[English] 日本語
Yorodumi
- EMDB-12965: Cryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1-CSN Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12965
TitleCryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1-CSN Complex
Map data
Sample
  • Complex: CRL4(DCAF1)-CSN
    • Protein or peptide: x 11 types
Function / homology
Function and homology information


cell competition in a multicellular organism / histone H2AT120 kinase activity / negative regulation of granulocyte differentiation / negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / V(D)J recombination / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / cellular response to chemical stress ...cell competition in a multicellular organism / histone H2AT120 kinase activity / negative regulation of granulocyte differentiation / negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / V(D)J recombination / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / cellular response to chemical stress / regulation of DNA damage checkpoint / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation by virus of viral protein levels in host cell / positive regulation of protein autoubiquitination / regulation of nucleotide-excision repair / RNA polymerase II transcription initiation surveillance / protein neddylation / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / NEDD8 ligase activity / protein K27-linked ubiquitination / negative regulation of response to oxidative stress / UV-damage excision repair / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / SCF ubiquitin ligase complex / biological process involved in interaction with symbiont / Cul2-RING ubiquitin ligase complex / regulation of mitotic cell cycle phase transition / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4-RING E3 ubiquitin ligase complex / negative regulation of mitophagy / Prolactin receptor signaling / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / hemopoiesis / somatic stem cell population maintenance / viral release from host cell / cullin family protein binding / protein monoubiquitination / ectopic germ cell programmed cell death / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of viral genome replication / ubiquitin-like ligase-substrate adaptor activity / site of DNA damage / signal transduction in response to DNA damage / Nuclear events stimulated by ALK signaling in cancer / transcription-coupled nucleotide-excision repair / protein K48-linked ubiquitination / negative regulation of insulin receptor signaling pathway / proteasomal protein catabolic process / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / intrinsic apoptotic signaling pathway / post-translational protein modification / positive regulation of gluconeogenesis / B cell differentiation / T cell activation / Regulation of BACH1 activity / nuclear estrogen receptor binding / negative regulation of canonical NF-kappaB signal transduction / nucleotide-excision repair / sperm end piece / cellular response to amino acid stimulus / Degradation of DVL / Degradation of CRY and PER proteins / G1/S transition of mitotic cell cycle / Degradation of GLI1 by the proteasome / negative regulation of canonical Wnt signaling pathway / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Recognition of DNA damage by PCNA-containing replication complex / Hedgehog 'on' state / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Vif-mediated degradation of APOBEC3G / regulation of circadian rhythm / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / RING-type E3 ubiquitin transferase / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / DNA Damage Recognition in GG-NER / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Regulation of expression of SLITs and ROBOs / fibrillar center
Similarity search - Function
VPRBP/DCAF1 family / Lissencephaly type-1-like homology motif / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Cullin, N-terminal / Cullin protein neddylation domain / : / Cullin, conserved site ...VPRBP/DCAF1 family / Lissencephaly type-1-like homology motif / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Cullin, N-terminal / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin alpha solenoid domain / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / : / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / Cullin-4A / DNA damage-binding protein 1 / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 23.0 Å
AuthorsMohamed WI / Schenk AD / Kempf G / Cavadini S / Thoma NH
CitationJournal: EMBO J / Year: 2021
Title: The CRL4 cullin-RING ubiquitin ligase is activated following a switch in oligomerization state.
Authors: Weaam I Mohamed / Andreas D Schenk / Georg Kempf / Simone Cavadini / Anja Basters / Alessandro Potenza / Wassim Abdul Rahman / Julius Rabl / Kurt Reichermeier / Nicolas H Thomä /
Abstract: The cullin-4-based RING-type (CRL4) family of E3 ubiquitin ligases functions together with dedicated substrate receptors. Out of the ˜29 CRL4 substrate receptors reported, the DDB1- and CUL4- ...The cullin-4-based RING-type (CRL4) family of E3 ubiquitin ligases functions together with dedicated substrate receptors. Out of the ˜29 CRL4 substrate receptors reported, the DDB1- and CUL4-associated factor 1 (DCAF1) is essential for cellular survival and growth, and its deregulation has been implicated in tumorigenesis. We carried out biochemical and structural studies to examine the structure and mechanism of the CRL4 ligase. In the 8.4 Å cryo-EM map of CRL4 , four CUL4-RBX1-DDB1-DCAF1 protomers are organized into two dimeric sub-assemblies. In this arrangement, the WD40 domain of DCAF1 mediates binding with the cullin C-terminal domain (CTD) and the RBX1 subunit of a neighboring CRL4 protomer. This renders RBX1, the catalytic subunit of the ligase, inaccessible to the E2 ubiquitin-conjugating enzymes. Upon CRL4 activation by neddylation, the interaction between the cullin CTD and the neighboring DCAF1 protomer is broken, and the complex assumes an active dimeric conformation. Accordingly, a tetramerization-deficient CRL4 mutant has higher ubiquitin ligase activity compared to the wild-type. This study identifies a novel mechanism by which unneddylated and substrate-free CUL4 ligases can be maintained in an inactive state.
History
DepositionMay 18, 2021-
Header (metadata) releaseOct 13, 2021-
Map releaseOct 13, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00129
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.00129
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12965.png

Downloads & links

-
Map

FileDownload / File: emd_12965.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 320 pix.
= 397.216 Å		1.24 Å/pix.
x 320 pix.
= 397.216 Å		1.24 Å/pix.
x 320 pix.
= 397.216 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2413 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00129 / Movie #1: 0.00129
Minimum - Maximum-0.005315238 - 0.0097976625
Average (Standard dev.)3.5354697e-05 (±0.0009297621)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 397.216 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.24131.24131.2413
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z397.216397.216397.216
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0050.0100.000

-
Supplemental data

-
Sample components

+
Entire : CRL4(DCAF1)-CSN

EntireName: CRL4(DCAF1)-CSN
Components
  • Complex: CRL4(DCAF1)-CSN
    • Protein or peptide: DCAF1
    • Protein or peptide: DDB1
    • Protein or peptide: Cul4A
    • Protein or peptide: Rbx1-CSN4
    • Protein or peptide: CSN1
    • Protein or peptide: CSN2
    • Protein or peptide: CSN3
    • Protein or peptide: CSN5
    • Protein or peptide: CSN6
    • Protein or peptide: CSN7
    • Protein or peptide: CSN8

+
Supramolecule #1: CRL4(DCAF1)-CSN

SupramoleculeName: CRL4(DCAF1)-CSN / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

+
Macromolecule #1: DCAF1

MacromoleculeName: DCAF1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MASWSHPQFE KLEVLFQGPT TVVVHVDSKA ELTTLLEQWE KEHGSGQDMV PILTRMSQLI EKETEEYRK GDPDPFDDRH PGRADPECML GHLLRILFKN DDFMNALVNA YVMTSREPPL N TAACRLLL DIMPGLETAV VFQEKEGIVE NLFKWAREAD QPLRTYSTGL ...String:
MASWSHPQFE KLEVLFQGPT TVVVHVDSKA ELTTLLEQWE KEHGSGQDMV PILTRMSQLI EKETEEYRK GDPDPFDDRH PGRADPECML GHLLRILFKN DDFMNALVNA YVMTSREPPL N TAACRLLL DIMPGLETAV VFQEKEGIVE NLFKWAREAD QPLRTYSTGL LGGAMENQDI AA NYRDENS QLVAIVLRRL RELQLQEVAL RQENKRPSPR KLSSEPLLPL DEEAVDMDYG DMA VDVVDG DQEEASGDME ISFHLDSGHK TSSRVNSTTK PEDGGLKKNK SAKQGDRENF RKAK QKLGF SSSDPDRMFV ELSNSSWSEM SPWVIGTNYT LYPMTPAIEQ RLILQYLTPL GEYQE LLPI FMQLGSRELM MFYIDLKQTN DVLLTFEALK HLASLLLHNK FATEFVAHGG VQKLLE IPR PSMAATGVSM CLYYLSYNQD AMERVCMHPH NVLSDVVNYT LWLMECSHAS GCCHATM FF SICFSFRAVL ELFDRYDGLR RLVNLISTLE ILNLEDQGAL LSDDEIFASR QTGKHTCM A LRKYFEAHLA IKLEQVKQSL QRTEGGILVH PQPPYKACSY THEQIVEMME FLIEYGPAQ LYWEPAEVFL KLSCVQLLLQ LISIACNWKT YYARNDTVRF ALDVLAILTV VPKIQLQLAE SVDVLDEAG STVSTVGISI ILGVAEGEFF IHDAEIQKSA LQIIINCVCG PDNRISSIGK F ISGTPRRK LPQNPKSSEH TLAKMWNVVQ SNNGIKVLLS LLSIKMPITD ADQIRALACK AL VGLSRSS TVRQIISKLP LFSSCQIQQL MKEPVLQDKR SDHVKFCKYA AELIERVSGK PLL IGTDVS LARLQKADVV AQSRISFPEK ELLLLIRNHL ISKGLGETAT VLTKEADLPM TAAS HSSAF TPVTAAASPV SLPRTPRIAN GIATRLGSHA AVGASAPSAP TAHPQPRPPQ GPLAL PGPS YAGNSPLIGR ISFIRERPSP CNGRKIRVLR QKSDHGAYSQ SPAIKKQLDR HLPSPP TLD SIITEYLREQ HARCKNPVAT CPPFSLFTPH QCPEPKQRRQ APINFTSRLN RRASFPK YG GVDGGCFDRH LIFSRFRPIS VFREANEDES GFTCCAFSAR ERFLMLGTCT GQLKLYNV F SGQEEASYNC HNSAITHLEP SRDGSLLLTS ATWSQPLSAL WGMKSVFDMK HSFTEDHYV EFSKHSQDRV IGTKGDIAHI YDIQTGNKLL TLFNPDLANN YKRNCATFNP TDDLVLNDGV LWDVRSAQA IHKFDKFNMN ISGVFHPNGL EVIINTEIWD LRTFHLLHTV PALDQCRVVF N HTGTVMYG AMLQADDEDD LMEERMKSPF GSSFRTFNAT DYKPIATIDV KRNIFDLCTD TK DCYLAVI ENQGSMDALN MDTVCRLYEV GRQRLAEDED EEEDQEEEEQ EEEDDDEDDD DTD DLDELD TDQLLEAELE EDDNNENAGE DGDNDFSPSD EELANLLEEG EDGEDEDSDA DEEV ELILG DTDSSDNSDL EDDIILSLNE

+
Macromolecule #2: DDB1

MacromoleculeName: DDB1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MHHHHHHVDE NLYFQGGGRM SYNYVVTAQK PTAVNGCVTG HFTSAEDLNL LIAKNTRLEI YVVTAEGLRP VKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI IGIIDPECR MIGLRLYDGL FKVIPLDRDN ...String:
MHHHHHHVDE NLYFQGGGRM SYNYVVTAQK PTAVNGCVTG HFTSAEDLNL LIAKNTRLEI YVVTAEGLRP VKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI IGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL EELHVIDVKF LYGCQAPTIC F VYQDPQGR HVKTYEVSLR EKEFNKGPWK QENVEAEASM VIAVPEPFGG AIIIGQESIT YH NGDKYLA IAPPIIKQST IVCHNRVDPN GSRYLLGDME GRLFMLLLEK EEQMDGTVTL KDL RVELLG ETSIAECLTY LDNGVVFVGS RLGDSQLVKL NVDSNEQGSY VVAMETFTNL GPIV DMCVV DLERQGQGQL VTCSGAFKEG SLRIIRNGIG IHEHASIDLP GIKGLWPLRS DPNRE TDDT LVLSFVGQTR VLMLNGEEVE ETELMGFVDD QQTFFCGNVA HQQLIQITSA SVRLVS QEP KALVSEWKEP QAKNISVASC NSSQVVVAVG RALYYLQIHP QELRQISHTE MEHEVAC LD ITPLGDSNGL SPLCAIGLWT DISARILKLP SFELLHKEML GGEIIPRSIL MTTFESSH Y LLCALGDGAL FYFGLNIETG LLSDRKKVTL GTQPTVLRTF RSLSTTNVFA CSDRPTVIY SSNHKLVFSN VNLKEVNYMC PLNSDGYPDS LALANNSTLT IGTIDEIQKL HIRTVPLYES PRKICYQEV SQCFGVLSSR IEVQDTSGGT TALRPSASTQ ALSSSVSSSK LFSSSTAPHE T SFGEEVEV HNLLIIDQHT FEVLHAHQFL QNEYALSLVS CKLGKDPNTY FIVGTAMVYP EE AEPKQGR IVVFQYSDGK LQTVAEKEVK GAVYSMVEFN GKLLASINST VRLYEWTTEK ELR TECNHY NNIMALYLKT KGDFILVGDL MRSVLLLAYK PMEGNFEEIA RDFNPNWMSA VEIL DDDNF LGAENAFNLF VCQKDSAATT DEERQHLQEV GLFHLGEFVN VFCHGSLVMQ NLGET STPT QGSVLFGTVN GMIGLVTSLS ESWYNLLLDM QNRLNKVIKS VGKIEHSFWR SFHTER KTE PATGFIDGDL IESFLDISRP KMQEVVANLQ YDDGSGMKRE ATADDLIKVV EELTRIH

+
Macromolecule #3: Cul4A

MacromoleculeName: Cul4A / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MHHHHHHVDE ENLYFQGGGR GGSKKLVIKN FRDRPRLPDN YTQDTWRKLH EAVRAVQSST SIRYNLEELY QAVENLCSHK VSPMLYKQL RQACEDHVQA QILPFREDSL DSVLFLKKIN TCWQDHCRQM IMIRSIFLFL D RTYVLQNS TLPSIWDMGL ELFRTHIISD ...String:
MHHHHHHVDE ENLYFQGGGR GGSKKLVIKN FRDRPRLPDN YTQDTWRKLH EAVRAVQSST SIRYNLEELY QAVENLCSHK VSPMLYKQL RQACEDHVQA QILPFREDSL DSVLFLKKIN TCWQDHCRQM IMIRSIFLFL D RTYVLQNS TLPSIWDMGL ELFRTHIISD KMVQSKTIDG ILLLIERERS GEAVDRSLLR SL LGMLSDL QVYKDSFELK FLEETNCLYA AEGQRLMQER EVPEYLNHVS KRLEEEGDRV ITY LDHSTQ KPLIACVEKQ LLGEHLTAIL QKGLDHLLDE NRVPDLAQMY QLFSRVRGGQ QALL QHWSE YIKTFGTAIV INPEKDKDMV QDLLDFKDKV DHVIEVCFQK NERFVNLMKE SFETF INKR PNKPAELIAK HVDSKLRAGN KEATDEELER TLDKIMILFR FIHGKDVFEA FYKKDL AKR LLVGKSASVD AEKSMLSKLK HECGAAFTSK LEGMFKDMEL SKDIMVHFKQ HMQNQSD SG PIDLTVNILT MGYWPTYTPM EVHLTPEMIK LQEVFKAFYL GKHSGRKLQW QTTLGHAV L KAEFKEGKKE FQVSLFQTLV LLMFNEGDGF SFEEIKMATG IEDSELRRTL QSLACGKAR VLIKSPKGKE VEDGDKFIFN GEFKHKLFRI KINQIQMKET VEEQVSTTER VFQDRQYQID AAIVRIMKM RKTLGHNLLV SELYNQLKFP VKPGDLKKRI ESLIDRDYME RDKDNPNQYH Y VA

+
Macromolecule #4: Rbx1-CSN4

MacromoleculeName: Rbx1-CSN4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MHHHHHHVDE NLYFQGGGRT NSGAGKKRFE VKKWNAVALW AWDIVVDNCA ICRNHIMDLC IECQANQASA TSEECTVAWG VCNHAFHFHC ISRWLKTRQV CPLDNREWEF QKYGHTG SG GSGGGGSGGG GSGGGGSGQY NVDYKLETYL KTARAYLEDD DPVQAEAY I ...String:
MHHHHHHVDE NLYFQGGGRT NSGAGKKRFE VKKWNAVALW AWDIVVDNCA ICRNHIMDLC IECQANQASA TSEECTVAWG VCNHAFHFHC ISRWLKTRQV CPLDNREWEF QKYGHTG SG GSGGGGSGGG GSGGGGSGQY NVDYKLETYL KTARAYLEDD DPVQAEAY I NRASLLQNES TNEQLQIHYK VCYARVLDYR RKFIEAAQRY NELSYKTIV HESERLEALK HALHCTILAS AGQQRSRMLA TLFKDERCQQ LAAYGILEKM YLDRIIRGN QLQEFAAMLM PHQKATTADG SSILDRAVIE HNLLSASKLY N NITFEELG ALLEIPAAKA EKIASQMITE GRMNGFIDQI DGIVHFETRE AL PTWDKQI QSLCFQVNNL LEKISQTAPE WTAQAMEAQM AQ

+
Macromolecule #5: CSN1

MacromoleculeName: CSN1 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MHHHHHHVDE NLYFQGGGRG AVEPMQIDVD PQEDPQNAPD VNYVVENPSL DLEQYAASYS GLMRIERLQF IADHCPTLRV EALKMALSFV QRTFNVDMYE EIHRKLSEAT RELQNAPDAI PESGVEPPAL DTAWVEATRK KALLKLEKLD TDLKNYKGNS IKESIRRGHD ...String:
MHHHHHHVDE NLYFQGGGRG AVEPMQIDVD PQEDPQNAPD VNYVVENPSL DLEQYAASYS GLMRIERLQF IADHCPTLRV EALKMALSFV QRTFNVDMYE EIHRKLSEAT RELQNAPDAI PESGVEPPAL DTAWVEATRK KALLKLEKLD TDLKNYKGNS IKESIRRGHD DLGDHYLDCG DLSNALKCYS RARDYCTSAK HVINMCLNVI KVSVYLQNWS HVLSYVSKAE STPEIAEQRG ERDSQTQAIL TKLKCAAGLA ELAARKYKQA AKCLLLASFD HCDFPELLSP SNVAIYGGLC ALATFDRQEL QRNVISSSSF KLFLELEPQV RDIIFKFYES KYASCLKMLD EMKDNLLLDM YLAPHVRTLY TQIRNRALIQ YFSPYVSADM HRMAAAFNTT VAALEDELTQ LILEGLISAR VDSHSKILYA RDVDQRSTTF EKSLLMGKEF QRRAKAMMLR AAVLRNQIHV KSPPREGSQG ELTPANSQSR MSTNM

+
Macromolecule #6: CSN2

MacromoleculeName: CSN2 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MHHHHHHVDE NLYFQGGGRM SDMEDDFMCD DEEDYDLEYS EDSNSEPNVD LENQYYNSKA LKEDDPKAAL SSFQKVLELE GEKGEWGFKA LKQMIKINFK LTNFPEMMNR YKQLLTYIRS AVTRNYSEKS INSILDYIST SKQMDLLQEF YETTLEALKD AKNDRLWFKT ...String:
MHHHHHHVDE NLYFQGGGRM SDMEDDFMCD DEEDYDLEYS EDSNSEPNVD LENQYYNSKA LKEDDPKAAL SSFQKVLELE GEKGEWGFKA LKQMIKINFK LTNFPEMMNR YKQLLTYIRS AVTRNYSEKS INSILDYIST SKQMDLLQEF YETTLEALKD AKNDRLWFKT NTKLGKLYLE REEYGKLQKI LRQLHQSCQT DDGEDDLKKG TQLLEIYALE IQMYTAQKNN KKLKALYEQS LHIKSAIPHP LIMGVIRECG GKMHLREGEF EKAHTDFFEA FKNYDESGSP RRTTCLKYLV LANMLMKSGI NPFDSQEAKP YKNDPEILAM TNLVSAYQNN DITEFEKILK TNHSNIMDDP FIREHIEELL RNIRTQVLIK LIKPYTRIHI PFISKELNID VADVESLLVQ CILDNTIHGR IDQVNQLLEL DHQKRGGARY TALDKWTNQL NSLNQAVVSK LA

+
Macromolecule #7: CSN3

MacromoleculeName: CSN3 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MHHHHHHVDE NLYFQGGGRM ASALEQFVNS VRQLSAQGQM TQLCELINKS GELLAKNLSH LDTVLGALDV QEHSLGVLAV LFVKFSMPSV PDFETLFSQV QLFISTCNGE HIRYATDTFA GLCHQLTNAL VERKQPLRGI GILKQAIDKM QMNTNQLTSI HADLCQLCLL ...String:
MHHHHHHVDE NLYFQGGGRM ASALEQFVNS VRQLSAQGQM TQLCELINKS GELLAKNLSH LDTVLGALDV QEHSLGVLAV LFVKFSMPSV PDFETLFSQV QLFISTCNGE HIRYATDTFA GLCHQLTNAL VERKQPLRGI GILKQAIDKM QMNTNQLTSI HADLCQLCLL AKCFKPALPY LDVDMMDICK ENGAYDAKHF LCYYYYGGMI YTGLKNFERA LYFYEQAITT PAMAVSHIML ESYKKYILVS LILLGKVQQL PKYTSQIVGR FIKPLSNAYH ELAQVYSTNN PSELRNLVNK HSETFTRDNN MGLVKQCLSS LYKKNIQRLT KTFLTLSLQD MASRVQLSGP QEAEKYVLHM IEDGEIFASI NQKDGMVSFH DNPEKYNNPA MLHNIDQEML KCIELDERLK AMDQEITVNP QFVQKSMGSQ EDDSGNKPSS YS

+
Macromolecule #8: CSN5

MacromoleculeName: CSN5 / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MHHHHHHVDE NLYFQGGGRM AASGSGMAQK TWELANNMQE AQSIDEIYKY DKKQQQEILA AKPWTKDHHY FKYCKISALA LLKMVMHARS GGNLAVMGLM LGKVDGETMI IMDSFALPVE GTETRVNAQA AAYEYMAAYI ENAKQVGRLE NAIGWYHSHP GYGCWLSGID ...String:
MHHHHHHVDE NLYFQGGGRM AASGSGMAQK TWELANNMQE AQSIDEIYKY DKKQQQEILA AKPWTKDHHY FKYCKISALA LLKMVMHARS GGNLAVMGLM LGKVDGETMI IMDSFALPVE GTETRVNAQA AAYEYMAAYI ENAKQVGRLE NAIGWYHSHP GYGCWLSGID VSTQMLNQQF QEPFVAVVID PTRTISAGKV NLGAFRTYPK GYKPPDEGPS EYQTIPLNKI EDFGVHCKQY YALEVSYFKS SLDRKLLELL WNKYWVNTLS SSSLLTNADY TTGQVFDLSE KLEQSEAQLG RGSFMLGLET HDRKSEDKLA KATRDSCKTT IEAIHGLMSQ VIKDKLFNQI NIS

+
Macromolecule #9: CSN6

MacromoleculeName: CSN6 / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MHHHHHHVDE NLYFQGGGRM AAAAAAAAAT NGTGGSSGME VDAAVVPSVM ACGVTGSVSV ALHPLVILNI SDHWIRMRSQ EGRPVQVIGA LIGKQEGRNI EVMNSFELLS HTVEEKIIID KEYYYTKEEQ FKQVFKELEF LGWYTTGGPP DPSDIHVHKQ VCEIIESPLF ...String:
MHHHHHHVDE NLYFQGGGRM AAAAAAAAAT NGTGGSSGME VDAAVVPSVM ACGVTGSVSV ALHPLVILNI SDHWIRMRSQ EGRPVQVIGA LIGKQEGRNI EVMNSFELLS HTVEEKIIID KEYYYTKEEQ FKQVFKELEF LGWYTTGGPP DPSDIHVHKQ VCEIIESPLF LKLNPMTKHT DLPVSVFESV IDIINGEATM LFAELTYTLA TEEAERIGVD HVARMTATGS GENSTVAEHL IAQHSAIKML HSRVKLILEY VKASEAGEVP FNHEILREAY ALCHCLPVLS TDKFKTDFYD QCNDVGLMAY LGTITKTCNT MNQFVNKFNV LYDRQGIGRR MRGLFF

+
Macromolecule #10: CSN7

MacromoleculeName: CSN7 / type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MHHHHHHVDE NLYFQGGGRM SAEVKVTGQN QEQFLLLAKS AKGAALATLI HQVLEAPGVY VFGELLDMPN VRELAESDFA STFRLLTVFA YGTYADYLAE ARNLPPLTEA QKNKLRHLSV VTLAAKVKCI PYAVLLEALA LRNVRQLEDL VIEAVYADVL RGSLDQRNQR ...String:
MHHHHHHVDE NLYFQGGGRM SAEVKVTGQN QEQFLLLAKS AKGAALATLI HQVLEAPGVY VFGELLDMPN VRELAESDFA STFRLLTVFA YGTYADYLAE ARNLPPLTEA QKNKLRHLSV VTLAAKVKCI PYAVLLEALA LRNVRQLEDL VIEAVYADVL RGSLDQRNQR LEVDYSIGRD IQRQDLSAIA RTLQEWCVGC EVVLSGIEEQ VSRANQHKEQ QLGLKQQIES EVANLKK

+
Macromolecule #11: CSN8

MacromoleculeName: CSN8 / type: protein_or_peptide / ID: 11 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MHHHHHHVDE NLYFQGGGRP VAVMAESAFS FKKLLDQCEN QELEAPGGIA TPPVYGQLLA LYLLHNDMNN ARYLWKRIPP AIKSANSELG GIWSVGQRIW QRDFPGIYTT INAHQWSETV QPIMEALRDA TRRRAFALVS QAYTSIIADD FAAFVGLPVE EAVKGILEQG ...String:
MHHHHHHVDE NLYFQGGGRP VAVMAESAFS FKKLLDQCEN QELEAPGGIA TPPVYGQLLA LYLLHNDMNN ARYLWKRIPP AIKSANSELG GIWSVGQRIW QRDFPGIYTT INAHQWSETV QPIMEALRDA TRRRAFALVS QAYTSIIADD FAAFVGLPVE EAVKGILEQG WQADSTTRMV LPRKPVAGAL DVSFNKFIPL SEPAPVPPIP NEQQLARLTD YVAFLEN

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26681
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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