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- EMDB-10585: Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7... -

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Basic information

Entry
Database: EMDB / ID: EMD-10585
TitleUbiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2
Map data
Sample
  • Complex: Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2
    • Complex: S-phase kinase-associated protein 1
      • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Complex: Cullin-1, E3 ubiquitin-protein ligase RBX1
      • Protein or peptide: S-phase kinase-associated protein 1
      • Protein or peptide: NEDD8
    • Complex: F-box/WD repeat-containing protein 1A, NEDD8, S-phase kinase-associated protein 1, Ubiquitin-conjugating enzyme E2 D2
      • Protein or peptide: F-box/WD repeat-containing protein 1A
      • Protein or peptide: Cullin-1
      • Protein or peptide: Ubiquitin-conjugating enzyme E2 D2
      • Protein or peptide: Polyubiquitin-C
    • Complex: Synthetic peptidePeptide synthesis
      • Protein or peptide: CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY
  • Ligand: ZINC ION
Function / homology
Function and homology information


I-kappaB/NF-kappaB complex / protein phosphorylated amino acid binding / cytoplasmic sequestering of NF-kappaB / Parkin-FBXW7-Cul1 ubiquitin ligase complex / negative regulation of myeloid cell differentiation / F-box domain binding / nucleotide-binding oligomerization domain containing 1 signaling pathway / IkBA variant leads to EDA-ID / PcG protein complex / (E3-independent) E2 ubiquitin-conjugating enzyme ...I-kappaB/NF-kappaB complex / protein phosphorylated amino acid binding / cytoplasmic sequestering of NF-kappaB / Parkin-FBXW7-Cul1 ubiquitin ligase complex / negative regulation of myeloid cell differentiation / F-box domain binding / nucleotide-binding oligomerization domain containing 1 signaling pathway / IkBA variant leads to EDA-ID / PcG protein complex / (E3-independent) E2 ubiquitin-conjugating enzyme / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / molecular sequestering activity / ubiquitin ligase activator activity / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / positive regulation of ubiquitin protein ligase activity / RIP-mediated NFkB activation via ZBP1 / maintenance of protein location in nucleus / regulation of proteolysis / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / SUMOylation of immune response proteins / positive regulation of circadian rhythm / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of protein autoubiquitination / protein neddylation / regulation of canonical Wnt signaling pathway / transcription regulator inhibitor activity / branching involved in mammary gland duct morphogenesis / NEDD8 ligase activity / regulation of canonical NF-kappaB signal transduction / Cul5-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-ubiquitin ligase activity / interleukin-1-mediated signaling pathway / mammary gland epithelial cell proliferation / cellular response to cold / Cul4A-RING E3 ubiquitin ligase complex / E2 ubiquitin-conjugating enzyme / Cul2-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / negative regulation of type I interferon production / toll-like receptor 4 signaling pathway / nuclear localization sequence binding / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / Cul3-RING ubiquitin ligase complex / negative regulation of NF-kappaB transcription factor activity / negative regulation of Notch signaling pathway / response to exogenous dsRNA / Prolactin receptor signaling / ubiquitin conjugating enzyme activity / protein monoubiquitination / TGF-beta receptor signaling activates SMADs / non-canonical NF-kappaB signal transduction / cullin family protein binding / positive regulation of proteolysis / TRAF6 mediated NF-kB activation / ligase activity / response to muramyl dipeptide / transcription factor binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ubiquitin-like ligase-substrate adaptor activity / cellular response to organic cyclic compound / NF-kappaB binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of cholesterol efflux / protein K48-linked ubiquitination / anatomical structure morphogenesis / canonical NF-kappaB signal transduction / protein autoubiquitination / Nuclear events stimulated by ALK signaling in cancer / ubiquitin ligase complex / negative regulation of smoothened signaling pathway / negative regulation of canonical NF-kappaB signal transduction / regulation of proteasomal protein catabolic process / Maturation of protein E / Notch signaling pathway / Maturation of protein E / ER Quality Control Compartment (ERQC) / lipopolysaccharide-mediated signaling pathway / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / positive regulation of TORC1 signaling
Similarity search - Function
D domain of beta-TrCP / D domain of beta-TrCP / D domain of beta-TrCP / Ankyrin repeats (many copies) / Nedd8-like ubiquitin / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation ...D domain of beta-TrCP / D domain of beta-TrCP / D domain of beta-TrCP / Ankyrin repeats (many copies) / Nedd8-like ubiquitin / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / SKP1/BTB/POZ domain superfamily / Ankyrin repeats (3 copies) / Ubiquitin conserved site / Ankyrin repeat profile. / Ubiquitin domain / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Zinc finger RING-type profile. / Zinc finger, RING-type / Ankyrin repeat-containing domain superfamily / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / G-protein beta WD-40 repeat / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Ring-box 1 / Polyubiquitin-C / NF-kappa-B inhibitor alpha / Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase RBX1 / S-phase kinase-associated protein 1 / Cullin-1 / NEDD8 / F-box/WD repeat-containing protein 1A
Similarity search - Component
Biological speciesPan troglodytes (chimpanzee) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBaek K / Prabu JR / Schulman BA
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nature / Year: 2020
Title: NEDD8 nucleates a multivalent cullin-RING-UBE2D ubiquitin ligation assembly.
Authors: Kheewoong Baek / David T Krist / J Rajan Prabu / Spencer Hill / Maren Klügel / Lisa-Marie Neumaier / Susanne von Gronau / Gary Kleiger / Brenda A Schulman /
Abstract: Eukaryotic cell biology depends on cullin-RING E3 ligase (CRL)-catalysed protein ubiquitylation, which is tightly controlled by the modification of cullin with the ubiquitin-like protein NEDD8. ...Eukaryotic cell biology depends on cullin-RING E3 ligase (CRL)-catalysed protein ubiquitylation, which is tightly controlled by the modification of cullin with the ubiquitin-like protein NEDD8. However, how CRLs catalyse ubiquitylation, and the basis of NEDD8 activation, remain unknown. Here we report the cryo-electron microscopy structure of a chemically trapped complex that represents the ubiquitylation intermediate, in which the neddylated CRL1 promotes the transfer of ubiquitin from the E2 ubiquitin-conjugating enzyme UBE2D to its recruited substrate, phosphorylated IκBα. NEDD8 acts as a nexus that binds disparate cullin elements and the RING-activated ubiquitin-linked UBE2D. Local structural remodelling of NEDD8 and large-scale movements of CRL domains converge to juxtapose the substrate and the ubiquitylation active site. These findings explain how a distinctive ubiquitin-like protein alters the functions of its targets, and show how numerous NEDD8-dependent interprotein interactions and conformational changes synergistically configure a catalytic CRL architecture that is both robust, to enable rapid ubiquitylation of the substrate, and fragile, to enable the subsequent functions of cullin-RING proteins.
History
DepositionDec 30, 2019-
Header (metadata) releaseFeb 12, 2020-
Map releaseFeb 12, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ttu
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10585.png

Downloads & links

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Map

FileDownload / File: emd_10585.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.016 / Movie #1: 0.016
Minimum - Maximum-0.052416746 - 0.093356736
Average (Standard dev.)0.0000803417 (±0.0014660304)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z339.200339.200339.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0520.0930.000

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Supplemental data

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Mask #1

Fileemd_10585_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused Refinement masking out C/R domain

Fileemd_10585_additional.map
AnnotationFocused Refinement masking out C/R domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10585_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_10585_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7...

EntireName: Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2
Components
  • Complex: Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2
    • Complex: S-phase kinase-associated protein 1
      • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Complex: Cullin-1, E3 ubiquitin-protein ligase RBX1
      • Protein or peptide: S-phase kinase-associated protein 1
      • Protein or peptide: NEDD8
    • Complex: F-box/WD repeat-containing protein 1A, NEDD8, S-phase kinase-associated protein 1, Ubiquitin-conjugating enzyme E2 D2
      • Protein or peptide: F-box/WD repeat-containing protein 1A
      • Protein or peptide: Cullin-1
      • Protein or peptide: Ubiquitin-conjugating enzyme E2 D2
      • Protein or peptide: Polyubiquitin-C
    • Complex: Synthetic peptidePeptide synthesis
      • Protein or peptide: CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY
  • Ligand: ZINC ION

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Supramolecule #1: Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7...

SupramoleculeName: Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Molecular weightTheoretical: 210 KDa

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Supramolecule #2: S-phase kinase-associated protein 1

SupramoleculeName: S-phase kinase-associated protein 1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Pan troglodytes (chimpanzee)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: Cullin-1, E3 ubiquitin-protein ligase RBX1

SupramoleculeName: Cullin-1, E3 ubiquitin-protein ligase RBX1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2, #4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Supramolecule #4: F-box/WD repeat-containing protein 1A, NEDD8, S-phase kinase-asso...

SupramoleculeName: F-box/WD repeat-containing protein 1A, NEDD8, S-phase kinase-associated protein 1, Ubiquitin-conjugating enzyme E2 D2
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #1, #3, #6-#7
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #5: Synthetic peptide

SupramoleculeName: Synthetic peptide / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #8
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Synthetic construct (others)

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Macromolecule #1: F-box/WD repeat-containing protein 1A

MacromoleculeName: F-box/WD repeat-containing protein 1A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.960797 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDPAEAVLQE KALKFMCSMP RSLWLGCSSL ADSMPSLRCL YNPGTGALTA FQNSSEREDC NNGEPPRKII PEKNSLRQTY NSCARLCLN QETVCLASTA MKTENCVAKT KLANGTSSMI VPKQRKLSAS YEKEKELCVK YFEQWSESDQ VEFVEHLISQ M CHYQHGHI ...String:
MDPAEAVLQE KALKFMCSMP RSLWLGCSSL ADSMPSLRCL YNPGTGALTA FQNSSEREDC NNGEPPRKII PEKNSLRQTY NSCARLCLN QETVCLASTA MKTENCVAKT KLANGTSSMI VPKQRKLSAS YEKEKELCVK YFEQWSESDQ VEFVEHLISQ M CHYQHGHI NSYLKPMLQR DFITALPARG LDHIAENILS YLDAKSLCAA ELVCKEWYRV TSDGMLWKKL IERMVRTDSL WR GLAERRG WGQYLFKNKP PDGNAPPNSF YRALYPKIIQ DIETIESNWR CGRHSLQRIH CRSETSKGVY CLQYDDQKIV SGL RDNTIK IWDKNTLECK RILTGHTGSV LCLQYDERVI ITGSSDSTVR VWDVNTGEML NTLIHHCEAV LHLRFNNGMM VTCS KDRSI AVWDMASPTD ITLRRVLVGH RAAVNVVDFD DKYIVSASGD RTIKVWNTST CEFVRTLNGH KRGIACLQYR DRLVV SGSS DNTIRLWDIE CGACLRVLEG HEELVRCIRF DNKRIVSGAY DGKIKVWDLV AALDPRAPAG TLCLRTLVEH SGRVFR LQF DEFQIVSSSH DDTILIWDFL NDPAAQAEPP RSPSRTYTYI SR

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Macromolecule #2: S-phase kinase-associated protein 1

MacromoleculeName: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 2
Details: SKP1 contains truncations of residues 38-43, 71-82.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.679965 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MPSIKLQSSD GEIFEVDVEI AKQSVTIKTM LEDLGMDDEG DDDPVPLPNV NAAILKKVIQ WCTHHKDDPP PPEDDENKEK RTDDIPVWD QEFLKVDQGT LFELILAANY LDIKGLLDVT CKTVANMIKG KTPEEIRKTF NIKNDFTEEE EAQVRKENQW C EEK

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Macromolecule #3: Cullin-1

MacromoleculeName: Cullin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.800367 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSTRSQNPH GLKQIGLDQI WDDLRAGIQQ VYTRQSMAKS RYMELYTHVY NYCTSVHQSN QARGAGVPPS KSKKGQTPGG AQFVGLELY KRLKEFLKNY LTNLLKDGED LMDESVLKFY TQQWEDYRFS SKVLNGICAY LNRHWVRREC DEGRKGIYEI Y SLALVTWR ...String:
MSSTRSQNPH GLKQIGLDQI WDDLRAGIQQ VYTRQSMAKS RYMELYTHVY NYCTSVHQSN QARGAGVPPS KSKKGQTPGG AQFVGLELY KRLKEFLKNY LTNLLKDGED LMDESVLKFY TQQWEDYRFS SKVLNGICAY LNRHWVRREC DEGRKGIYEI Y SLALVTWR DCLFRPLNKQ VTNAVLKLIE KERNGETINT RLISGVVQSY VELGLNEDDA FAKGPTLTVY KESFESQFLA DT ERFYTRE STEFLQQNPV TEYMKKAEAR LLEEQRRVQV YLHESTQDEL ARKCEQVLIE KHLEIFHTEF QNLLDADKNE DLG RMYNLV SRIQDGLGEL KKLLETHIHN QGLAAIEKCG EAALNDPKMY VQTVLDVHKK YNALVMSAFN NDAGFVAALD KACG RFINN NAVTKMAQSS SKSPELLARY CDSLLKKSSK NPEEAELEDT LNQVMVVFKY IEDKDVFQKF YAKMLAKRLV HQNSA SDDA EASMISKLKQ ACGFEYTSKL QRMFQDIGVS KDLNEQFKKH LTNSEPLDLD FSIQVLSSGS WPFQQSCTFA LPSELE RSY QRFTAFYASR HSGRKLTWLY QLSKGELVTN CFKNRYTLQA STFQMAILLQ YNTEDAYTVQ QLTDSTQIKM DILAQVL QI LLKSKLLVLE DENANVDEVE LKPDTLIKLY LGYKNKKLRV NINVPMKTEQ KQEQETTHKN IEEDRKLLIQ AAIVRIMK M RKVLKHQQLL GEVLTQLSSR FKPRVPVIKK CIDILIEKEY LERVDGEKDT YSYLA

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Macromolecule #4: NEDD8

MacromoleculeName: NEDD8 / type: protein_or_peptide / ID: 4
Details: Residue 1, Ser, comes from the linker. NEDD8 residue starts from MET.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.661055 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
SMLIKVKTLT GKEIEIDIEP TDKVERIKER VEEKEGIPPQ QQRLIYSGKQ MNDEKTAADY KILGGSVLHL VLALRGG

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Macromolecule #5: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 5
Details: RBX1 contains mutation Asn98Arg (N98R). There are 3 Zinc ions coordinated throughout. This is not meant to align to the C-terminus of the protein.
Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.333067 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDRR EWEFQKYGH

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Macromolecule #6: Ubiquitin-conjugating enzyme E2 D2

MacromoleculeName: Ubiquitin-conjugating enzyme E2 D2 / type: protein_or_peptide / ID: 6
Details: UBE2D2 contains mutations of the following: Cys21Ile, Cys107Ala, Cys111Asp.
Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.745121 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MALKRIHKEL NDLARDPPAQ ISAGPVGDDM FHWQATIMGP NDSPYQGGVF FLTIHFPTDY PFKPPKVAFT TRIYHPNINS NGSICLDIL RSQWSPALTI SKVLLSIASL LDDPNPDDPL VPEIARIYKT DREKYNRIAR EWTQKYAM

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Macromolecule #7: Polyubiquitin-C

MacromoleculeName: Polyubiquitin-C / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

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Macromolecule #8: CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY

MacromoleculeName: CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY / type: protein_or_peptide / ID: 8 / Details: Phosphorylated peptide derived from IkBa. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.782819 KDa
SequenceString:
CKKERLLDDR HD(SEP)GLD(SEP)MKD EEDYKDDDDK

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / 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: 7.8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 70.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 106257
FSC plot (resolution estimation)

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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

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