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- EMDB-60832: CryoEM structure of Plant-Complex-C-5b -

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Basic information

Entry
Database: EMDB / ID: EMD-60832
TitleCryoEM structure of Plant-Complex-C-5b
Map data
Sample
  • Complex: Complex of plant c5b
    • Protein or peptide: COP9 signalosome complex subunit 1
    • Protein or peptide: COP9 signalosome complex subunit 8
    • Protein or peptide: COP9 signalosome complex subunit 7
    • Protein or peptide: COP9 signalosome complex subunit 6b
    • Protein or peptide: COP9 signalosome complex subunit 5b
    • Protein or peptide: COP9 signalosome complex subunit 3
    • Protein or peptide: COP9 signalosome complex subunit 4
    • Protein or peptide: COP9 signalosome complex subunit 2
  • Ligand: ZINC ION
Keywordscomplex / PLANT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsWang JZ / Zhao J / Li XH / Xu B
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271253 China
CitationJournal: To Be Published
Title: Plant protein complex CC5b
Authors: Wang JZ / Zhao J / Li XH / Xu B
History
DepositionJul 17, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60832.png

Downloads & links

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Map

FileDownload / File: emd_60832.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.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0862
Minimum - Maximum-0.41447902 - 0.68721133
Average (Standard dev.)0.000574599 (±0.019450014)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60832_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60832_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of plant c5b

EntireName: Complex of plant c5b
Components
  • Complex: Complex of plant c5b
    • Protein or peptide: COP9 signalosome complex subunit 1
    • Protein or peptide: COP9 signalosome complex subunit 8
    • Protein or peptide: COP9 signalosome complex subunit 7
    • Protein or peptide: COP9 signalosome complex subunit 6b
    • Protein or peptide: COP9 signalosome complex subunit 5b
    • Protein or peptide: COP9 signalosome complex subunit 3
    • Protein or peptide: COP9 signalosome complex subunit 4
    • Protein or peptide: COP9 signalosome complex subunit 2
  • Ligand: ZINC ION

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Supramolecule #1: Complex of plant c5b

SupramoleculeName: Complex of plant c5b / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 50.650867 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MERDEEASGP MMEMCTNGGE ETSNRRPIIS GEPLDIEAYA ALYKGRTKIM RLLFIANHCG GNHALQFDAL RMAYDEIKKG ENTQLFREV VNKIGNRLGE KYGMDLAWCE AVDRRAEQKK VKLENELSSY RTNLIKESIR MGYNDFGDFY YACGMLGDAF K NYIRTRDY ...String:
MERDEEASGP MMEMCTNGGE ETSNRRPIIS GEPLDIEAYA ALYKGRTKIM RLLFIANHCG GNHALQFDAL RMAYDEIKKG ENTQLFREV VNKIGNRLGE KYGMDLAWCE AVDRRAEQKK VKLENELSSY RTNLIKESIR MGYNDFGDFY YACGMLGDAF K NYIRTRDY CTTTKHIIHM CMNAILVSIE MGQFTHVTSY VNKAEQNPET LEPMVNAKLR CASGLAHLEL KKYKLAARKF LD VNPELGN SYNEVIAPQD IATYGGLCAL ASFDRSELKQ KVIDNINFRN FLELVPDVRE LINDFYSSRY ASCLEYLASL KSN LLLDIH LHDHVDTLYD QIRKKALIQY TLPFVSVDLS RMADAFKTSV SGLEKELEAL ITDNQIQARI DSHNKILYAR HADQ RNATF QKVLQMGNEF DRDVRAMLLR ANLLKHEYHA RSARKL

UniProtKB: COP9 signalosome complex subunit 1

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Macromolecule #2: COP9 signalosome complex subunit 8

MacromoleculeName: COP9 signalosome complex subunit 8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 22.573637 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDLSPVKEAL AAKSFDKIAD ICDTLMLQVA SEGIEYHDDW PYAIHLLGYF YVDDCDSARF LWKRIPTAIK ERKPEVVAAW GIGQKLWTH DYAGVYEAIR GYDWSQEAKD MVAAFSDLYT KRMFQLLLSA YSTITIHDLA LFLGMTEDDA TTYVVENGWT V DAASQMAS ...String:
MDLSPVKEAL AAKSFDKIAD ICDTLMLQVA SEGIEYHDDW PYAIHLLGYF YVDDCDSARF LWKRIPTAIK ERKPEVVAAW GIGQKLWTH DYAGVYEAIR GYDWSQEAKD MVAAFSDLYT KRMFQLLLSA YSTITIHDLA LFLGMTEDDA TTYVVENGWT V DAASQMAS VKKQAVKREQ KVDSSKLQRL TEYVFHLEH

UniProtKB: COP9 signalosome complex subunit 8

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Macromolecule #3: COP9 signalosome complex subunit 7

MacromoleculeName: COP9 signalosome complex subunit 7 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 29.508859 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDIEQKQAEI IDQLVKRAST CKSEALGPLI IEATSHPSLF AFSEILALPN VAQLEGTTDS VYLDLLRLFA HGTWGDYKCN ATRLPHLSP DQILKLKQLT VLTLAESNKV LPYDTLMVEL DVSNVRELED FLINECMYAG IVRGKLDQLK RCFEVPFAAG R DLRPGQLG ...String:
MDIEQKQAEI IDQLVKRAST CKSEALGPLI IEATSHPSLF AFSEILALPN VAQLEGTTDS VYLDLLRLFA HGTWGDYKCN ATRLPHLSP DQILKLKQLT VLTLAESNKV LPYDTLMVEL DVSNVRELED FLINECMYAG IVRGKLDQLK RCFEVPFAAG R DLRPGQLG NMLHTLSNWL NTSENLLISI QDKIKWADNM SEMDKKHRKE AEEGVEEVKK SLSMKGDVDI RGNKEMFGEP SG VMDYEED GIRPKRRRHP VTR

UniProtKB: COP9 signalosome complex subunit 7

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Macromolecule #4: COP9 signalosome complex subunit 6b

MacromoleculeName: COP9 signalosome complex subunit 6b / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 35.44634 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAPSSSSGLT FKLHPLVMLN ISDHFTRVKT QLNPPAASCA TGNGSNNADA MLLQNPRVYG CVIGLQRGRT VEIFNSFELI FDPALDTLD RSFLEKKQEL YKKVFPDFYV LGWYSTGSDA TESDMHIHKA LMDINESPVY VLLNPAINHA QKDLPVTIYE S EFHVIDGI ...String:
MAPSSSSGLT FKLHPLVMLN ISDHFTRVKT QLNPPAASCA TGNGSNNADA MLLQNPRVYG CVIGLQRGRT VEIFNSFELI FDPALDTLD RSFLEKKQEL YKKVFPDFYV LGWYSTGSDA TESDMHIHKA LMDINESPVY VLLNPAINHA QKDLPVTIYE S EFHVIDGI PQSIFVHTSY TIETVEAERI SVDHVAHLKP SDGGSAATQL AAHLTGIHSA IKMLNSRIRV LYQHIVAMQK GD KPCENSV LRQVSSLLRS LPAAESEKFN ENFLMEYNDK LLMSYLAMIT NCTSNMNEVV DKFNTAYDKH SRRGGRTAFM

UniProtKB: COP9 signalosome complex subunit 6b

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Macromolecule #5: COP9 signalosome complex subunit 5b

MacromoleculeName: COP9 signalosome complex subunit 5b / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 40.361953 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEGSSSTIAR KTWELENSIL TVDSPDSTSD NIFYYDDTSQ TRFQQEKPWE NDPHYFKRVK ISALALLKMV VHARSGGTIE IMGLMQGKT DGDTIIVMDA FALPVEGTET RVNAQDDAYE YMVEYSQTNK LAGRLENVVG WYHSHPGYGC WLSGIDVSTQ R LNQQHQEP ...String:
MEGSSSTIAR KTWELENSIL TVDSPDSTSD NIFYYDDTSQ TRFQQEKPWE NDPHYFKRVK ISALALLKMV VHARSGGTIE IMGLMQGKT DGDTIIVMDA FALPVEGTET RVNAQDDAYE YMVEYSQTNK LAGRLENVVG WYHSHPGYGC WLSGIDVSTQ R LNQQHQEP FLAVVIDPTR TVSAGKVEIG AFRTYSKGYK PPDEPVSEYQ TIPLNKIEDF GVHCKQYYSL DVTYFKSSLD SH LLDLLWN KYWVNTLSSS PLLGNGDYVA GQISDLAEKL EQAESHLVQS RFGGVVPSSL HKKKEDESQL TKITRDSAKI TVE QVHGLM SQVIKDELFN SMRQSNNKSP TDSSDPDPMI TY

UniProtKB: COP9 signalosome complex subunit 5b

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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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 47.792895 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MIGAVNSVEA VITSIQGLSG SPEDLSALHD LLRGAQDSLR AEPGVNFSTL DQLDASKHSL GYLYFLEVLT CGPVSKEKAA YEIPIIARF INSCDAGQIR LASYKFVSLC KILKDHVIAL GDPLRGVGPL LNAVQKLQVS SKRLTALHPD VLQLCLQAKS Y KSGFSILS ...String:
MIGAVNSVEA VITSIQGLSG SPEDLSALHD LLRGAQDSLR AEPGVNFSTL DQLDASKHSL GYLYFLEVLT CGPVSKEKAA YEIPIIARF INSCDAGQIR LASYKFVSLC KILKDHVIAL GDPLRGVGPL LNAVQKLQVS SKRLTALHPD VLQLCLQAKS Y KSGFSILS DDIVEIDQPR DFFLYSYYGG MICIGLKRFQ KALELLYNVV TAPMHQVNAI ALEAYKKYIL VSLIHNGQFT NT LPKCAST AAQRSFKNYT GPYIELGNCY NDGKIGELEA LVVARNAEFE EDKNLGLVKQ AVSSLYKRNI LRLTQKYLTL SLQ DIANMV QLGNAKEAEM HVLQMIQDGQ IHALINQKDG MVRFLEDPEQ YKSSEMIEIM DSVIQRTIGL SKNLLAMDES LSCD PLYLG KVGRERQRYD FGDDFDTVPQ KFSM

UniProtKB: COP9 signalosome complex subunit 3

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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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 45.007125 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDEALTNASA IGDQRQKIEQ YKLILSSVLS SNDLLQAQRF IDHILSDDVP LVVSRQLLQS FAQELGRLEP ETQKEIAQFT LTQIQPRVV SFEEQALVIR EKLAGLYESE QEWSKAAQML SGIDLDSGMR AVDDNFKLSK CIQIARLYLE DDDAVNAEAF I NKASFLVS ...String:
MDEALTNASA IGDQRQKIEQ YKLILSSVLS SNDLLQAQRF IDHILSDDVP LVVSRQLLQS FAQELGRLEP ETQKEIAQFT LTQIQPRVV SFEEQALVIR EKLAGLYESE QEWSKAAQML SGIDLDSGMR AVDDNFKLSK CIQIARLYLE DDDAVNAEAF I NKASFLVS NSQNEVLNLQ YKVCYARILD MKRKFLEAAL RYYGISQIEQ RQIGDEEIDE NALEQALSAA VTCTILAGAG PQ RSRVLAT LYKDERCSKL KIYPILQKVY LERILRRPEI DAFSEELRPH QKASLPDKST VLDRAMIEHN LLSASKLYTN IRF DELGTL LAIDPRKAEK IAANMIGQDR MRGSIDQEEA VIHFEDDVEE LQQWDQQISG LCQALNDILD GMAKKGMSVP V

UniProtKB: COP9 signalosome complex subunit 4

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Macromolecule #8: COP9 signalosome complex subunit 2

MacromoleculeName: COP9 signalosome complex subunit 2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 51.254418 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASDADMEDY GFEYSDEEQE EQDVDIENQY YNSKGMVETE PEEALSGFAE VVQMEPEKAD WGFKALKQTV KIYYRLGKYK EMMEAYTEM LTYIKSAVTR NYSEKCINNI MDFVSGSASQ NTGLLQEFYQ TTLKALEEAK NERLWFKTNL KLCNIWFDIG E YRRMTKIL ...String:
MASDADMEDY GFEYSDEEQE EQDVDIENQY YNSKGMVETE PEEALSGFAE VVQMEPEKAD WGFKALKQTV KIYYRLGKYK EMMEAYTEM LTYIKSAVTR NYSEKCINNI MDFVSGSASQ NTGLLQEFYQ TTLKALEEAK NERLWFKTNL KLCNIWFDIG E YRRMTKIL KELHKSCQKE DGTDDQKKGS QLLEVYAIEI QIYTETKDNK KLKQLYHKAL AIKSAIPHPR IMGIIRECGG KM HMAERQW EEAATDFFEA FKNYDEAGNQ RRIQCLKYLV LANMLMESEV NPFDGQEAKP YKNDPEILAM TNLIAAYQRN EII EFERIL KSNRRTIMDD PFIRNYMEDL LKKVRTQVLL KLIKPYTKIG IPFISKELNV PETDVTELLV SLILDSRIDG HIDE MNRYL LRGDSGNGRK LHKAVDKWNS QLKSLSSNIT SRVC

UniProtKB: COP9 signalosome complex subunit 2

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 1 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69921
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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