[English] 日本語
Yorodumi
- EMDB-4741: Structural basis of Cullin-2 RING E3 ligase regulation by the COP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4741
TitleStructural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome
Map dataStructural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome
Sample
  • Complex: Ternary complex of COP9 signalosome (CSN1-CSN8) with Cullin-Ring E3 Ligase deneddylated Cullin-2, Rbx1, Elongin-B and ElonginC
    • Protein or peptide: x 12 types
KeywordsCullin-Ring E3 Ligases (CRLs) COP9 signalosome (CSN) deneddylation / LIGASE
Function / homology
Function and homology information


regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / deNEDDylase activity / GTPase inhibitor activity / regulation of protein neddylation / eukaryotic translation initiation factor 3 complex ...regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / deNEDDylase activity / GTPase inhibitor activity / regulation of protein neddylation / eukaryotic translation initiation factor 3 complex / protein deneddylation / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / COP9 signalosome / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / activation of NF-kappaB-inducing kinase activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / target-directed miRNA degradation / elongin complex / VCB complex / positive regulation of protein autoubiquitination / protein neddylation / metal-dependent deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases) / NEDD8 ligase activity / RHOBTB1 GTPase cycle / Cul5-RING ubiquitin ligase complex / negative regulation of response to oxidative stress / ubiquitin-ubiquitin ligase activity / Cul4A-RING E3 ubiquitin ligase complex / SCF ubiquitin ligase complex / inner cell mass cell proliferation / Cul2-RING ubiquitin ligase complex / negative regulation of type I interferon production / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / protein deubiquitination / Prolactin receptor signaling / skeletal muscle cell differentiation / protein monoubiquitination / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / cullin family protein binding / regulation of JNK cascade / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / response to light stimulus / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / protein K48-linked ubiquitination / Formation of HIV elongation complex in the absence of HIV Tat / Nuclear events stimulated by ALK signaling in cancer / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / JNK cascade / positive regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / T cell activation / translation initiation factor activity / Regulation of BACH1 activity / intrinsic apoptotic signaling pathway / post-translational protein modification / transcription corepressor binding / Degradation of DVL / transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / Recognition of DNA damage by PCNA-containing replication complex / Degradation of GLI1 by the proteasome / Negative regulation of NOTCH4 signaling / cellular response to amino acid stimulus / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / DNA Damage Recognition in GG-NER / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / RING-type E3 ubiquitin transferase / Degradation of beta-catenin by the destruction complex / negative regulation of canonical Wnt signaling pathway / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / neuron differentiation / Inactivation of CSF3 (G-CSF) signaling / Dual Incision in GG-NER / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Regulation of expression of SLITs and ROBOs / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / positive regulation of DNA-binding transcription factor activity / Formation of Incision Complex in GG-NER / Interleukin-1 signaling
Similarity search - Function
COP9 signalosome, subunit CSN8 / COP9 signalosome complex subunit 7, helix I / : / : / COP9 signalosome complex subunit 7a helix I domain / COP9 signalosome complex subunit 1, C-terminal helix / COP9 signalosome complex subunit 3-like, C-terminal helix / COP9 signalosome subunit 6 / Cop9 signalosome subunit 5 C-terminal domain / COP9 signalosome complex subunit 4, helix turn helix domain ...COP9 signalosome, subunit CSN8 / COP9 signalosome complex subunit 7, helix I / : / : / COP9 signalosome complex subunit 7a helix I domain / COP9 signalosome complex subunit 1, C-terminal helix / COP9 signalosome complex subunit 3-like, C-terminal helix / COP9 signalosome subunit 6 / Cop9 signalosome subunit 5 C-terminal domain / COP9 signalosome complex subunit 4, helix turn helix domain / Cop9 signalosome subunit 5 C-terminal domain / CSN4/RPN5/eIF3a helix turn helix domain / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome subunit RPN7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / PCI/PINT associated module / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Elongin B / Cullin / Elongin-C / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / Cullin / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Proteasome component (PCI) domain / PCI domain profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / SKP1/BTB/POZ domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
COP9 signalosome complex subunit 2 / E3 ubiquitin-protein ligase RBX1 / COP9 signalosome complex subunit 1 / Cullin-2 / Elongin-C / Elongin-B / COP9 signalosome complex subunit 6 / COP9 signalosome complex subunit 5 / COP9 signalosome complex subunit 8 / COP9 signalosome complex subunit 4 ...COP9 signalosome complex subunit 2 / E3 ubiquitin-protein ligase RBX1 / COP9 signalosome complex subunit 1 / Cullin-2 / Elongin-C / Elongin-B / COP9 signalosome complex subunit 6 / COP9 signalosome complex subunit 5 / COP9 signalosome complex subunit 8 / COP9 signalosome complex subunit 4 / COP9 signalosome complex subunit 7b / COP9 signalosome complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsFaull SV / Lau AMC
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis of Cullin 2 RING E3 ligase regulation by the COP9 signalosome.
Authors: Sarah V Faull / Andy M C Lau / Chloe Martens / Zainab Ahdash / Kjetil Hansen / Hugo Yebenes / Carla Schmidt / Fabienne Beuron / Nora B Cronin / Edward P Morris / Argyris Politis /
Abstract: Cullin-Ring E3 Ligases (CRLs) regulate a multitude of cellular pathways through specific substrate receptors. The COP9 signalosome (CSN) deactivates CRLs by removing NEDD8 from activated Cullins. ...Cullin-Ring E3 Ligases (CRLs) regulate a multitude of cellular pathways through specific substrate receptors. The COP9 signalosome (CSN) deactivates CRLs by removing NEDD8 from activated Cullins. Here we present structures of the neddylated and deneddylated CSN-CRL2 complexes by combining single-particle cryo-electron microscopy (cryo-EM) with chemical cross-linking mass spectrometry (XL-MS). These structures suggest a conserved mechanism of CSN activation, consisting of conformational clamping of the CRL2 substrate by CSN2/CSN4, release of the catalytic CSN5/CSN6 heterodimer and finally activation of the CSN5 deneddylation machinery. Using hydrogen-deuterium exchange (HDX)-MS we show that CRL2 activates CSN5/CSN6 in a neddylation-independent manner. The presence of NEDD8 is required to activate the CSN5 active site. Overall, by synergising cryo-EM with MS, we identify sensory regions of the CSN that mediate its stepwise activation and provide a framework for understanding the regulatory mechanism of other Cullin family members.
History
DepositionMar 28, 2019-
Header (metadata) releaseAug 28, 2019-
Map releaseAug 28, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6r7h
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4741.png

Downloads & links

-
Map

FileDownload / File: emd_4741.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 6.0 / Movie #1: 6
Minimum - Maximum-1.4705892 - 10.037419999999999
Average (Standard dev.)0.000000024428235 (±1.0000002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-148-148-148
Dimensions300300300
Spacing300300300
CellA=B=C: 317.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z318.000318.000318.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ132132232
MAP C/R/S123
start NC/NR/NS-148-148-148
NC/NR/NS300300300
D min/max/mean-1.47110.0370.000

-
Supplemental data

-
Sample components

+
Entire : Ternary complex of COP9 signalosome (CSN1-CSN8) with Cullin-Ring ...

EntireName: Ternary complex of COP9 signalosome (CSN1-CSN8) with Cullin-Ring E3 Ligase deneddylated Cullin-2, Rbx1, Elongin-B and ElonginC
Components
  • Complex: Ternary complex of COP9 signalosome (CSN1-CSN8) with Cullin-Ring E3 Ligase deneddylated Cullin-2, Rbx1, Elongin-B and ElonginC
    • Protein or peptide: COP9 signalosome complex subunit 1
    • Protein or peptide: Elongin-C
    • Protein or peptide: Cullin-2
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: COP9 signalosome complex subunit 2
    • Protein or peptide: COP9 signalosome complex subunit 3
    • Protein or peptide: COP9 signalosome complex subunit 4
    • Protein or peptide: COP9 signalosome complex subunit 5
    • Protein or peptide: COP9 signalosome complex subunit 6
    • Protein or peptide: COP9 signalosome complex subunit 7b
    • Protein or peptide: COP9 signalosome complex subunit 8
    • Protein or peptide: Elongin-B

+
Supramolecule #1: Ternary complex of COP9 signalosome (CSN1-CSN8) with Cullin-Ring ...

SupramoleculeName: Ternary complex of COP9 signalosome (CSN1-CSN8) with Cullin-Ring E3 Ligase deneddylated Cullin-2, Rbx1, Elongin-B and ElonginC
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: COP9 signalosome complex subunit 1

MacromoleculeName: COP9 signalosome complex subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.253535 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: VENPSLDLEQ YAASYSGLMR IERLQFIADH CPTLRVEALK MALSFVQRTF NVDMYEEIHR KLSEATRSSL RELQNAPDAI PESGVEPPA LDTAWVEATR KKALLKLEKL DTDLKNYKGN SIKESIRRGH DDLGDHYLDC GDLSNALKCY SRARDYCTSA K HVINMCLN ...String:
VENPSLDLEQ YAASYSGLMR IERLQFIADH CPTLRVEALK MALSFVQRTF NVDMYEEIHR KLSEATRSSL RELQNAPDAI PESGVEPPA LDTAWVEATR KKALLKLEKL DTDLKNYKGN SIKESIRRGH DDLGDHYLDC GDLSNALKCY SRARDYCTSA K HVINMCLN VIKVSVYLQN WSHVLSYVSK AESTPEIAEQ RGERDSQTQA ILTKLKCAAG LAELAARKYK QAAKCLLLAS FD HCDFPEL LSPSNVAIYG GLCALATFDR QELQRNVISS SSFKLFLELE PQVRDIIFKF YESKYASCLK MLDEMKDNLL LDM YLAPHV RTLYTQIRNR ALIQYFSPYV SADMHRMAAA FNTTVAALED ELTQLILEGL ISARVDSHSK ILYARDVDQR STTF EKSLL MGKEFQRRAK AMMLRAAVLR NQIHVKSP

UniProtKB: COP9 signalosome complex subunit 1

+
Macromolecule #2: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.485135 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MDGEEKTYGG CEGPDAMYVK LISSDGHEFI VKREHALTSG TIKAMLSGPG QFAENETNEV NFREIPSHVL SKVCMYFTYK VRYTNSSTE IPEFPIAPEI ALELLMAANF LDC

UniProtKB: Elongin-C

+
Macromolecule #3: Cullin-2

MacromoleculeName: Cullin-2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.520719 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSLKPRVVDF DETWNKLLTT IKAVVMLEYV ERATWNDRFS DIYALCVAYP EPLGERLYTE TKIFLENHVR HLHKRVLESE EQVLVMYHR YWEEYSKGAD YMDCLYRYLN TQFIKKNKLT EADLQYGYGG VDMNEPLMEI GELALDMWRK LMVEPLQAIL I RMLLREIK ...String:
MSLKPRVVDF DETWNKLLTT IKAVVMLEYV ERATWNDRFS DIYALCVAYP EPLGERLYTE TKIFLENHVR HLHKRVLESE EQVLVMYHR YWEEYSKGAD YMDCLYRYLN TQFIKKNKLT EADLQYGYGG VDMNEPLMEI GELALDMWRK LMVEPLQAIL I RMLLREIK NDRGGEDPNQ KVIHGVINSF VHVEQYKKKF PLKFYQEIFE SPFLTETGEY YKQEASNLLQ ESNCSQYMEK VL GRLKDEE IRCRKYLHPS SYTKVIHECQ QRMVADHLQF LHAECHNIIR QEKKNDMANM YVLLRAVSTG LPHMIQELQN HIH DEGLRA TSNLTQENMP TLFVESVLEV HGKFVQLINT VLNGDQHFMS ALDKALTSVV NYREPKSVCK APELLAKYCD NLLK KSAKG MTENEVEDRL TSFITVFKYI DDKDVFQKFY ARMLAKRLIH GLSMSMDSEE AMINKLKQAC GYEFTSKLHR MYTDM SVSA DLNNKFNNFI KNQDTVIDLG ISFQIYVLQA GAWPLTQAPS STFAIPQELE KSVQMFELFY SQHFSGRKLT WLHYLC TGE VKMNYLGKPY VAMVTTYQMA VLLAFNNSET VSYKELQDST QMNEKELTKT IKSLLDVKMI NHDSEKEDID AESSFSL NM NFSSKRTKFK IT

UniProtKB: Cullin-2

+
Macromolecule #4: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.655229 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
KKRFEVKKWN AVALWAWDIV VDNCAICRNH IMDLCIECQA NQASATSEEC TVAWGVCNHA FHFHCISRWL KTRQVCPLDN REWEFQKYG H

+
Macromolecule #5: COP9 signalosome complex subunit 2

MacromoleculeName: COP9 signalosome complex subunit 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.212152 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: VDLENQYYNS KALKEDDPKA ALSSFQKVLE LEGEKGEWGF KALKQMIKIN FKLTNFPEMM NRYKQLLTYI RSAVTRNYSE KSINSILDY ISTSKQMDLL QEFYETTLEA LKDAKNDRLW FKTNTKLGKL YLEREEYGKL QKILRQLHQS CQTDDGEDDL K KGTQLLEI ...String:
VDLENQYYNS KALKEDDPKA ALSSFQKVLE LEGEKGEWGF KALKQMIKIN FKLTNFPEMM NRYKQLLTYI RSAVTRNYSE KSINSILDY ISTSKQMDLL QEFYETTLEA LKDAKNDRLW FKTNTKLGKL YLEREEYGKL QKILRQLHQS CQTDDGEDDL K KGTQLLEI YALEIQMYTA QKNNKKLKAL YEQSLHIKSA IPHPLIMGVI RECGGKMHLR EGEFEKAHTD FFEAFKNYDE SG SPRRTTC LKYLVLANML MKSGINPFDS QEAKPYKNDP EILAMTNLVS AYQNNDITEF EKILKTNHSN IMDDPFIREH IEE LLRNIR TQVLIKLIKP YTRIHIPFIS KELNIDVADV ESLLVQCILD NTIHGRIDQV NQLLELDHQK RGGARYTALD KWTN QLNSL NQAVVSKLA

UniProtKB: COP9 signalosome complex subunit 2

+
Macromolecule #6: COP9 signalosome complex subunit 3

MacromoleculeName: COP9 signalosome complex subunit 3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.808816 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MASALEQFVN SVRQLSAQGQ MTQLCELINK SGELLAKNLS HLDTVLGALD VQEHSLGVLA VLFVKFSMPS VPDFETLFSQ VQLFISTCN GEHIRYATDT FAGLCHQLTN ALVERKQPLR GIGILKQAID KMQMNTNQLT SIHADLCQLC LLAKCFKPAL P YLDVDMMD ...String:
MASALEQFVN SVRQLSAQGQ MTQLCELINK SGELLAKNLS HLDTVLGALD VQEHSLGVLA VLFVKFSMPS VPDFETLFSQ VQLFISTCN GEHIRYATDT FAGLCHQLTN ALVERKQPLR GIGILKQAID KMQMNTNQLT SIHADLCQLC LLAKCFKPAL P YLDVDMMD ICKENGAYDA KHFLCYYYYG GMIYTGLKNF ERALYFYEQA ITTPAMAVSH IMLESYKKYI LVSLILLGKV QQ LPKYTSQ IVGRFIKPLS NAYHELAQVY STNNPSELRN LVNKHSETFT RDNNMGLVKQ CLSSLYKKNI QRLTKTFLTL SLQ DMASRV QLSGPQEAEK YVLHMIEDGE IFASINQKDG MVSFHDNPEK YNNPAMLHNI DQEMLKCIEL DERLKAMDQE ITVN PQF

UniProtKB: COP9 signalosome complex subunit 3

+
Macromolecule #7: COP9 signalosome complex subunit 4

MacromoleculeName: COP9 signalosome complex subunit 4 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.322688 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAAVRQDLA QLMNSSGSHK DLAGKYRQIL EKAIQLSGAE QLEALKAFVE AMVNENVSLV ISRQLLTDFC THLPNLPDST AKEIYHFTL EKIQPRVISF EEQVASIRQH LASIYEKEED WRNAAQVLVG IPLETGQKQY NVDYKLETYL KIARLYLEDD D PVQAEAYI ...String:
MAAAVRQDLA QLMNSSGSHK DLAGKYRQIL EKAIQLSGAE QLEALKAFVE AMVNENVSLV ISRQLLTDFC THLPNLPDST AKEIYHFTL EKIQPRVISF EEQVASIRQH LASIYEKEED WRNAAQVLVG IPLETGQKQY NVDYKLETYL KIARLYLEDD D PVQAEAYI NRASLLQNES TNEQLQIHYK VCYARVLDYR RKFIEAAQRY NELSYKTIVH ESERLEALKH ALHCTILASA GQ QRSRMLA TLFKDERCQQ LAAYGILEKM YLDRIIRGNQ LQEFAAMLMP HQKATTADGS SILDRAVIEH NLLSASKLYN NIT FEELGA LLEIPAAKAE KIASQMITEG RMNGFIDQID GIVHFETREA LPTWDKQIQS LCFQVNNLLE KISQTAPEWT AQAM EAQMA Q

UniProtKB: COP9 signalosome complex subunit 4

+
Macromolecule #8: COP9 signalosome complex subunit 5

MacromoleculeName: COP9 signalosome complex subunit 5 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.184059 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SIDEIYKYDK KQQQEILAAK PWTKDHHYFK YCKISALALL KMVMHARSGG NLEVMGLMLG KVDGETMIIM DSFALPVEGT ETRVNAQAA AYEYMAAYIE NAKQVGRLEN AIGWYHSHPG YGCWLSGIDV STQMLNQQFQ EPFVAVVIDP TRTISAGKVN L GAFRTYPK ...String:
SIDEIYKYDK KQQQEILAAK PWTKDHHYFK YCKISALALL KMVMHARSGG NLEVMGLMLG KVDGETMIIM DSFALPVEGT ETRVNAQAA AYEYMAAYIE NAKQVGRLEN AIGWYHSHPG YGCWLSGIDV STQMLNQQFQ EPFVAVVIDP TRTISAGKVN L GAFRTYPK GYKPPDEGPS EYQTIPLNKI EDFGVHCKQY YALEVSYFKS SLDRKLLELL WNKYWVNTLS SSSLLTNADY TT GQVFDLS EKLEQSEAQL GRGSFMLGLE THDRKSEDKL AKATRDSCKT TIEAIHGLMS QVIKDKLFNQ INIS

UniProtKB: COP9 signalosome complex subunit 5

+
Macromolecule #9: COP9 signalosome complex subunit 6

MacromoleculeName: COP9 signalosome complex subunit 6 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.507193 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SVMACGVTGS VSVALHPLVI LNISDHWIRM RSQEGRPVQV IGALIGKQEG RNIEVMNSFE LLSHTVEEKI IIDKEYYYTK EEQFKQVFK ELEFLGWYTT GGPPDPSDIH VHKQVCEIIE SPLFLKLNPM TKHTDLPVSV FESVIDIING EATMLFAELT Y TLATEEAE ...String:
SVMACGVTGS VSVALHPLVI LNISDHWIRM RSQEGRPVQV IGALIGKQEG RNIEVMNSFE LLSHTVEEKI IIDKEYYYTK EEQFKQVFK ELEFLGWYTT GGPPDPSDIH VHKQVCEIIE SPLFLKLNPM TKHTDLPVSV FESVIDIING EATMLFAELT Y TLATEEAE RIGVDHVARM TATGSGENST VAEHLIAQHS AIKMLHSRVK LILEYVKASE AGEVPFNHEI LREAYALCHC LP VLSTDKF KTDFYDQCND VGLMAYLGTI TKTCNTMNQF VNKFNVLYDR Q

UniProtKB: COP9 signalosome complex subunit 6

+
Macromolecule #10: COP9 signalosome complex subunit 7b

MacromoleculeName: COP9 signalosome complex subunit 7b / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.429709 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SSNLLEQFIL LAKGTSGSAL TALISQVLEA PGVYVFGELL ELANVQELAE GANAAYLQLL NLFAYGTYPD YIANKESLPE LSTAQQNKL KHLTIVSLAS RMKCIPYSVL LKDLEMRNLR ELEDLIIEAV YTDIIQGKLD QRNQLLEVDF CIGRDIRKKD I NNIVKTLH ...String:
SSNLLEQFIL LAKGTSGSAL TALISQVLEA PGVYVFGELL ELANVQELAE GANAAYLQLL NLFAYGTYPD YIANKESLPE LSTAQQNKL KHLTIVSLAS RMKCIPYSVL LKDLEMRNLR ELEDLIIEAV YTDIIQGKLD QRNQLLEVDF CIGRDIRKKD I NNIVKTLH EWCDGCEAVL LGIEQQVLRA NQYKENHNRT QQQVEAEVTN

UniProtKB: COP9 signalosome complex subunit 7b

+
Macromolecule #11: COP9 signalosome complex subunit 8

MacromoleculeName: COP9 signalosome complex subunit 8 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.258342 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: FSFKKLLDQC ENQELEAPGG IATPPVYGQL LALYLLHNDM NNARYLWKRI PPAIKSANSE LGGIWSVGQR IWQRDFPGIY TTINAHQWS ETVQPIMEAL RDATRRRAFA LVSQAYTSII ADDFAAFVGL PVEEAVKGIL EQGWQADSTT RMVLPRKPVA G ALDVSFNK ...String:
FSFKKLLDQC ENQELEAPGG IATPPVYGQL LALYLLHNDM NNARYLWKRI PPAIKSANSE LGGIWSVGQR IWQRDFPGIY TTINAHQWS ETVQPIMEAL RDATRRRAFA LVSQAYTSII ADDFAAFVGL PVEEAVKGIL EQGWQADSTT RMVLPRKPVA G ALDVSFNK FIPLSEPAPV PPIPNEQQLA RLTDYVAFLE N

UniProtKB: COP9 signalosome complex subunit 8

+
Macromolecule #12: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.748406 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMK

UniProtKB: Elongin-B

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Details: 15 mM HEPES pH 7.5 100 mM NaCl 0.5 mM DTT 1% Glycerol
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 83.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17191
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://pdbjlvh1.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