRERF VHKVLRSYAQ DDSGLLTPDQ LRSALDRLHT GLDAAEKDRI VARVAPAQHG KVHYMDFIRS LESPQPLGGP G LGVGFPGV ...String:
MATYEPPRSP GSRRVRRHAM GVSNASSIDE CEASSSARST VTLIQSGRLV RLQPHERPTD SVARETRTED RPIVDKVHDK LFKAHRERF VHKVLRSYAQ DDSGLLTPDQ LRSALDRLHT GLDAAEKDRI VARVAPAQHG KVHYMDFIRS LESPQPLGGP G LGVGFPGV TPQRAAAAGT APTFWNWQRH KKQHVPGLLE EVREGTFEQA QSDALLTSLM STKLNQYRDK LRLIFRQMDG NR NSLIDRE EFIRGIAKLR INVSKAQVER LFDLCDVDKS GELDYEEFVN RFEENGLASA ARNQTRAQPQ QPDGAPATVP LAQ SLGLTQ DEVAGALSHP MVHELARSLY GKASGATSVF VRNDLTRCGQ LPVRDMTRCC QALVPGISER QVAAVMAVVD PNSA GGVDY RAFVQKLTET GVANPRMLHS APARGEGFTA TGALTRFGEG GSLTAPDALP SAGSRSLSAV GTCRSPGGSG TTVLP ISAG LGVVLQPGGT LPPGAVTTRP AADRTSLDDL HDVCVAPFLE SLSRAGNNDL PAQHDNNNNN GGAGGPATSL PSVTRS IDM GTLSRSASLP NAHGGSPTRF GGAGGGGGFG GTAAGLSATG SKAPTHATGR FSRFWDRRYA DTSHITSVDP CSASYAP SE GTYVRKGWGS GDASSDFLTY QGADRDQRAR QRQAVAVRTT ARSEVEAKLS GLDDASGLDD GRLQVARATK QRYEERAE M YDRTRQQHEG GSCIFGRLPP FHEHQLEAAN TPARVFW

+
Macromolecule #6: Unknown protein

MacromoleculeName: Unknown protein / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 57.734598 KDa
SequenceString: MPPQLGREVQ ERVKVYGPLN ELTYEGRLLT QTLQDELNRS ISAPAGPRSP WYEGDPELES MRERVRQQRA IREAQRRRDH AALTASIQK RNLQEEQRRD AMLGSLLGDV IGGLTDPNSP LAEAEAALSH ADKVRRKKKE SLHNEWSTQV FDTIQGRLQA A VDARDPAA ...String:
MPPQLGREVQ ERVKVYGPLN ELTYEGRLLT QTLQDELNRS ISAPAGPRSP WYEGDPELES MRERVRQQRA IREAQRRRDH AALTASIQK RNLQEEQRRD AMLGSLLGDV IGGLTDPNSP LAEAEAALSH ADKVRRKKKE SLHNEWSTQV FDTIQGRLQA A VDARDPAA IESRLKTQYD QYLHTTNTKV AVFRDVIIEQ DYNPLAAADA AIRVPTGDIR DPLKRDVLKG EYERRLMTGG RG GGGASPT GRGGAAAAGA GSIYGPLGKE TLGTQQWGEL AVKATPYGHC TDGQGGYVAR PLSGSAVALR ASRVPMDHYD YPV GNAAAA AEVPPGKRIV PGPEQRRGRQ DLFDVVQHTV HLKPQGYTGG DQWLEHKGKG NAPGPEQRRG RRDLADVLQQ KAVA DGPRG TSAPARGDQL QHKEQGDAWL DAKGKRRVEG PEMRRGRQGL YETLQQTSNP YQGGNKVGDA WLEHKGRKVQ PRPEP EAAA ALSAVPPLPT VRPPRVGDDK KYAVNIEAAM GQMTVKDGAK VTGW

+
Macromolecule #7: FAP65

MacromoleculeName: FAP65 / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 46.26157 KDa
SequenceString: MSERPHQSGP RSWAEDCNQY RTTRGSKSYS TLEDAGRVPE RYSRTNYVPF LAERHPLYSY NDLGEDGKGK VRLDPATQAD RFSRHGWGD VSLLKQEGLA GQPHPRSSEA GPTRSGRLRP GSPRGADGRN GLYGVLQMTE AGGTDSWVGH PQIDPTKGKR A VAPPPDPK ...String:
MSERPHQSGP RSWAEDCNQY RTTRGSKSYS TLEDAGRVPE RYSRTNYVPF LAERHPLYSY NDLGEDGKGK VRLDPATQAD RFSRHGWGD VSLLKQEGLA GQPHPRSSEA GPTRSGRLRP GSPRGADGRN GLYGVLQMTE AGGTDSWVGH PQIDPTKGKR A VAPPPDPK GRRDLFDVLH ARSPGMPADD SWLGHQKIDP ARGKAHPPGP EQSRGRRDLT ELFTMNILHD PRRLELLQKG AD KHGDAWC GNILIDPARG KKPVEDVAAA GQNLHGATFK PLPAGTPLPD APRRHTRPAP APASDAYAAE VIRGEAAGDD WGP RTKRSV PDMPKPNAFD GRTDLYAHMQ YRPLSNGEQG KYAKAFDDRG TRGRRQLHTP GDADPAKEAL LTWKPEMRVG QFVK NGGLA QENRVRGHTL RATAGR

UniProtKB: Abnormal spindle-like microcephaly-associated protein ASH domain-containing protein

+
Macromolecule #8: FAP70

MacromoleculeName: FAP70 / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 10.089324 KDa
SequenceString:
MFRQEEQPKT GVRQFGTHTT GKVDHMLGTH ATVRPEYKDP PPKRTVPTSQ LEAVRNIETQ YIKARKAAED ARERQGTSHL YAAGKGWGH

UniProtKB: Cilia- and flagella-associated protein 70

+
Macromolecule #9: FAP147

MacromoleculeName: FAP147 / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 22.193566 KDa
SequenceString:
MFKNAFQSGF LSVLYSIGSK PLEIWDKQVS NGHIKRITDA DIQSSVLEIM GQNVSTTYIT CPADPNKTLG IKLPFLVLII KNLNKYFSF EVQVLDDKNV RRRFRASNYQ STTRVKPFIC TMPMRLDSGW NQIQFNLSDF TRRAYGTNYI ETLRVQVHAN C RIRRIYFS DRLYSEEELP AEFKLFLPIQ KS

UniProtKB: Flagellar associated protein

+
Macromolecule #10: FAP178

MacromoleculeName: FAP178 / type: protein_or_peptide / ID: 10 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 65.929133 KDa
SequenceString: MAAAGLDTLR LEDSDDDFKY EEVDVMSDGE DDASEDLDAA LRKLQQFTSK QEAATGPART TEVKPGQVVK KPEVIDDFLR NFFIKMGLS RTCECFEAEW YELKATGRLD NSTTVPDVYL RNAELEDDVA GLRRELAEAK SIAGRASATW DKFRKERDFH R MHHKRVAQ ...String:
MAAAGLDTLR LEDSDDDFKY EEVDVMSDGE DDASEDLDAA LRKLQQFTSK QEAATGPART TEVKPGQVVK KPEVIDDFLR NFFIKMGLS RTCECFEAEW YELKATGRLD NSTTVPDVYL RNAELEDDVA GLRRELAEAK SIAGRASATW DKFRKERDFH R MHHKRVAQ EKNKLLTDLR RLKEHYAKYE PTILELKKKY ETLMKEKMMM SLERDKLAAR VDALEQVASS PLPGAERSLG GQ STAAAGG GASGRALGAT NRALTGDVPP AAGAAAAAAT GRSGAVSAGP RSGWASLNAP PRRNPYADLE FPAAPVKMLS LNK TFKGHL LSVANLALHP TKPILVTASD DKTWKMWHMP GGDLIMCGEG HKDWVAGVDF HPAGTCLASG GGDSAVKIWD FEKQ RCVTT FTDHKQAIWS VRFHHLGEVV ASGSLDHTVR LWDLPAGKCR MALRGHVDSV NDLAWQPFSS SLATASSDKT VSVWD ARAG LCTQTYYGHQ NSCNGVSFNI LGTQLASTDA DGVVKLWDTR MTAEVATINT GKHPANKSCF DRSGQVLAVA CDDGKV KAY STTDGVLQAE LAGHEDAVQA VLFDPAGQYL VSCGSDNTFR LWS

UniProtKB: Calponin-homology (CH) domain-containing protein

+
Macromolecule #11: Flagellar WD repeat-containing protein Pf20

MacromoleculeName: Flagellar WD repeat-containing protein Pf20 / type: protein_or_peptide / ID: 11 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 10.336616 KDa
SequenceString:
MSESQKETFR KYLEQAGAID VLVKVLVQLY EEPSKPKTAL DYIKQCLGSP TPAEYEAVVA ERDGLQKQLE EANQLIAELQ SRVQSLEAA AETA

UniProtKB: Flagellar WD repeat-containing protein Pf20

+
Macromolecule #12: Flagellar associated protein

MacromoleculeName: Flagellar associated protein / type: protein_or_peptide / ID: 12 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 233.221547 KDa
SequenceString: MPASNGADQG TAPGGTMAYG VLSREQRKQM FGLDCPEQLE WRHWNPGTEY VKQLVLKNVS TSVLKIRFKQ PTSKAFGMDF PEPFKLRPG MSQPLKVVFR PLKQQHYSDN VELFVGNVSC LVPVHAYTPV THIEVPPALD FGFTPTKETV TAQLPVRNTG D VRVDVLWK ...String:
MPASNGADQG TAPGGTMAYG VLSREQRKQM FGLDCPEQLE WRHWNPGTEY VKQLVLKNVS TSVLKIRFKQ PTSKAFGMDF PEPFKLRPG MSQPLKVVFR PLKQQHYSDN VELFVGNVSC LVPVHAYTPV THIEVPPALD FGFTPTKETV TAQLPVRNTG D VRVDVLWK LDAPFSISPL FASLAPGEVV AFTASFTPPE ACSYTASAAC QLESGAAAIC KISGIGKFPY LSVEQAGVDF GA VVVGQRV ERLVRFGNHS VVPAHFAVTH DEAGPDDGVF TVGPARGTLG PEEYSMLKLS YTPRATGTFS SETFHIGTAG GNR VALNLR GTAVAPLVTL STRAFNFGNV AAGATASRVL YIRNHSAVPV PYDFQVDPLD VFAISRTRGV LAPDSTAHVT ITFR PMAGL AANLWRRVTL LLKDAEPQGV DLVATAYTDK SRPPPLSQRH VERYMARVLS GGPAVEESQL DSKPPSAATG AGGLD GASE GGAGPLLAGG GFGSLLPPLG DAAEGGEGAA SKLLGPDGWS LLFGGQDPAA ALTVDSDALD FGSCSRLSAS EYRSVT VTN HTPAKLTAFV LVPEWADPGA APGDAPQRVF QVFPESADMR PYGQATFKVA FRPPRDAAFF SQQLALVAHT KSQRNFR LV AEHQVLPAWC VPLRATGNTF LHSNPEFGPK VELSSRAVAF PPCRPGERVH QTLLIANSGD TPVAFSFGAA GAALGPLF S AKPAAGVVPP QGHVLVALRF APTDTRPAAA NALVTFNGVA SNAVSVSLRG AAHTPRLTTD LPSSTLYFRP TCVGASSQR AVTLHNPSRV PVAFRWRLPA RLQGLVTVSP AAGALRGNES VQLQWSFTPA AQKLYEARAA CLVMSPPEAA NGNAAGATAS AASLFPGAG LATGIEWYEG AGATAALAGM GEEEAADAVL LSLVGEGTQG AVALEPPSLE LGDLRVGHPV RRPLLLQNCS D GVLRYSLE VGPAEDDQPP AGDATLVDFT AGLDSAAEGG VGGGAGGAGG AALECWVDEP EGALPARASK TVMVTLFPRY RK RYSLQVR CRSSTVAPLL TGPNRPPSGG AGPRPLDAGS EAAAAAAAAA AAAAAPLPPP VIAPLTASTT FPTLEVTDVY CEG LPKQLL WQLLGLNDLN HHLRTEVTAT ELRLRAAQDR GALTTEAASA AMRPFLMEFG THGLGGRPRV VHVEISNPTP LPAS WQLHS FDDPDGVELE NWVEPGRPRT EGERMRDLIA EYKLFEMRPR SGELEPGARC TVTIEFRPSV EGSFELPVFL HITDG KRLR LQLQAVTTPE PLQLLALPPP LRTFRLEPVA LGERAPPLQM YVLRNGGPAP LHWRLDTAPL AALAEASWGH PVLELV GPE EGDIEEGGVA AINWRFSPLE AKEYRVEVPV LLGDGGIEVI ELLGRGFAPP PAPPHGAAAV QLIGPGAATS PAAPTTA AE DDDTPAAALD SVGGDAEAEA ARAAAAADRD WITWRGLSSA PSAGMAGRLA LVDHDLVSLG VTPVRGLTRR IIVLTNKS R YPLAFDWDLG CLAPPPPPGL AATQRAAAAS AMMGLGGGSL LPASQLQLLA GRPLQGALAI SPAAGSLEPG ERLVCRVSL HAGVTPQVFE GEVRCHVRID DDAVAEAEAA AAAAAAAGAA AVAAELPFVE QVEEVIAEAP VRGPPAPPPA VAAAQRASRL RSRLPVHQY MTTAVRTRIE PLNAAFTATM EARTRRLADA TRPPSWPEPQ SISVTLRGRI LDERQLGALR YVPPHERAAA R AAVVAGAA WVPPAMVPFW EEEGRSTPAV SAQPSSQGGG GYGVGGYGGG YGSGGSQGGE ASVAPSGGDP GGYSPRGGMA DS WPSLEPG LGMEETVVGP PTVGLDLSLS LQHAGGAGGA PGGDGDSDSR PGTPSMTAAA HHHHHHPRHA GPAPGSGTAE VME VTFSGD QQPTGGPMPS PPSISGAPDP DSATPDDDFA TSDAAVNAAA AVRAAGGGMG SPQPVDPGGS AAAAASELAP PALP PAPPR GGDIEYDALV SAREVLAGLF AELMEDADVV RAVAFLPEHE VPSFAEVRAT PPPCYDPAVR AAAEAARAEA EARAA AEAA TKAAAEAEAV AARAAAMLGP KHEASSSSSS SSSSSSSSSS SSSSSSAASS PGASPTGKAP VVEAATPRLV SAVGGM APS QPALALRPAP STPPRTPPKP SQGAAFAIPA AAAQAATEPP ALEDELAADT ELARVLVAPE WRAFADFVLE SAVLGLM QE SAAGDWEMPE EEVGR

UniProtKB: Flagellar associated protein 174

+
Macromolecule #13: FAP196

MacromoleculeName: FAP196 / type: protein_or_peptide / ID: 13 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 111.116258 KDa
SequenceString: MAPKKKEDKD APPPEDTNPY GVFVSVTMPS ATVVLDVQDD AAAQRETHIT LNIPGCHVPW ASAHTAPSEG GVYQYSVVKH FRRSGGQDG LLQLINGVLT VTVNDSATNA VLASATVDQL QGFAIGQNTW STEGLDLVPA AEVPEGVPKA RSARLAFASI A LQERPLPE ...String:
MAPKKKEDKD APPPEDTNPY GVFVSVTMPS ATVVLDVQDD AAAQRETHIT LNIPGCHVPW ASAHTAPSEG GVYQYSVVKH FRRSGGQDG LLQLINGVLT VTVNDSATNA VLASATVDQL QGFAIGQNTW STEGLDLVPA AEVPEGVPKA RSARLAFASI A LQERPLPE GADAAALAAA PPPPEAELPP LLPYSYVSGE AAEKGNMVEL VVSGLSPLPP NLQAAADAAG GKLHVTVGLA LP GGGPAVA VSLAVAGGRV AAPAFRRELL PPGCLQALQY ALEDGLPVVL EVARYVSAEG MADPAFEGYH AAAAAPALAA GLG AAGATE AAAEGLSLTA WAASGAKTCL PPYTAPAGKP KPVEAEVPPA GTCLWEKAGA QLAVSLRFAR PVVPAWRPPP PPPR PLLEL IPPRDLTPKP PPTTAVDEFK AKVRVIARAL AEEYKAVLPP PDASVAAAAA GGGAEGRHKA LIFELNRSGK YAQMR DSLK TAVVSLVREK YRKSGSMSPN EMALLYNDLY GSLLAAVHSS LNDLVDAAAA RPRAPPPAPV PDKQRLGELL ELAAQA EAM GDTDRAELLH QRRLLAKNDA QVWYEYGTYC LRRGGAKRGR AEECFREALA LEPAHRGALL ALLGCSVAAG RNTDPAY LE SAEAAAHRLL DVAGRSSLDA WAALAVVYRA YGEAKRAELA SCEQEMARLE KQQLAAAAAA ASAGVSPSPS YGEGRAGG N GGGVPATEPS TASAGSVAGS AGELQARSFI SLANTLLESL ALPAEAALAL ELAAGLRHWP SVGPDTRTLH ALAGALAEQ ALARAAGGGA ASAAAEAMLT PGSSVLSMMR ADAGEAVSSV AAEAAWRCRL LVAQLHKARG ATDEAIRFYQ EYIEAARSSG RLAEVPLSA WLELAEAYAA RGQARFAADV FLLGASARPG CAVLWRGAGR CFVGAEELGP ADMALSEANV LDPEDPEAWG W LALVALRE GRAEDAEKAL AFGLRCGLGD PGLLLDIAAE YRAAGQRRAE QRVLQEVAVK LMPESCSARL LLARCLVAQR CG AEAAEAV AAARQLAAHE DDEAAVAELE AELRGMA

UniProtKB: Uncharacterized protein

+
Macromolecule #14: FAP213

MacromoleculeName: FAP213 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 102.141609 KDa
SequenceString: MVGPSEPAGL PPKAKLKAYK VLGDVGEFQE RLAATLPPPK APEPPNVFNI SDTSEFPPDV WFAATISPDN GVAVIASYRE LCKARALYQ SQLTNIHTAR RQYGMGGSMG PGAGAPLPLP PAQQAAAENR TIAETMRVAA DTRKLGKFEQ QQAKWDEVSS T LAYRVGRA ...String:
MVGPSEPAGL PPKAKLKAYK VLGDVGEFQE RLAATLPPPK APEPPNVFNI SDTSEFPPDV WFAATISPDN GVAVIASYRE LCKARALYQ SQLTNIHTAR RQYGMGGSMG PGAGAPLPLP PAQQAAAENR TIAETMRVAA DTRKLGKFEQ QQAKWDEVSS T LAYRVGRA PTELAMQRGP AWRTRAELTE LLYRAQPRDA RGSNPDEVWT ASLRDAWERI LPLGSIFSGL AIKIRDRPGE LP ATRAARV GRPLDPLLAP LGGGGTTLSP ATLGHPAAAA AHAQHVATLA ANGVMLGATT NKPPLGRSLS ARGRAWEDSE MLK QRVAEY GTRLRALAPH DPDFGALVVA GEALESQLEA LAGAPITLAE VESHVRGHAP EAFEAYKAVK DEMEAQLRAA LEAE EAQRA AQEAAAAAAA PQPGPHVAFS SPFVSLACHV GEKAHGSVTL VSRGTAAVNW SWRRVPAPQH AHAATELSQP PCFAA SLQS GVLLPGQSLT VAVTFEAAAA GTYREAWELV TRPPLQGSEG PCLTLRLRGA AEVRDESGTG RGALEEALAE KEKRAK VAA ALERVLRDVR MPRRPQPHES VEELAAGDAW DRVNGCAAGA VGGPYAWPPL FHSPGVQSEL AEVYREAEAA LAAALKP SV DEDPKKKKKE TSARKGKKGD EPPPPPPKYP PSWTEPAPAG AGCSLAVLDE LLTELAAAAP AAAAPLAVRA EEAKARAR V PPNNRKVLRR AMRVLVGKMV DAVEEKFNVI RTDLEAKSAA EAAAAAAAAA AAAGEDGDDA DGEASAISVG AVKEKDKEK EKDGKEKKGG AKEKPGAKGG AGKDKKGGSA SHTDDGAAPE PGAGLPNVEH LQPVFHDKAT TAAKAAIKAA LNTLLDEVHR HKVAAGDAL EANIRSLDSR IEAAQADAQA NQEPAAAEAA AAAGLALFAP AAGGVPAPGP GPAARARSAE LEQLYWERLC V LRTWTGLG IPTRADVR

UniProtKB: Flagellar associated protein

+
Macromolecule #15: FAP225

MacromoleculeName: FAP225 / type: protein_or_peptide / ID: 15 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 23.511406 KDa
SequenceString: MTNRATLSQT ATSLTSTTGR RDRLQRQEDT TLFGYESPPD TPALHRDVLK WVQGLDLSQS LKNCRRDVAN GFLVAEIFSR YFPADIQMH SFANAASSHF KRDNWTQLQA FCGRQGINLP GDLVEGCVQG VHGAAIALLE HLYEAFTGKK VPRLKVPDAA A AAAAAAAA ...String:
MTNRATLSQT ATSLTSTTGR RDRLQRQEDT TLFGYESPPD TPALHRDVLK WVQGLDLSQS LKNCRRDVAN GFLVAEIFSR YFPADIQMH SFANAASSHF KRDNWTQLQA FCGRQGINLP GDLVEGCVQG VHGAAIALLE HLYEAFTGKK VPRLKVPDAA A AAAAAAAA RGGPGAVGGS GEGAKLISST VKTAQNLEFG AVTTQQLAGA DATALRRRLA GGTS

UniProtKB: EF-hand domain-containing protein

+
Macromolecule #16: FAP239

MacromoleculeName: FAP239 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.103049 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

UniProtKB: Flagellar associated protein

+
Macromolecule #17: FAP388

MacromoleculeName: FAP388 / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 6.571091 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

UniProtKB: Uncharacterized protein

+
Macromolecule #18: FAP424

MacromoleculeName: FAP424 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.017944 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

UniProtKB: Predicted protein

+
Macromolecule #19: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 19 / Number of copies: 74 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

+
Macromolecule #20: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 20 / Number of copies: 74 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

+
Macromolecule #21: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 21 / Number of copies: 74 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.4
GridModel: C-flat-1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 39.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

9385

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104806
FSC plot (resolution estimation)

+
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