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- EMDB-4744: Structural basis of Cullin-2 RING E3 ligase regulation by the COP... -

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Basic information

Entry
Database: EMDB / ID: EMD-4744
TitleStructural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome
Map dataNone
Sample
  • Complex: CNS (COP9 Signalosome) with CSN5/CSN6 the catalytic heterodimer complexed with CUL2 (CUL2, ElonginB, ElongingC, Rbx1 and VDL)
    • Protein or peptide: x 10 types
  • Ligand: x 1 types
KeywordsCullin-Ring E3 Ligases (CRLs) COP9 signalosome (CSN) deneddylation VHL tumour suppressor substrate receptor / LIGASE
Function / homology
Function and homology information


COP9 signalosome assembly / trophectodermal cell proliferation / GTPase inhibitor activity / deNEDDylase activity / protein deneddylation / regulation of protein neddylation / activation of NF-kappaB-inducing kinase activity / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / COP9 signalosome ...COP9 signalosome assembly / trophectodermal cell proliferation / GTPase inhibitor activity / deNEDDylase activity / protein deneddylation / regulation of protein neddylation / activation of NF-kappaB-inducing kinase activity / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / COP9 signalosome / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / target-directed miRNA degradation / elongin complex / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / protein neddylation / NEDD8 ligase activity / RHOBTB1 GTPase cycle / VCB complex / negative regulation of response to oxidative stress / regulation of DNA damage response, signal transduction by p53 class mediator / Cul5-RING ubiquitin ligase complex / inner cell mass cell proliferation / SCF ubiquitin ligase complex / negative regulation of type I interferon production / ubiquitin-ubiquitin ligase activity / Cul2-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / negative regulation of mitophagy / Prolactin receptor signaling / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / response to light stimulus / cullin family protein binding / skeletal muscle cell differentiation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / protein monoubiquitination / 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 / transcription-coupled nucleotide-excision repair / RNA Polymerase II Pre-transcription Events / positive regulation of TORC1 signaling / regulation of cellular response to insulin stimulus / intrinsic apoptotic signaling pathway / negative regulation of insulin receptor signaling pathway / post-translational protein modification / Regulation of BACH1 activity / T cell activation / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / cellular response to amino acid stimulus / Degradation of DVL / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / Recognition of DNA damage by PCNA-containing replication complex / Vif-mediated degradation of APOBEC3G / G1/S transition of mitotic cell cycle / Hedgehog 'on' state / negative regulation of canonical Wnt signaling pathway / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Inactivation of CSF3 (G-CSF) signaling / Degradation of beta-catenin by the destruction complex / RING-type E3 ubiquitin transferase / DNA Damage Recognition in GG-NER / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / Interleukin-1 signaling / Orc1 removal from chromatin / protein polyubiquitination / neuron differentiation / Regulation of RAS by GAPs
Similarity search - Function
COP9 signalosome complex subunit 7, helix I / : / COP9 signalosome complex subunit 7a helix I domain / COP9 signalosome complex subunit 3-like, C-terminal helix / CSN7 helical bundle subdomain / COP9 signalosome, subunit CSN8 / COP9 signalosome complex subunit 4, helix turn helix domain / : / CSN4/RPN5/eIF3a helix turn helix domain / COP9 signalosome complex subunit 3, N-terminal helical repeats ...COP9 signalosome complex subunit 7, helix I / : / COP9 signalosome complex subunit 7a helix I domain / COP9 signalosome complex subunit 3-like, C-terminal helix / CSN7 helical bundle subdomain / COP9 signalosome, subunit CSN8 / COP9 signalosome complex subunit 4, helix turn helix domain / : / CSN4/RPN5/eIF3a helix turn helix domain / COP9 signalosome complex subunit 3, N-terminal helical repeats / : / COP9 signalosome complex subunit 1, C-terminal helix / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin protein neddylation domain / : / : / PSMD12/CSN4, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome subunit RPN7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / : / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / PCI/PINT associated module / Elongin-C / Elongin B / Cullin / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin alpha solenoid domain / Cullin family profile. / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / 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 / 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 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: 6.5 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 29, 2019-
Header (metadata) releaseAug 28, 2019-
Map releaseAug 28, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.65
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3.65
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6r7n
  • Surface level: 3.65
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4744.png

Downloads & links

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Map

FileDownload / File: emd_4744.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.65 / Movie #1: 3.65
Minimum - Maximum-7.0971975 - 19.606954999999999
Average (Standard dev.)0.000000011842336 (±0.99999976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
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-150-150-150
NC/NR/NS300300300
D min/max/mean-7.09719.6070.000

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Supplemental data

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Sample components

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Entire : CNS (COP9 Signalosome) with CSN5/CSN6 the catalytic heterodimer c...

EntireName: CNS (COP9 Signalosome) with CSN5/CSN6 the catalytic heterodimer complexed with CUL2 (CUL2, ElonginB, ElongingC, Rbx1 and VDL)
Components
  • Complex: CNS (COP9 Signalosome) with CSN5/CSN6 the catalytic heterodimer complexed with CUL2 (CUL2, ElonginB, ElongingC, Rbx1 and VDL)
    • Protein or peptide: COP9 signalosome complex subunit 1
    • Protein or peptide: COP9 signalosome complex subunit 4
    • Protein or peptide: COP9 signalosome complex subunit 8
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • Protein or peptide: RBX1 E3 ubiquitin-protein ligase
    • Protein or peptide: COP9 signalosome complex subunit 3
    • Protein or peptide: CSN7B_HUMAN
    • Protein or peptide: Cullin-2
    • Protein or peptide: COP9 signalosome complex subunit 2
  • Ligand: ZINC ION

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Supramolecule #1: CNS (COP9 Signalosome) with CSN5/CSN6 the catalytic heterodimer c...

SupramoleculeName: CNS (COP9 Signalosome) with CSN5/CSN6 the catalytic heterodimer complexed with CUL2 (CUL2, ElonginB, ElongingC, Rbx1 and VDL)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Homo sapiens (human)

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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: 55.606496 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPLPVQVFNL QGAVEPMQID VDPQEDPQNA PDVNYVVENP SLDLEQYAAS YSGLMRIERL QFIADHCPTL RVEALKMALS FVQRTFNVD MYEEIHRKLS EATRSSLREL QNAPDAIPES GVEPPALDTA WVEATRKKAL LKLEKLDTDL KNYKGNSIKE S IRRGHDDL ...String:
MPLPVQVFNL QGAVEPMQID VDPQEDPQNA PDVNYVVENP SLDLEQYAAS YSGLMRIERL QFIADHCPTL RVEALKMALS FVQRTFNVD MYEEIHRKLS EATRSSLREL QNAPDAIPES GVEPPALDTA WVEATRKKAL LKLEKLDTDL KNYKGNSIKE S IRRGHDDL GDHYLDCGDL SNALKCYSRA RDYCTSAKHV INMCLNVIKV SVYLQNWSHV LSYVSKAEST PEIAEQRGER DS QTQAILT KLKCAAGLAE LAARKYKQAA KCLLLASFDH CDFPELLSPS NVAIYGGLCA LATFDRQELQ RNVISSSSFK LFL ELEPQV RDIIFKFYES KYASCLKMLD EMKDNLLLDM YLAPHVRTLY TQIRNRALIQ YFSPYVSADM HRMAAAFNTT VAAL EDELT QLILEGLISA RVDSHSKILY ARDVDQRSTT FEKSLLMGKE FQRRAKAMML RAAVLRNQIH VKSPPREGSQ GELTP ANSQ SRMSTNM

UniProtKB: COP9 signalosome complex subunit 1

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Macromolecule #2: COP9 signalosome complex subunit 4

MacromoleculeName: COP9 signalosome complex subunit 4 / type: protein_or_peptide / ID: 2 / 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

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Macromolecule #3: COP9 signalosome complex subunit 8

MacromoleculeName: COP9 signalosome complex subunit 8 / type: protein_or_peptide / ID: 3 / 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

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Macromolecule #4: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 4 / 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

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Macromolecule #5: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 5 / 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

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Macromolecule #6: RBX1 E3 ubiquitin-protein ligase

MacromoleculeName: RBX1 E3 ubiquitin-protein ligase / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.092631 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
AKKKRFEVKK WNAVALWAWD IVVDNCAICR NHIMDLCIEC QANQASATSE ECTVAWGVCN HAFHFHCISR WLKTRQVCPL DNREWE

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Macromolecule #7: COP9 signalosome complex subunit 3

MacromoleculeName: COP9 signalosome complex subunit 3 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.606543 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SALEQFVNSV RQLSAQGQMT QLCELINKSG ELLAKNLSHL DTVLGALDVQ EHSLGVLAVL FVKFSMPSVP DFETLFSQVQ LFISTCNGE HIRYATDTFA GLCHQLTNAL VERKQPLRGI GILKQAIDKM QMNTNQLTSI HADLCQLCLL AKCFKPALPY L DVDMMDIC ...String:
SALEQFVNSV RQLSAQGQMT QLCELINKSG ELLAKNLSHL DTVLGALDVQ EHSLGVLAVL FVKFSMPSVP DFETLFSQVQ LFISTCNGE HIRYATDTFA GLCHQLTNAL VERKQPLRGI GILKQAIDKM QMNTNQLTSI HADLCQLCLL AKCFKPALPY L DVDMMDIC KENGAYDAKH FLCYYYYGGM IYTGLKNFER ALYFYEQAIT TPAMAVSHIM LESYKKYILV SLILLGKVQQ LP KYTSQIV GRFIKPLSNA YHELAQVYST NNPSELRNLV NKHSETFTRD NNMGLVKQCL SSLYKKNIQR LTKTFLTLSL QDM ASRVQL SGPQEAEKYV LHMIEDGEIF ASINQKDGMV SFHDNPEKYN NPAMLHNIDQ EMLKCIELDE RLKAMDQEIT VNPQ F

UniProtKB: COP9 signalosome complex subunit 3

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Macromolecule #8: CSN7B_HUMAN

MacromoleculeName: CSN7B_HUMAN / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.9444 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAGEQKPSSN LLEQFILLAK GTSGSALTAL ISQVLEAPGV YVFGELLELA NVQELAEGAN AAYLQLLNLF AYGTYPDYIA NKESLPELS TAQQNKLKHL TIVSLASRMK CIPYSVLLKD LEMRNLRELE DLIIEAVYTD IIQGKLDQRN QLLEVDFCIG R DIRKKDLS ...String:
MAGEQKPSSN LLEQFILLAK GTSGSALTAL ISQVLEAPGV YVFGELLELA NVQELAEGAN AAYLQLLNLF AYGTYPDYIA NKESLPELS TAQQNKLKHL TIVSLASRMK CIPYSVLLKD LEMRNLRELE DLIIEAVYTD IIQGKLDQRN QLLEVDFCIG R DIRKKDLS AIARTLQEWC VGCEVVLSGI EEQVSRANQH KEQQLGLKQQ IESEVAN

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Macromolecule #9: Cullin-2

MacromoleculeName: Cullin-2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.09893 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 ITTSMQKDTP QEMEQTRSAV DEDRKMYLQA AIVRIMKARK VLRHNALIQE VISQSRARFN PSISMIKK C IEVLIDKQYI ERSQASADEY SYVA

UniProtKB: Cullin-2

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Macromolecule #10: COP9 signalosome complex subunit 2

MacromoleculeName: COP9 signalosome complex subunit 2 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.66457 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSDMEDDFMC DDEEDYDLEY SEDSNSEPNV DLENQYYNSK ALKEDDPKAA LSSFQKVLEL EGEKGEWGFK ALKQMIKINF KLTNFPEMM NRYKQLLTYI RSAVTRNYSE KSINSILDYI STSKQMDLLQ EFYETTLEAL KDAKNDRLWF KTNTKLGKLY L EREEYGKL ...String:
MSDMEDDFMC DDEEDYDLEY SEDSNSEPNV DLENQYYNSK ALKEDDPKAA LSSFQKVLEL EGEKGEWGFK ALKQMIKINF KLTNFPEMM NRYKQLLTYI RSAVTRNYSE KSINSILDYI STSKQMDLLQ EFYETTLEAL KDAKNDRLWF KTNTKLGKLY L EREEYGKL QKILRQLHQS CQTDDGEDDL KKGTQLLEIY ALEIQMYTAQ KNNKKLKALY EQSLHIKSAI PHPLIMGVIR EC GGKMHLR EGEFEKAHTD FFEAFKNYDE SGSPRRTTCL KYLVLANMLM KSGINPFDSQ EAKPYKNDPE ILAMTNLVSA YQN NDITEF EKILKTNHSN IMDDPFIREH IEELLRNIRT QVLIKLIKPY TRIHIPFISK ELNIDVADVE SLLVQCILDN TIHG RIDQV NQLLELDHQK RGGARYTALD KWTNQLNSLN QAVVSKLA

UniProtKB: COP9 signalosome complex subunit 2

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / 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 / 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

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22471
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6r7n:
Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome

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