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- EMDB-28827: Human CCC complex -

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Basic information

Entry
Database: EMDB / ID: EMD-28827
TitleHuman CCC complex
Map dataPost-processed sharpened map. B factor -24
Sample
  • Complex: Human CCC complex
    • Protein or peptide: x 12 types
Function / homology
Function and homology information


negative regulation of sodium ion transmembrane transport / cytoplasmic sequestering of NF-kappaB / plasma membrane to endosome transport / regulation of proteasomal ubiquitin-dependent protein catabolic process / copper ion homeostasis / negative regulation of protein localization to cell surface / Golgi to plasma membrane transport / phosphatidic acid binding / positive regulation of ubiquitin-dependent protein catabolic process / endocytic recycling ...negative regulation of sodium ion transmembrane transport / cytoplasmic sequestering of NF-kappaB / plasma membrane to endosome transport / regulation of proteasomal ubiquitin-dependent protein catabolic process / copper ion homeostasis / negative regulation of protein localization to cell surface / Golgi to plasma membrane transport / phosphatidic acid binding / positive regulation of ubiquitin-dependent protein catabolic process / endocytic recycling / phosphatidylinositol-3,4-bisphosphate binding / sodium channel inhibitor activity / phosphatidylinositol-3,5-bisphosphate binding / Cul2-RING ubiquitin ligase complex / sodium ion transport / negative regulation of NF-kappaB transcription factor activity / cullin family protein binding / phosphatidylinositol-3,4,5-trisphosphate binding / intracellular copper ion homeostasis / NF-kappaB binding / negative regulation of canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / phosphatidylinositol-4,5-bisphosphate binding / cholesterol homeostasis / positive regulation of protein ubiquitination / nucleotide-excision repair / recycling endosome / protein transport / Neddylation / cytoplasmic vesicle / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / ficolin-1-rich granule lumen / early endosome / endosome membrane / endosome / copper ion binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / centrosome / Neutrophil degranulation / Golgi apparatus / protein homodimerization activity / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
COMM domain-containing protein 2 / COMM domain-containing protein 3 / COMM domain-containing protein 4 / : / COMMD1 N-terminal domain / COMM domain-containing protein 1 / COMM domain-containing protein 5 / COMM domain-containing protein 7 / COMM domain-containing protein 10 / : ...COMM domain-containing protein 2 / COMM domain-containing protein 3 / COMM domain-containing protein 4 / : / COMMD1 N-terminal domain / COMM domain-containing protein 1 / COMM domain-containing protein 5 / COMM domain-containing protein 7 / COMM domain-containing protein 10 / : / COMMD1 N-terminal domain / COMMD protein HN domain / Coiled-coil domain-containing protein 22 / CCDC93, coiled-coil domain / Coiled-coil domain-containing protein 93 / : / : / : / CCDC22 protein coiled-coil region / CCDC93 coiled-coil domain / CCDC93 protein N-terminal domain / CCDC22 protein N-terminal domain / COMM domain-containing protein 9 / : / COMMD9, N-terminal domain / COMM domain / COMM domain / COMM domain profile.
Similarity search - Domain/homology
Coiled-coil domain-containing protein 22 / Coiled-coil domain-containing protein 93 / COMM domain-containing protein 6 / COMM domain-containing protein 7 / COMM domain-containing protein 2 / COMM domain-containing protein 1 / COMM domain-containing protein 5 / COMM domain-containing protein 4 / COMM domain-containing protein 8 / COMM domain-containing protein 9 ...Coiled-coil domain-containing protein 22 / Coiled-coil domain-containing protein 93 / COMM domain-containing protein 6 / COMM domain-containing protein 7 / COMM domain-containing protein 2 / COMM domain-containing protein 1 / COMM domain-containing protein 5 / COMM domain-containing protein 4 / COMM domain-containing protein 8 / COMM domain-containing protein 9 / COMM domain-containing protein 3 / COMM domain-containing protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsHealy MD / McNally KE / Butkovic R / Chilton M / Kato K / Sacharz J / McConville C / Moody ERR / Shaw S / Planelles-Herrero VJ ...Healy MD / McNally KE / Butkovic R / Chilton M / Kato K / Sacharz J / McConville C / Moody ERR / Shaw S / Planelles-Herrero VJ / Kadapalakere SY / Ross J / Borucu U / Palmer CS / Chen K / Croll TI / Hall RJ / Caruana NJ / Ghai R / Nguyen THD / Heesom KJ / Saitoh S / Berger I / Berger-Schaffitzel C / Williams TA / Stroud DA / Derivery E / Collins BM / Cullen PJ
Funding support United Kingdom, Australia, 9 items
OrganizationGrant numberCountry
Wellcome Trust104568/Z/14/Z United Kingdom
Wellcome Trust220260/Z/20/Z United Kingdom
Wellcome Trust220480/Z/20/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/L007363/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/P018807/1 United Kingdom
The Lister Institute of Preventive Medicine United Kingdom
Royal SocietyRSRP/R1/211004 United Kingdom
National Health and Medical Research Council (NHMRC, Australia)APP1136021 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1156493 Australia
CitationJournal: Cell / Year: 2023
Title: Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome.
Authors: Michael D Healy / Kerrie E McNally / Rebeka Butkovič / Molly Chilton / Kohji Kato / Joanna Sacharz / Calum McConville / Edmund R R Moody / Shrestha Shaw / Vicente J Planelles-Herrero / ...Authors: Michael D Healy / Kerrie E McNally / Rebeka Butkovič / Molly Chilton / Kohji Kato / Joanna Sacharz / Calum McConville / Edmund R R Moody / Shrestha Shaw / Vicente J Planelles-Herrero / Sathish K N Yadav / Jennifer Ross / Ufuk Borucu / Catherine S Palmer / Kai-En Chen / Tristan I Croll / Ryan J Hall / Nikeisha J Caruana / Rajesh Ghai / Thi H D Nguyen / Kate J Heesom / Shinji Saitoh / Imre Berger / Christiane Schaffitzel / Tom A Williams / David A Stroud / Emmanuel Derivery / Brett M Collins / Peter J Cullen /
Abstract: The Commander complex is required for endosomal recycling of diverse transmembrane cargos and is mutated in Ritscher-Schinzel syndrome. It comprises two sub-assemblies: Retriever composed of VPS35L, ...The Commander complex is required for endosomal recycling of diverse transmembrane cargos and is mutated in Ritscher-Schinzel syndrome. It comprises two sub-assemblies: Retriever composed of VPS35L, VPS26C, and VPS29; and the CCC complex which contains twelve subunits: COMMD1-COMMD10 and the coiled-coil domain-containing (CCDC) proteins CCDC22 and CCDC93. Combining X-ray crystallography, electron cryomicroscopy, and in silico predictions, we have assembled a complete structural model of Commander. Retriever is distantly related to the endosomal Retromer complex but has unique features preventing the shared VPS29 subunit from interacting with Retromer-associated factors. The COMMD proteins form a distinctive hetero-decameric ring stabilized by extensive interactions with CCDC22 and CCDC93. These adopt a coiled-coil structure that connects the CCC and Retriever assemblies and recruits a 16th subunit, DENND10, to form the complete Commander complex. The structure allows mapping of disease-causing mutations and reveals the molecular features required for the function of this evolutionarily conserved trafficking machinery.
History
DepositionNov 8, 2022-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateMay 24, 2023-
Current statusMay 24, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28827.png

Downloads & links

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Map

FileDownload / File: emd_28827.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed sharpened map. B factor -24
Voxel sizeX=Y=Z: 1.084 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.035145126 - 0.06553532
Average (Standard dev.)-0.00023393621 (±0.003132012)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 286.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Refine 3D map

Fileemd_28827_additional_1.map
AnnotationRefine 3D map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_28827_half_map_1.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_28827_half_map_2.map
AnnotationHalf map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Human CCC complex

EntireName: Human CCC complex
Components
  • Complex: Human CCC complex
    • Protein or peptide: COMM domain-containing protein 1
    • Protein or peptide: COMM domain-containing protein 2
    • Protein or peptide: COMM domain-containing protein 3
    • Protein or peptide: COMM domain-containing protein 4
    • Protein or peptide: COMM domain-containing protein 5
    • Protein or peptide: COMM domain-containing protein 6
    • Protein or peptide: COMM domain-containing protein 7
    • Protein or peptide: COMM domain-containing protein 8
    • Protein or peptide: COMM domain-containing protein 9
    • Protein or peptide: COMM domain-containing protein 10
    • Protein or peptide: Coiled-coil domain-containing protein 93
    • Protein or peptide: Coiled-coil domain-containing protein 22

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Supramolecule #1: Human CCC complex

SupramoleculeName: Human CCC complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: COMM domain-containing protein 1

MacromoleculeName: COMM domain-containing protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.203061 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString:
MAAGELEGGK PLSGLLNALA QDTFHGYPGI TEELLRSQLY PEVPPEEFRP FLAKMRGILK SIASADMDFN QLEAFLTAQT KKQGGITSD QAAVISKFWK SHKTKIRESL MNQSRWNSGL RGLSWRVDGK SQSRHSAQIH TPVAIIELEL GKYGQESEFL C LEFDEVKV NQILKTLSEV EESISTLISQ PN

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Macromolecule #2: COMM domain-containing protein 2

MacromoleculeName: COMM domain-containing protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.776113 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MLLELSEEHK EHLAFLPQVD SAVVAEFGRI AVEFLRRGAN PKIYEGAARK LNVSSDTVQH GVEGLTYLLT ESSKLMISEL DFQDSVFVL GFSEELNKLL LQLYLDNRKE IRTILSELAP SLPSYHNLEW RLDVQLASRS LRQQIKPAVT IKLHLNQNGD H NTKVLQTD ...String:
MLLELSEEHK EHLAFLPQVD SAVVAEFGRI AVEFLRRGAN PKIYEGAARK LNVSSDTVQH GVEGLTYLLT ESSKLMISEL DFQDSVFVL GFSEELNKLL LQLYLDNRKE IRTILSELAP SLPSYHNLEW RLDVQLASRS LRQQIKPAVT IKLHLNQNGD H NTKVLQTD PATLLHLVQQ LEQALEEMKT NHCRRVVRNI K

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Macromolecule #3: COMM domain-containing protein 3

MacromoleculeName: COMM domain-containing protein 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.179117 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MELSESVQKG FQMLADPRSF DSNAFTLLLR AAFQSLLDAQ ADEAVLDHPD LKHIDPVVLK HCHAAAATYI LEAGKHRADK STLSTYLED CKFDRERIEL FCTEYQNNKN SLEILLGSIG RSLPHITDVS WRLEYQIKTN QLHRMYRPAY LVTLSVQNTD S PSYPEISF ...String:
MELSESVQKG FQMLADPRSF DSNAFTLLLR AAFQSLLDAQ ADEAVLDHPD LKHIDPVVLK HCHAAAATYI LEAGKHRADK STLSTYLED CKFDRERIEL FCTEYQNNKN SLEILLGSIG RSLPHITDVS WRLEYQIKTN QLHRMYRPAY LVTLSVQNTD S PSYPEISF SCSMEQLQDL VGKLKDASKS LERATQL

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Macromolecule #4: COMM domain-containing protein 4

MacromoleculeName: COMM domain-containing protein 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.790354 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MRFRFCGDLD CPDWVLAEIS TLAKMSSVKL RLLCSQVLKE LLGQGIDYEK ILKLTADAKF ESGDVKATVA VLSFILSSAA KHSVDGESL SSELQQLGLP KEHAASLCRC YEEKQSPLQK HLRVCSLRMN RLAGVGWRVD YTLSSSLLQS VEEPMVHLRL E VAAAPGTP ...String:
MRFRFCGDLD CPDWVLAEIS TLAKMSSVKL RLLCSQVLKE LLGQGIDYEK ILKLTADAKF ESGDVKATVA VLSFILSSAA KHSVDGESL SSELQQLGLP KEHAASLCRC YEEKQSPLQK HLRVCSLRMN RLAGVGWRVD YTLSSSLLQS VEEPMVHLRL E VAAAPGTP AQPVAMSLSA DKFQVLLAEL KQAQTLMSSL G

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Macromolecule #5: COMM domain-containing protein 5

MacromoleculeName: COMM domain-containing protein 5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.346219 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MSAVGAATPY LHHPGDSHSG RVSFLGAQLP PEVAAMARLL GDLDRSTFRK LLKFVVSSLQ GEDCREAVQR LGVSANLPEE QLGALLAGM HTLLQQALRL PPTSLKPDTF RDQLQELCIP QDLVGDLASV VFGSQRPLLD SVAQQQGAWL PHVADFRWRV D VAISTSAL ...String:
MSAVGAATPY LHHPGDSHSG RVSFLGAQLP PEVAAMARLL GDLDRSTFRK LLKFVVSSLQ GEDCREAVQR LGVSANLPEE QLGALLAGM HTLLQQALRL PPTSLKPDTF RDQLQELCIP QDLVGDLASV VFGSQRPLLD SVAQQQGAWL PHVADFRWRV D VAISTSAL ARSLQPSVLM QLKLSDGSAY RFEVPTAKFQ ELRYSVALVL KEMADLEKRC ERRLQDGSLF QGPWSHPQFE KG GGSGGGS GGSSAWSHPQ FEK

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Macromolecule #6: COMM domain-containing protein 6

MacromoleculeName: COMM domain-containing protein 6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.648074 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString:
MEASSEPPLD AKSDVTNQLV DFQWKLGMAV SSDTCRSLKY PYVAVMLKVA DHSGQVKTKC FEMTIPQFQN FYRQFKEIAA VIETV

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Macromolecule #7: COMM domain-containing protein 7

MacromoleculeName: COMM domain-containing protein 7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.561953 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MGRLHCTEDP VPEAVGGDMQ QLNQLGAQQF SALTEVLFHF LTEPKEVERF LAQLSEFATT NQISLGSLRS IVKSLLLVPN GALKKSLTA KQVQADFITL GLSEEKATYF SEKWKQNAPT LARWAIGQTL MINQLIDMEW KFGVTSGSSE LEKVGSIFLQ L KLVVKKGN ...String:
MGRLHCTEDP VPEAVGGDMQ QLNQLGAQQF SALTEVLFHF LTEPKEVERF LAQLSEFATT NQISLGSLRS IVKSLLLVPN GALKKSLTA KQVQADFITL GLSEEKATYF SEKWKQNAPT LARWAIGQTL MINQLIDMEW KFGVTSGSSE LEKVGSIFLQ L KLVVKKGN QTENVYIELT LPQFYSFLHE MERVRTSMEC FC

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Macromolecule #8: COMM domain-containing protein 8

MacromoleculeName: COMM domain-containing protein 8 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.116342 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString:
MEPEEGTPLW RLQKLPAELG PQLLHKIIDG ICGRAYPVYQ DYHTVWESEE WMHVLEDIAK FFKAIVGKNL PDEEIFQQLN QLNSLHQET IMKCVKSRKD EIKQALSREI VAISSAQLQD FDWQVKLALS SDKIAALRMP LLSLHLDVKE NGEVKPYSIE M SREELQNL IQSLEAANKV VLQLK

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Macromolecule #9: COMM domain-containing protein 9

MacromoleculeName: COMM domain-containing protein 9 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.844117 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MAALTAEHFA ALQSLLKASS KDVVRQLCQE SFSSSALGLK KLLDVTCSSL SVTQEEAEEL LQALHRLTRL VAFRDLSSAE AILALFPEN FHQNLKNLLT KIILEHVSTW RTEAQANQIS LPRLVDLDWR VDIKTSSDSI SRMAVPTCLL QMKIQEDPSL C GDKPSISA ...String:
MAALTAEHFA ALQSLLKASS KDVVRQLCQE SFSSSALGLK KLLDVTCSSL SVTQEEAEEL LQALHRLTRL VAFRDLSSAE AILALFPEN FHQNLKNLLT KIILEHVSTW RTEAQANQIS LPRLVDLDWR VDIKTSSDSI SRMAVPTCLL QMKIQEDPSL C GDKPSISA VTVELSKETL DTMLDGLGRI RDQLSAVASK

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Macromolecule #10: COMM domain-containing protein 10

MacromoleculeName: COMM domain-containing protein 10 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.376871 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MAVPAALILR ESPSMKKAVS LINAIDTGRF PRLLTRILQK LHLKAESSFS EEEEEKLQAA FSLEKQDLHL VLETISFILE QAVYHNVKP AALQQQLENI HLRQDKAEAF VNTWSSMGQE TVEKFRQRIL APCKLETVGW QLNLQMAHSA QAKLKSPQAV L QLGVNNED ...String:
MAVPAALILR ESPSMKKAVS LINAIDTGRF PRLLTRILQK LHLKAESSFS EEEEEKLQAA FSLEKQDLHL VLETISFILE QAVYHNVKP AALQQQLENI HLRQDKAEAF VNTWSSMGQE TVEKFRQRIL APCKLETVGW QLNLQMAHSA QAKLKSPQAV L QLGVNNED SKSLEKVLVE FSHKELFDFY NKLETIQAQL DSLTHHHHHH HHHH

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Macromolecule #11: Coiled-coil domain-containing protein 93

MacromoleculeName: Coiled-coil domain-containing protein 93 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.319734 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MGLPRGPEGQ GLPEVETRED EEQNVKLTEI LELLVAAGYF RARIKGLSPF DKVVGGMTWC ITTCNFDVDV DLLFQENSTI GQKIALSEK IVSVLPRMKC PHQLEPHQIQ GMDFIHIFPV VQWLVKRAIE TKEEMGDYIR SYSVSQFQKT YSLPEDDDFI K RKEKAIKT ...String:
MGLPRGPEGQ GLPEVETRED EEQNVKLTEI LELLVAAGYF RARIKGLSPF DKVVGGMTWC ITTCNFDVDV DLLFQENSTI GQKIALSEK IVSVLPRMKC PHQLEPHQIQ GMDFIHIFPV VQWLVKRAIE TKEEMGDYIR SYSVSQFQKT YSLPEDDDFI K RKEKAIKT VVDLSEVYKP RRKYKRHQGA EELLDEESRI HATLLEYGRR YGFSRQSKME KAEDKKTALP AGLSATEKAD AH EEDELRA AEEQRIQSLM TKMTAMANEE SRLTASSVGQ IVGLCSAEIK QIVSEYAEKQ SELSAEESPE KLGTSQLHRR KVI SLNKQI AQKTKHLEEL RASHTSLQAR YNEAKKTLTE LKTYSEKLDK EQAALEKIES KADPSILQNL RALVAMNENL KSQE QEFKA HCREEMTRLQ QEIENLKAER APRGDEKTLS SGEPPGTLTS AMTHDEDLDR RYNMEKEKLY KIRLLQARRN REIAI LHRK IDEVPSRAEL IQYQKRFIEL YRQISAVHKE TKQFFTLYNT LDDKKVYLEK EISLLNSIHE NFSQAMASPA ARDQFL RQM EQIVEGIKQS RMKMEKKKQE NKMRRDQLND QYLELLEKQR LYFKTVKEFK EEGRKNEMLL SKVKAKAS

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Macromolecule #12: Coiled-coil domain-containing protein 22

MacromoleculeName: Coiled-coil domain-containing protein 22 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.856555 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MEEADRILIH SLRQAGTAVP PDVQTLRAFT TELVVEAVVR CLRVINPAVG SGLSPLLPLA MSARFRLAMS LAQACMDLGY PLELGYQNF LYPSEPDLRD LLLFLAERLP TDASEDADQP AGDSAILLRA IGSQIRDQLA LPWVPPHLRT PKLQHLQGSA L QKPFHASR ...String:
MEEADRILIH SLRQAGTAVP PDVQTLRAFT TELVVEAVVR CLRVINPAVG SGLSPLLPLA MSARFRLAMS LAQACMDLGY PLELGYQNF LYPSEPDLRD LLLFLAERLP TDASEDADQP AGDSAILLRA IGSQIRDQLA LPWVPPHLRT PKLQHLQGSA L QKPFHASR LVVPELSSRG EPREFQASPL LLPVPTQVPQ PVGRVASLLE HHALQLCQQT GRDRPGDEDW VHRTSRLPPQ ED TRAQRQR LQKQLTEHLR QSWGLLGAPI QARDLGELLQ AWGAGAKTGA PKGSRFTHSE KFTFHLEPQA QATQVSDVPA TSR RPEQVT WAAQEQELES LREQLEGVNR SIEEVEADMK TLGVSFVQAE SECRHSKLST AEREQALRLK SRAVELLPDG TANL AKLQL VVENSAQRVI HLAGQWEKHR VPLLAEYRHL RKLQDCRELE SSRRLAEIQE LHQSVRAAAE EARRKEEVYK QLMSE LETL PRDVSRLAYT QRILEIVGNI RKQKEEITKI LSDTKELQKE INSLSGKLDR TFAVTDELVF KDAKKDDAVR KAYKYL AAL HENCSQLIQT IEDTGTIMRE VRDLEEQIET ELGKKTLSNL EKIREDYRAL RQENAGLLGR VREA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.2
Details: 50 mM HEPES pH7.2, 150 mM NaCl, 2mM beta-mercaptoethanol, 0.01% Triton-X100
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsHuman CCC complex cross-linked with 1 mM BS3

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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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 5651 / Average exposure time: 9.01 sec. / Average electron dose: 43.14 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationSoftware - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 20034
FSC plot (resolution estimation)

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  • 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

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