[English] 日本語
Yorodumi
- EMDB-32544: Architecture of the human NALCN channelosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32544
TitleArchitecture of the human NALCN channelosome
Map dataOverall map
Sample
  • Complex: NALCN channelosome
    • Protein or peptide: Protein unc-80 homolog
    • Protein or peptide: Protein unc-79 homolog
    • Protein or peptide: Calmodulin-1
    • Protein or peptide: Sodium leak channel non-selective protein,Extended tegument protein pp150
    • Protein or peptide: Transmembrane protein FAM155ATransmembrane protein
Function / homology
Function and homology information


monoatomic cation homeostasis / positive regulation of synaptic transmission, cholinergic / leak channel activity / regulation of resting membrane potential / viral tegument / cation channel complex / sodium channel activity / voltage-gated sodium channel activity / CaM pathway / Cam-PDE 1 activation ...monoatomic cation homeostasis / positive regulation of synaptic transmission, cholinergic / leak channel activity / regulation of resting membrane potential / viral tegument / cation channel complex / sodium channel activity / voltage-gated sodium channel activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / monoatomic ion channel complex / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / Activation of RAC1 downstream of NMDARs / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / Unblocking of NMDA receptors, glutamate binding and activation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / calcium ion import across plasma membrane / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / sodium ion transmembrane transport / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / monoatomic cation channel activity / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of protein autophosphorylation / potassium ion transmembrane transport / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / protein serine/threonine kinase activator activity / bioluminescence / sarcomere / monoatomic ion transmembrane transport / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / generation of precursor metabolites and energy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / positive regulation of synaptic transmission, GABAergic / calcium ion transmembrane transport / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / spindle pole / cellular response to type II interferon
Similarity search - Function
Protein UNC80, C-terminal / Cation-channel complex subunit UNC-79 / Protein UNC80 C-terminal region / UNC79 / Cation channel complex component UNC80, N-terminal / Protein UNC80, central region / UNC80 N-terminal / Protein UNC80 central region / Sodium leak channel NALCN / Herpesvirus UL11/UL32 ...Protein UNC80, C-terminal / Cation-channel complex subunit UNC-79 / Protein UNC80 C-terminal region / UNC79 / Cation channel complex component UNC80, N-terminal / Protein UNC80, central region / UNC80 N-terminal / Protein UNC80 central region / Sodium leak channel NALCN / Herpesvirus UL11/UL32 / Herpesvirus large structural phosphoprotein UL32 / Voltage-dependent channel domain superfamily / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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 / Ion transport domain / Ion transport protein / EF-hand domain pair / Armadillo-type fold
Similarity search - Domain/homology
Extended tegument protein pp150 / NALCN channel auxiliary factor 1 / Calmodulin-1 / Sodium leak channel NALCN / Protein unc-80 homolog / Protein unc-79 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsWu JP / Yan Z / Zhou L / Liu H / Zhao Q
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Discov / Year: 2022
Title: Architecture of the human NALCN channelosome.
Authors: Lunni Zhou / Haobin Liu / Qingqing Zhao / Jianping Wu / Zhen Yan /
Abstract: NALCN regulates the resting membrane potential by mediating the Na leak current in neurons, and it functions as a channelosome in complex with FAM155A, UNC79, and UNC80. Dysfunction of the NALCN ...NALCN regulates the resting membrane potential by mediating the Na leak current in neurons, and it functions as a channelosome in complex with FAM155A, UNC79, and UNC80. Dysfunction of the NALCN channelosome causes a broad range of neurological and developmental diseases called NALCN channelopathies in humans. How the auxiliary subunits, especially the two large components UNC79 and UNC80, assemble with NALCN and regulate its function remains unclear. Here we report an overall architecture of the human NALCN channelosome. UNC79 and UNC80 each adopt an S-shape super-helical structure consisting of HEAT and armadillo repeats, forming a super-coiled heterodimeric assembly in the cytoplasmic side, which may provide a scaffold for the binding of other potential modulators of the channelosome. The UNC79-UNC80 assembly specifically associates with the NALCN-FAM155A subcomplex through the intracellular II-III linker of NALCN. Disruptions of the interaction interfaces between UNC79 and UNC80, and between the II-III linker of NALCN and the UNC79-UNC80 assembly, significantly reduce the NALCN-mediated currents in HEK293T system, suggesting the importance of the UNC79-UNC80 assembly in regulating channelosome function. Cross-linking mass spectrometry analysis identified an additional calmodulin (CaM) bound in the carboxyl-terminal domain of NALCN. Our study thus provides a structural basis for understanding the unique assembly mechanism and functional regulation of the NALCN channelosome, and also provides an opportunity for the interpretation of many disease-related mutations in UNC80.
History
DepositionJan 6, 2022-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateApr 20, 2022-
Current statusApr 20, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32544.png

Downloads & links

-
Map

FileDownload / File: emd_32544.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall map
Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.0551169 - 1.947338
Average (Standard dev.)-0.0010802363 (±0.036794893)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 556.544 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Local map of UNC79 N-ter with UNC80 C-ter

Fileemd_32544_additional_1.map
AnnotationLocal map of UNC79 N-ter with UNC80 C-ter
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half2 map of the overall map

Fileemd_32544_half_map_1.map
AnnotationHalf2 map of the overall map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half1 map of the overall map

Fileemd_32544_half_map_2.map
AnnotationHalf1 map of the overall map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : NALCN channelosome

EntireName: NALCN channelosome
Components
  • Complex: NALCN channelosome
    • Protein or peptide: Protein unc-80 homolog
    • Protein or peptide: Protein unc-79 homolog
    • Protein or peptide: Calmodulin-1
    • Protein or peptide: Sodium leak channel non-selective protein,Extended tegument protein pp150
    • Protein or peptide: Transmembrane protein FAM155ATransmembrane protein

-
Supramolecule #1: NALCN channelosome

SupramoleculeName: NALCN channelosome / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all / Details: NALCN-FAM155A-UNC79-UNC80-CaM
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 900 KDa

-
Macromolecule #1: Protein unc-80 homolog

MacromoleculeName: Protein unc-80 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 363.856188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVKRKSSEGQ EQDGGRGIPL PIQTFLWRQT SAFLRPKLGK QYEASCVSFE RVLVENKLHG LSPALSEAIQ SISRWELVQA ALPHVLHCT ATLLSNRNKL GHQDKLGVAE TKLLHTLHWM LLEAPQDCNN ERFGGTDRGS SWGGSSSAFI HQVENQGSPG Q PCQSSSND ...String:
MVKRKSSEGQ EQDGGRGIPL PIQTFLWRQT SAFLRPKLGK QYEASCVSFE RVLVENKLHG LSPALSEAIQ SISRWELVQA ALPHVLHCT ATLLSNRNKL GHQDKLGVAE TKLLHTLHWM LLEAPQDCNN ERFGGTDRGS SWGGSSSAFI HQVENQGSPG Q PCQSSSND EEENNRRKIF QNSMATVELF VFLFAPLVHR IKESDLTFRL ASGLVIWQPM WEHRQPGVSG FTALVKPIRN II TAKRSSP INSQSRTCES PNQDARHLEG LQVVCETFQS DSISPKATIS GCHRGNSFDG SLSSQTSQER GPSHSRASLV IPP CQRSRY ATYFDVAVLR CLLQPHWSEE GTQWSLMYYL QRLRHMLEEK PEKPPEPDIP LLPRPRSSSM VAAAPSLVNT HKTQ DLTMK CNEEEKSLSS EAFSKVSLTN LRRSAVPDLS SDLGMNIFKK FKSRKEDRER KGSIPFHHTG KRRPRRMGVP FLLHE DHLD VSPTRSTFSF GSFSGLGEDR RGIEKGGWQT TILGKLTRRG SSDAATEMES LSARHSHSHH TLVSDLPDPS NSHGEN TVK EVRSQISTIT VATFNTTLAS FNVGYADFFN EHMRKLCNQV PIPEMPHEPL ACANLPRSLT DSCINYSYLE DTEHIDG TN NFVHKNGMLD LSVVLKAVYL VLNHDISSRI CDVALNIVEC LLQLGVVPCV EKNRKKSENK ENETLEKRPS EGAFQFKG V SGSSTCGFGG PAVSGAGDGG GEEGGGGDGG GGGGDGGGGG GGGGGPYEKN DKNQEKDEST PVSNHRLALT MLIKIVKSL GCAYGCGEGH RGLSGDRLRH QVFRENAQNC LTKLYKLDKM QFRQTMRDYV NKDSLNNVVD FLHALLGFCM EPVTDNKAGF GNNFTTVDN KSTAQNVEGI IVSAMFKSLI TRCASTTHEL HSPENLGLYC DIRQLVQFIK EAHGNVFRRV ALSALLDSAE K LAPGKKVE ENEQESKPAG SKRSEAGSIV DKGQVSSAPE ECRSFMSGRP SQTPEHDEQM QGANLGRKDF WRKMFKSQSA AS DTSSQSE QDTSECTTAH SGTTSDRRAR SRSRRISLRK KLKLPIGKRN WLKRSSLSGL ADGVEDLLDI SSVDRLSFIR QSS KVKFTS AVKLSEGGPG SGMENGRDEE ENFFKRLGCH SFDDHLSPNQ DGGKSKNVVN LGAIRQGMKR FQFLLNCCEP GTIP DASIL AAALDLEAPV VARAALFLEC ARFVHRCNRG NWPEWMKGHH VNITKKGLSR GRSPIVGNKR NQKLQWNAAK LFYQW GDAI GVRLNELCHG ESESPANLLG LIYDEETKRR LRKEDEEEDF LDDSTVNPSK CGCPFALKMA ACQLLLEITT FLRETF SCL PRPRTEPLVD LESCRLRLDP ELDRHRYERK ISFAGVLDEN EDSKDSLHSS SHTLKSDAGV EEKKEGSPWS ASEPSIE PE GMSNAGAEEN YHRNMSWLHV MILLCNQQSF ICTHVDYCHP HCYLHHSRSC ARLVRAIKLL YGDSVDSLRE SSNISSVA L RGKKQKECSD KSCLRTPSLK KRVSDANLEG KKDSGMLKYI RLQVMSLSPA PLSLLIKAAP ILTEEMYGDI QPAAWELLL SMDEHMAGAA AAMFLLCAVK VPEAVSDMLM SEFHHPETVQ RLNAVLKFHT LWRFRYQVWP RMEEGAQQIF KIPPPSINFT LPSPVLGMP SVPMFDPPWV PQCSGSVQDP INEDQSKSFS ARAVSRSHQR AEHILKNLQQ EEEKKRLGRE ASLITAIPIT Q EACYEPTC TPNSEPEEEV EEVTNLASRR LSVSPSCTSS TSHRNYSFRR GSVWSVRSAV SAEDEEHTTE HTPNHHVPQP PQ AVFPACI CAAVLPIVHL MEDGEVREDG VAVSAVAQQV LWNCLIEDPS TVLRHFLEKL TISNRQDELM YMLRKLLLNI GDF PAQTSH ILFNYLVGLI MYFVRTPCEW GMDAISATLT FLWEVVGYVE GLFFKDLKQT MKKEQCEVKL LVTASMPGTK TLVV HGQNE CDIPTQLPVH EDTQFEALLK ECLEFFNIPE SQSTHYFLMD KRWNLIHYNK TYVRDIYPFR RSVSPQLNLV HMHPE KGQE LIQKQVFTRK LEEVGRVLFL ISLTQKIPTA HKQSHVSMLQ EDLLRLPSFP RSAIDAEFSL FSDPQAGKEL FGLDTL QKS LWIQLLEEMF LGMPSEFPWG DEIMLFLNVF NGALILHPED SALLRQYAAT VINTAVHFNH LFSLSGYQWI LPTMLQV YS DYESNPQLRQ AIEFACHQFY ILHRKPFVLQ LFASVAPLLE FPDAANNGPS KGVSAQCLFD LLQSLEGETT DILDILEL V KAEKPLKSLD FCYGNEDLTF SISEAIKLCV TVVAYAPESF RSLQMLMVLE ALVPCYLQKL KRQTSQVETV PAAREEIAA TAALATSLQA LLYSVEVLTR PMTAPQMSRC DQGHKGTTTA NHTMSSGVNT RYQEQGAKLH FIRENLHLLE EGQGIPREEL DERIAREEF RRPRESLLNI CTEFYKHCGP RLKILQNLAG EPRVIALELL DVKSHMRLAE IAHSLLKLAP YDTQTMESRG L RRYIMEML PITDWTAEAV RPALILILKR LDRMFNKIHK MPTLRRQVEW EPASNLIEGV CLTLQRQPII SFLPHLRSLI NV CVNLVMG VVGPSSVADG LPLLHLSPYL SPPLPFSTAV VRLVALQIQA LKEDFPLSHV ISPFTNQERR EGMLLNLLIP FVL TVGSGS KDSPWLEQPE VQLLLQTVIN VLLPPRIIST SRSKNFMLES SPAHCSTPGD AGKDLRREGL AESTSQAAYL ALKV ILVCF ERQLGSQWYW LSLQVKEMAL RKVGGLALWD FLDFIVRTRI PIFVLLRPFI QCKLLAQPAE NHEELSARQH IADQL ERRF IPRPLCKSSL IAEFNSELKI LKEAVHSGSA YQGKTSISTV GTSTSAYRLS LATMSRSNTG TGTVWEQDSE PSQQAS QDT LSRTDEEDEE NDSISMPSVV SEQEAYLLSA IGRRRFSSHV SSMSVPQAEV GMLPSQSEPN VLDDSQGLAA EGSLSRV AS IQSEPGQQNL LVQQPLGRKR GLRQLRRPLL SRQKTQTEPR NRQGARLSTT RRSIQPKTKP SADQKRSVTF IEAQPEPA A APTDALPATG QLQGCSPAPS RKPEAMDEPV LTSSPAIVVA DLHSVSPKQS ENFPTEEGEK EEDTEAQGAT AHSPLSAQL SDPDDFTGLE TSSLLQHGDT VLHISEENGM ENPLLSSQFT FTPTELGKTD AVLDESHV

-
Macromolecule #2: Protein unc-79 homolog

MacromoleculeName: Protein unc-79 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 298.239656 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSTKAEQFAS KIRYLQEYHN RVLHNIYPVP SGTDIANTLK YFSQTLLSIL SRTGKKENQD ASNLTVPMTM CLFPVPFPLT PSLRPQVSS INPTVTRSLL YSVLRDAPSE RGPQSRDAQL SDYPSLDYQG LYVTLVTLLD LVPLLQHGQH DLGQSIFYTT T CLLPFLND ...String:
MSTKAEQFAS KIRYLQEYHN RVLHNIYPVP SGTDIANTLK YFSQTLLSIL SRTGKKENQD ASNLTVPMTM CLFPVPFPLT PSLRPQVSS INPTVTRSLL YSVLRDAPSE RGPQSRDAQL SDYPSLDYQG LYVTLVTLLD LVPLLQHGQH DLGQSIFYTT T CLLPFLND DILSTLPYTM ISTLATFPPF LHKDIIEYLS TSFLPMAILG SSRREGVPAH VNLSASSMLM IAMQYTSNPV YH CQLLECL MKYKQEVWKD LLYVIAYGPS QVKPPAVQML FHYWPNLKPP GAISEYRGLQ YTAWNPIHCQ HIECHNAINK PAV KMCIDP SLSVALGDKP PPLYLCEECS ERIAGDHSEW LIDVLLPQAE ISAICQKKNC SSHVRRAVVT CFSAGCCGRH GNRP VRYCK RCHSNHHSNE VGAAAETHLY QTSPPPINTR ECGAEELVCA VEAVISLLKE AEFHAEQREH ELNRRRQLGL SSSHH SLDN ADFDNKDDDK HDQRLLSQFG IWFLVSLCTP SENTPTESLA RLVAMVFQWF HSTAYMMDDE VGSLVEKLKP QFVTKW LKT VCDVRFDVMV MCLLPKPMEF ARVGGYWDKS CSTVTQLKEG LNRILCLIPY NVINQSVWEC IMPEWLEAIR TEVPDNQ LK EFREVLSKMF DIELCPLPFS MEEMFGFISC RFTGYPSSVQ EQALLWLHVL SELDIMVPLQ LLISMFSDGV NSVKELAN Q RKSRVSELAG NLASRRVSVA SDPGRRVQHN MLSPFHSPFQ SPFRSPLRSP FRSPFKNFGH PGGRTIDFDC EDDEMNLNC FILMFDLLLK QMELQDDGIT MGLEHSLSKD IISIINNVFQ APWGGSHTCQ KDEKAIECNL CQSSILCYQL ACELLERLAP KEESRLVEP TDSLEDSLLS SRPEFIIGPE GEEEENPASK HGENPGNCTE PVEHAAVKND TERKFCYQQL PVTLRLIYTI F QEMAKFEE PDILFNMLNC LKILCLHGEC LYIARKDHPQ FLAYIQDHML IASLWRVVKS EFSQLSSLAV PLLLHALSLP HG ADIFWTI INGNFNSKDW KMRFEAVEKV AVICRFLDIH SVTKNHLLKY SLAHAFCCFL TAVEDVNPAV ATRAGLLLDT IKR PALQGL CLCLDFQFDT VVKDRPTILS KLLLLHFLKQ DIPALSWEFF VNRFETLSLE AQLHLDCNKE FPFPTTITAV RTNV ANLSD AALWKIKRAR FARNRQKSVR SLRDSVKGPV ESKRALSLPE TLTSKIRQQS PENDNTIKDL LPEDAGIDHQ TVHQL ITVL MKFMAKDESS AESDISSAKA FNTVKRHLYV LLGYDQQEGC FMIAPQKMRL STCFNAFIAG IAQVMDYNIN LGKHLL PLV VQVLKYCSCP QLRHYFQQPP RCSLWSLKPH IRQMWLKALL VILYKYPYRD CDISKILLHL IHITVNTLNA QYHSCKP HA TAGPLYSDNS NISRYSEKEK GEIELAEYRE TGALQDSLLH CVREESIPKK KLRSFKQKSL DIGNADSLLF TLDEHRRK S CIDRCDIEKP PTQAAYIAQR PNDPGRSRQN SATRPDNSEI PENPAMEGFP DARRPVIPEV RLNCMETFEV KVDSPVKPA PKEDLDLIDL SSDSTSGPEK HSILSTSDSD SLVFEPLPPL RIVESDEEEE TMNQGDDGPS GKNAASSPSV PSHPSVLSLS TAPLVQVSV EDCSKDFSSK DSGNNQSAGN TDSALITLED PMDAEGSSKP EELPEFSCGS PLTLKQKRDL LQKSFALPEM S LDDHPDPG TEGEKPGELM PSSGAKTVLL KVPEDAENPT ESEKPDTSAE SDTEQNPERK VEEDGAEESE FKIQIVPRQR KQ RKIAVSA IQREYLDISF NILDKLGEQK DPDPSTKGLS TLEMPRESSS APTLDAGVPE TSSHSSISTQ YRQMKRGSLG VLT MSQLMK RQLEHQSSAP HNISNWDTEQ IQPGKRQCNV PTCLNPDLEG QPLRMRGATK SSLLSAPSIV SMFVPAPEEF TDEQ PTVMT DKCHDCGAIL EEYDEETLGL AIVVLSTFIH LSPDLAAPLL LDIMQSVGRL ASSTTFSNQA ESMMVPGNAA GVAKQ FLRC IFHQLAPNGI FPQLFQSTIK DGTFLRTLAS SLMDFNELSS IAALSQLLEG LNNKKNLPAG GAMIRCLENI ATFMEA LPM DSPSSLWTTI SNQFQTFFAK LPCVLPLKCS LDSSLRIMIC LLKIPSTNAT RSLLEPFSKL LSFVIQNAVF TLAYLVE LC GLCYRAFTKE RDKFYLSRSV VLELLQALKL KSPLPDTNLL LLVQFICADA GTKLAESTIL SKQMIASVPG CGTAAMEC V RQYINEVLDF MADMHTLTKL KSHMKTCSQP LHEDTFGGHL KVGLAQIAAM DISRGNHRDN KAVIRYLPWL YHPPSAMQQ GPKEFIECVS HIRLLSWLLL GSLTHNAVCP NASSPCLPIP LDAGSHVADH LIVILIGFPE QSKTSVLHMC SLFHAFIFAQ LWTVYCEQS AVATNLQNQN EFSFTAILTA LEFWSRVTPS ILQLMAHNKV MVEMVCLHVI SLMEALQECN STIFVKLIPM W LPMIQSNI KHLSAGLQLR LQAIQNHVNH HSLRTLPGSG QSSAGLAALR KWLQCTQFKM AQVEIQSSEA ASQFYPLDEV DA GSDYKDD DKGSDYKDDD K

-
Macromolecule #3: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.852545 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTAK

-
Macromolecule #4: Sodium leak channel non-selective protein,Extended tegument prote...

MacromoleculeName: Sodium leak channel non-selective protein,Extended tegument protein pp150
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 229.017703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLKRKQSSRV EAQPVTDFGP DESLSDNADI LWINKPWVHS LLRICAIISV ISVCMNTPMT FEHYPPLQYV TFTLDTLLMF LYTAEMIAK MHIRGIVKGD SSYVKDRWCV FDGFMVFCLW VSLVLQVFEI ADIVDQMSPW GMLRIPRPLI MIRAFRIYFR F ELPRTRIT ...String:
MLKRKQSSRV EAQPVTDFGP DESLSDNADI LWINKPWVHS LLRICAIISV ISVCMNTPMT FEHYPPLQYV TFTLDTLLMF LYTAEMIAK MHIRGIVKGD SSYVKDRWCV FDGFMVFCLW VSLVLQVFEI ADIVDQMSPW GMLRIPRPLI MIRAFRIYFR F ELPRTRIT NILKRSGEQI WSVSIFLLFF LLLYGILGVQ MFGTFTYHCV VNDTKPGNVT WNSLAIPDTH CSPELEEGYQ CP PGFKCMD LEDLGLSRQE LGYSGFNEIG TSIFTVYEAA SQEGWVFLMY RAIDSFPRWR SYFYFITLIF FLAWLVKNVF IAV IIETFA EIRVQFQQMW GSRSSTTSTA TTQMFHEDAA GGWQLVAVDV NKPQGRAPAC LQKMMRSSVF HMFILSMVTV DVIV AASNY YKGENFRRQY DEFYLAEVAF TVLFDLEALL KIWCLGFTGY ISSSLHKFEL LLVIGTTLHV YPDLYHSQFT YFQVL RVVR LIKISPALED FVYKIFGPGK KLGSLVVFTA SLLIVMSAIS LQMFCFVEEL DRFTTFPRAF MSMFQILTQE GWVDVM DQT LNAVGHMWAP VVAIYFILYH LFATLILLSL FVAVILDNLE LDEDLKKLKQ LKQSEANADT KEKLPLRLRI FEKFPNR PQ MVKISKLPSD FTVPKIRESF MKQFIDRQQQ DTCCLLRSLP TTSSSSCDHS KRSAIEDNKY IDQKLRKSVF SIRARNLL E KETAVTKILR ACTRQRMLSG SFEGQPAKER SILSVQHHIR QERRSLRHGS NSQRISRGKS LETLTQDHSN TVRYRNAQR EDSEIKMIQE KKEQAEMKRK VQEEELRENH PYFDKPLFIV GREHRFRNFC RVVVRARFNA SKTDPVTGAV KNTKYHQLYD LLGLVTYLD WVMIIVTICS CISMMFESPF RRVMHAPTLQ IAEYVFVIFM SIELNLKIMA DGLFFTPTAV IRDFGGVMDI F IYLVSLIF LCWMPQNVPA ESGAQLLMVL RCLRPLRIFK LVPQMRKVVR ELFSGFKEIF LVSILLLTLM LVFASFGVQL FA GKLAKCN DPNIIRREDC NGIFRINVSV SKNLNLKLRP GEKKPGFWVP RVWANPRNFN FDNVGNAMLA LFEVLSLKGW VEV RDVIIH RVGPIHGIYI HVFVFLGCMI GLTLFVGVVI ANFNENKGTA LLTVDQRRWE DLKSRLKIAQ PLHLPPRPDN DGFR AKMYD ITQHPFFKRT IALLVLAQSV LLSVKWDVED PVTVPLATMS VVFTFIFVLE VTMKIIAMSP AGFWQSRRNR YDLLV TSLG VVWVVLHFAL LNAYTYMMGA CVIVFRFFSI CGKHVTLKML LLTVVVSMYK SFFIIVGMFL LLLCYAFAGV VLFGTV KYG ENINRHANFS SAGKAITVLF RIVTGEDWNK IMHDCMVQPP FCTPDEFTYW ATDCGNYAGA LMYFCSFYVI IAYIMLN LL VAIIVENFSL FYSTEEDQLL SYNDLRHFQI IWNMVDDKRE GVIPTFRVKF LLRLLRGRLE VDLDKDKLLF KHMCYEME R LHNGGDVTFH DVLSMLSYRS VDIRKSLQLE ELLAREQLEY TIEEEVAKQT IRMWLKKCLK RIRAKQQQSC SIIHSLRES QQQELSRFLN PPSIETTQPS EDTNANSQDN SMQPETSSQQ QLLSPTLSDR GGSRQDAADA GKPQRKFGQW RLPSAPKPIS HSVSSVNLR FGGRTTMKSV VCKMNPMTDA ASCGSEVKKW WTRQLTVESD ESGDDLLDIL EGSENLYFQG GGGSMVSKGE E LFTGVVPI LVELDGDVNG HKFSVSGEGE GDATYGKLTL KFICTTGKLP VPWPTLVTTL TYGVQCFSRY PDHMKQHDFF KS AMPEGYV QERTIFFKDD GNYKTRAEVK FEGDTLVNRI ELKGIDFKED GNILGHKLEY NYNSHNVYIM ADKQKNGIKV NFK IRHNIE DGSVQLADHY QQNTPIGDGP VLLPDNHYLS TQSALSKDPN EKRDHMVLLE FVTAAGITLG MDELYK

-
Macromolecule #5: Transmembrane protein FAM155A

MacromoleculeName: Transmembrane protein FAM155A / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.550484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTRGAWMCRQ YDDGLKIWLA APRENEKPFI DSERAQKWRL SLASLLFFTV LLSDHLWFCA EAKLTRARDK EHQQQQRQQQ QQQQQQRQR QQQQQQRRQQ EPSWPALLAS MGESSPAAQA HRLLSASSSP TLPPSPGDGG GGGGKGNRGK DDRGKALFLG N SAKPVWRL ...String:
MTRGAWMCRQ YDDGLKIWLA APRENEKPFI DSERAQKWRL SLASLLFFTV LLSDHLWFCA EAKLTRARDK EHQQQQRQQQ QQQQQQRQR QQQQQQRRQQ EPSWPALLAS MGESSPAAQA HRLLSASSSP TLPPSPGDGG GGGGKGNRGK DDRGKALFLG N SAKPVWRL ETCYPQGASS GQCFTVENAD AVCARNWSRG AAGGDGQEVR SKHPTPLWNL SDFYLSFCNS YTLWELFSGL SS PNTLNCS LDVVLKEGGE MTTCRQCVEA YQDYDHHAQE KYEEFESVLH KYLQSEEYSV KSCPEDCKIV YKAWLCSQYF EVT QFNCRK TIPCKQYCLE VQTRCPFILP DNDEVIYGGL SSFICTGLYE TFLTNDEPEC CDVRREEKSN NPSKGTVEKS GSCH RTSLT VSSATRLCNS RLKLCVLVLI LLHTVLTASA AQNTAGLSFG GINTLEENST NEE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K

-
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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: COMMON LINE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 174294

+
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