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- PDB-9is6: CryoEM structure of Plant-Complex-C-5b -

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Basic information

Entry
Database: PDB / ID: 9is6
TitleCryoEM structure of Plant-Complex-C-5b
Components(COP9 signalosome complex subunit ...) x 8
KeywordsPLANT PROTEIN / complex
Function / homology
Function and homology information


negative regulation of photomorphogenesis / regulation of L-ascorbic acid biosynthetic process / response to absence of light / COP9 signalosome assembly / red, far-red light phototransduction / response to jasmonic acid / response to auxin / protein deneddylation / embryo development ending in seed dormancy / COP9 signalosome ...negative regulation of photomorphogenesis / regulation of L-ascorbic acid biosynthetic process / response to absence of light / COP9 signalosome assembly / red, far-red light phototransduction / response to jasmonic acid / response to auxin / protein deneddylation / embryo development ending in seed dormancy / COP9 signalosome / Hydrolases; Acting on peptide bonds (peptidases) / hyperosmotic response / response to light stimulus / response to salt stress / positive regulation of G2/M transition of mitotic cell cycle / protein catabolic process / metalloendopeptidase activity / positive regulation of protein catabolic process / metallopeptidase activity / protein-containing complex assembly / protein-containing complex / proteolysis / metal ion binding / nucleus / cytoplasm
Similarity search - Function
COP9 signalosome, subunit CSN8 / : / COP9 signalosome complex subunit 3, N-terminal helical repeats / COP9 signalosome subunit 6 / : / COP9 signalosome complex subunit 1, C-terminal helix / Cop9 signalosome subunit 5 C-terminal domain / Cop9 signalosome subunit 5 C-terminal domain / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / : ...COP9 signalosome, subunit CSN8 / : / COP9 signalosome complex subunit 3, N-terminal helical repeats / COP9 signalosome subunit 6 / : / COP9 signalosome complex subunit 1, C-terminal helix / Cop9 signalosome subunit 5 C-terminal domain / Cop9 signalosome subunit 5 C-terminal domain / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / : / : / : / 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 / PCI/PINT associated module / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / : / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
COP9 signalosome complex subunit 8 / COP9 signalosome complex subunit 1 / COP9 signalosome complex subunit 4 / COP9 signalosome complex subunit 6b / COP9 signalosome complex subunit 2 / COP9 signalosome complex subunit 3 / COP9 signalosome complex subunit 7 / COP9 signalosome complex subunit 5b
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsWang, J.Z. / Zhao, J. / Li, X.H. / Xu, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271253 China
CitationJournal: To Be Published
Title: Plant protein complex CC5b
Authors: Wang, J.Z. / Zhao, J. / Li, X.H. / Xu, B.
History
DepositionJul 17, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COP9 signalosome complex subunit 1
H: COP9 signalosome complex subunit 8
G: COP9 signalosome complex subunit 7
F: COP9 signalosome complex subunit 6b
E: COP9 signalosome complex subunit 5b
C: COP9 signalosome complex subunit 3
D: COP9 signalosome complex subunit 4
B: COP9 signalosome complex subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,6629
Polymers322,5968
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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COP9 signalosome complex subunit ... , 8 types, 8 molecules AHGFECDB

#1: Protein COP9 signalosome complex subunit 1 / CSN complex subunit 1 / Constitutive photomorphogenesis protein 11 / Protein FUSCA 6


Mass: 50650.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CSN1, COP11, FUS6, At3g61140, T20K12.40 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P45432
#2: Protein COP9 signalosome complex subunit 8 / CSN complex subunit 8 / Constitutive photomorphogenesis protein 9 / Protein FUSCA 7


Mass: 22573.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CSN8, COP9, FUS7, At4g14110, dl3095c / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P43255
#3: Protein COP9 signalosome complex subunit 7 / CSN complex subunit 7 / Protein FUSCA 5


Mass: 29508.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CSN7, FUS5, At1g02090, T7I23.24, T7I23.25 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q94JU3
#4: Protein COP9 signalosome complex subunit 6b / AtCSN6b / Signalosome subunit 6b


Mass: 35446.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CSN6B, At4g26430, M3E9.140 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8W1P0
#5: Protein COP9 signalosome complex subunit 5b / Signalosome subunit 5b / Jun activation domain-binding homolog 2


Mass: 40361.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CSN5B, AJH2, CSN5A, At1g71230, F3I17.12 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9FVU9, Hydrolases; Acting on peptide bonds (peptidases)
#6: Protein COP9 signalosome complex subunit 3 / Signalosome subunit 3 / Protein FUSCA 11


Mass: 47792.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CSN3, FUS11, At5g14250, F18O22.40 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8W575
#7: Protein COP9 signalosome complex subunit 4 / AtS4 / Signalosome subunit 4 / Constitutive photomorphogenesis protein 8 / Protein FUSCA 4


Mass: 45007.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CSN4, COP8, FUS4, At5g42970, MBD2.17 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8L5U0
#8: Protein COP9 signalosome complex subunit 2 / Signalosome subunit 2 / Protein FUSCA 12


Mass: 51254.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CSN2, FUS12, At2g26990, T20P8.4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8W207

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Non-polymers , 1 types, 1 molecules

#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of plant c5b / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69921 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00215159
ELECTRON MICROSCOPYf_angle_d0.50620557
ELECTRON MICROSCOPYf_dihedral_angle_d4.1862125
ELECTRON MICROSCOPYf_chiral_restr0.0362389
ELECTRON MICROSCOPYf_plane_restr0.0032657

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