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- EMDB-12040: Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 s... -

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Basic information

Entry
Database: EMDB / ID: EMD-12040
TitleUbiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2
Map data
Sample
  • Complex: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1
    • Complex: Cullin-1, E3 ubiquitin-protein ligase RBX1
      • Protein or peptide: Cullin-1
      • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Complex: ARIH1, SKP2, CKS1B, SKP1, UBC
      • Protein or peptide: E3 ubiquitin-protein ligase ARIH1
      • Protein or peptide: S-phase kinase-associated protein 2
      • Protein or peptide: Cyclin-dependent kinases regulatory subunit 1
      • Protein or peptide: S-phase kinase-associated protein 1
      • Protein or peptide: Polyubiquitin-C
    • Complex: Cyclin-dependent kinase inhibitor 1B
      • Protein or peptide: Cyclin-dependent kinase inhibitor 1B
  • Ligand: ZINC ION
Keywordsubiquitin / ubiquitin ligase / E3 ligase / F-box protein / RBR ligase / Cullin-RING-Ligase / CRL / SCF / NEDD8 / Post-translational modification / ubiquitylation / LIGASE
Function / homology
Function and homology information


PKR/eIFalpha signaling / cyclin-dependent protein kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cyclin-dependent protein kinase activity / negative regulation of cardiac muscle tissue regeneration / negative regulation of kinase activity / positive regulation of protein polyubiquitination / ubiquitin-like protein transferase activity / autophagic cell death / FOXO-mediated transcription of cell cycle genes ...PKR/eIFalpha signaling / cyclin-dependent protein kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cyclin-dependent protein kinase activity / negative regulation of cardiac muscle tissue regeneration / negative regulation of kinase activity / positive regulation of protein polyubiquitination / ubiquitin-like protein transferase activity / autophagic cell death / FOXO-mediated transcription of cell cycle genes / Parkin-FBXW7-Cul1 ubiquitin ligase complex / Lewy body / RBR-type E3 ubiquitin transferase / negative regulation of epithelial cell proliferation involved in prostate gland development / F-box domain binding / negative regulation of cyclin-dependent protein serine/threonine kinase activity / cellular response to cell-matrix adhesion / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of cell cycle G1/S phase transition / PcG protein complex / regulation of exit from mitosis / cullin-RING-type E3 NEDD8 transferase / negative regulation of epithelial cell apoptotic process / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / epithelial cell proliferation involved in prostate gland development / positive regulation of ubiquitin protein ligase activity / cellular response to chemical stress / cyclin-dependent protein serine/threonine kinase inhibitor activity / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / ubiquitin ligase activator activity / RHO GTPases activate CIT / regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / cyclin-dependent protein serine/threonine kinase activator activity / protein neddylation / nuclear export / ubiquitin conjugating enzyme binding / negative regulation of mitotic cell cycle / Modulation of host responses by IFN-stimulated genes / NEDD8 ligase activity / AKT phosphorylates targets in the cytosol / VCB complex / negative regulation of response to oxidative stress / epithelial cell apoptotic process / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / cellular response to antibiotic / Cul2-RING ubiquitin ligase complex / negative regulation of type I interferon production / ubiquitin-ubiquitin ligase activity / Cul4A-RING E3 ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / molecular function inhibitor activity / Cul4-RING E3 ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / cellular response to lithium ion / positive regulation of intracellular estrogen receptor signaling pathway / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of mitophagy / Prolactin receptor signaling / p53-Dependent G1 DNA Damage Response / protein kinase inhibitor activity / RSV-host interactions / PTK6 Regulates Cell Cycle / Constitutive Signaling by AKT1 E17K in Cancer / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / inner ear development / negative regulation of vascular associated smooth muscle cell proliferation / regulation of G1/S transition of mitotic cell cycle / cullin family protein binding / protein K63-linked ubiquitination / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Maturation of protein E / Maturation of protein E / protein monoubiquitination / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / ubiquitin ligase complex / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation
Similarity search - Function
: / E3 ubiquitin-protein ligase ARIH1, UBA-like domain / Ariadne domain / Ariadne domain / E3 ubiquitin ligase RBR family / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily ...: / E3 ubiquitin-protein ligase ARIH1, UBA-like domain / Ariadne domain / Ariadne domain / E3 ubiquitin ligase RBR family / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / IBR domain, a half RING-finger domain / IBR domain / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / IBR domain / A Receptor for Ubiquitination Targets / In Between Ring fingers / TRIAD supradomain / F-box domain profile. / TRIAD supradomain profile. / F-box-like / F-box-like domain superfamily / 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 repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / 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 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / SKP1/BTB/POZ domain superfamily / Ring finger / : / Leucine-rich repeat domain superfamily / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / Cyclin-dependent kinase inhibitor 1B / Cyclin-dependent kinases regulatory subunit 1 / E3 ubiquitin-protein ligase RBX1 / S-phase kinase-associated protein 1 / S-phase kinase-associated protein 2 / Cullin-1 / E3 ubiquitin-protein ligase ARIH1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.91 Å
AuthorsHorn-Ghetko D / Prabu JR / Schulman BA
Funding support Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)H2020 789016-NEDD8Activate Germany
German Research Foundation (DFG)SCHU 3196/1-1 Germany
CitationJournal: Nature / Year: 2021
Title: Ubiquitin ligation to F-box protein targets by SCF-RBR E3-E3 super-assembly.
Authors: Horn-Ghetko D / Krist DT / Prabu JR / Baek K / Mulder MPC / Klugel M / Scott DC / Ovaa H / Kleiger G / Schulman BA
History
DepositionDec 5, 2020-
Header (metadata) releaseFeb 17, 2021-
Map releaseFeb 17, 2021-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0185
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0185
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7b5m
  • Surface level: 0.0185
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_12040.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.0185 / Movie #1: 0.0185
Minimum - Maximum-0.05181092 - 0.10555756
Average (Standard dev.)0.00016817033 (±0.002099611)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions312312312
Spacing312312312
CellA=B=C: 340.08002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z312312312
origin x/y/z0.0000.0000.000
length x/y/z340.080340.080340.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS312312312
D min/max/mean-0.0520.1060.000

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Supplemental data

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Sample components

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Entire : CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1

EntireName: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1
Components
  • Complex: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1
    • Complex: Cullin-1, E3 ubiquitin-protein ligase RBX1
      • Protein or peptide: Cullin-1
      • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Complex: ARIH1, SKP2, CKS1B, SKP1, UBC
      • Protein or peptide: E3 ubiquitin-protein ligase ARIH1
      • Protein or peptide: S-phase kinase-associated protein 2
      • Protein or peptide: Cyclin-dependent kinases regulatory subunit 1
      • Protein or peptide: S-phase kinase-associated protein 1
      • Protein or peptide: Polyubiquitin-C
    • Complex: Cyclin-dependent kinase inhibitor 1B
      • Protein or peptide: Cyclin-dependent kinase inhibitor 1B
  • Ligand: ZINC ION

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Supramolecule #1: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1

SupramoleculeName: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Molecular weightTheoretical: 250 KDa

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Supramolecule #2: Cullin-1, E3 ubiquitin-protein ligase RBX1

SupramoleculeName: Cullin-1, E3 ubiquitin-protein ligase RBX1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: ARIH1, SKP2, CKS1B, SKP1, UBC

SupramoleculeName: ARIH1, SKP2, CKS1B, SKP1, UBC / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#6
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Cyclin-dependent kinase inhibitor 1B

SupramoleculeName: Cyclin-dependent kinase inhibitor 1B / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cullin-1

MacromoleculeName: Cullin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.800367 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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

UniProtKB: Cullin-1

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Macromolecule #2: E3 ubiquitin-protein ligase ARIH1

MacromoleculeName: E3 ubiquitin-protein ligase ARIH1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RBR-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.005605 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDSDEGYNYE FDEDEECSEE DSGAEEEEDE DDDEPDDDTL DLGEVELVEP GLGVGGERDG LLCGETGGGG GSALGPGGGG GGGGGGGGG GPGHEQEEDY RYEVLTAEQI LQHMVECIRE VNEVIQNPAT ITRILLSHFN WDKEKLMERY FDGNLEKLFA E CHVINPSK ...String:
MDSDEGYNYE FDEDEECSEE DSGAEEEEDE DDDEPDDDTL DLGEVELVEP GLGVGGERDG LLCGETGGGG GSALGPGGGG GGGGGGGGG GPGHEQEEDY RYEVLTAEQI LQHMVECIRE VNEVIQNPAT ITRILLSHFN WDKEKLMERY FDGNLEKLFA E CHVINPSK KSRTRQMNTR SSAQDMPCQI CYLNYPNSYF TGLECGHKFC MQCWSEYLTT KIMEEGMGQT ISCPAHGCDI LV DDNTVMR LITDSKVKLK YQHLITNSFV ECNRLLKWCP APDCHHVVKV QYPDAKPVRC KCGRQFCFNC GENWHDPVKC KWL KKWIKK CDDDSETSNW IAANTKECPK CHVTIEKDGG CNHMVCRNQN CKAEFCWVCL GPWEPHGSAW YNCNRYNEDD AKAA RDAQE RSRAALQRYL FYCNRYMNHM QSLRAAHKLY AQVKQKMEEM QQHNMSWIEV QFLKKAVDVL CQCRATLMYT YVFAF YLKK NNQSIIFENN QADLENATAV LSGYLERDIS QDSLQDIKQK VQDKYRYCES RRRVLLQHVH EGYEKDLWEY IED

UniProtKB: E3 ubiquitin-protein ligase ARIH1

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Macromolecule #3: S-phase kinase-associated protein 2

MacromoleculeName: S-phase kinase-associated protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.817785 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHRKHLQEIP DLSSNVATSF TWGWDSSKTS ELLSGMGVSA LEKEEPDSEN IPQELLSNLG HPESPPRKRL KSKGSDKDFV IVRRPKLNR ENFPGVSWDS LPDELLLGIF SCLCLPELLK VSGVCKRWYR LASDESLWQT LDLTGKNLHP DVTGRLLSQG V IAFRCPRS ...String:
MHRKHLQEIP DLSSNVATSF TWGWDSSKTS ELLSGMGVSA LEKEEPDSEN IPQELLSNLG HPESPPRKRL KSKGSDKDFV IVRRPKLNR ENFPGVSWDS LPDELLLGIF SCLCLPELLK VSGVCKRWYR LASDESLWQT LDLTGKNLHP DVTGRLLSQG V IAFRCPRS FMDQPLAEHF SPFRVQHMDL SNSVIEVSTL HGILSQCSKL QNLSLEGLRL SDPIVNTLAK NSNLVRLNLS GC SGFSEFA LQTLLSSCSR LDELNLSWCF DFTEKHVQVA VAHVSETITQ LNLSGYRKNL QKSDLSTLVR RCPNLVHLDL SDS VMLKND CFQEFFQLNY LQHLSLSRCY DIIPETLLEL GEIPTLKTLQ VFGIVPDGTL QLLKEALPHL QINCSHFTTI ARPT IGNKK NQEIWGIKCR LTLQKPSCL

UniProtKB: S-phase kinase-associated protein 2

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Macromolecule #4: Cyclin-dependent kinases regulatory subunit 1

MacromoleculeName: Cyclin-dependent kinases regulatory subunit 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.679211 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSHKQIYYSD KYDDEEFEYR HVMLPKDIAK LVPKTHLMSE SEWRNLGVQQ SQGWVHYMIH EPEPHILLFR RPLPKKPKK

UniProtKB: Cyclin-dependent kinases regulatory subunit 1

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Macromolecule #5: S-phase kinase-associated protein 1

MacromoleculeName: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.679965 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPSIKLQSSD GEIFEVDVEI AKQSVTIKTM LEDLGMDDEG DDDPVPLPNV NAAILKKVIQ WCTHHKDDPP PPEDDENKEK RTDDIPVWD QEFLKVDQGT LFELILAANY LDIKGLLDVT CKTVANMIKG KTPEEIRKTF NIKNDFTEEE EAQVRKENQW C EEK

UniProtKB: S-phase kinase-associated protein 1

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Macromolecule #6: Polyubiquitin-C

MacromoleculeName: Polyubiquitin-C / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.519778 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRG

UniProtKB: Polyubiquitin-C

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Macromolecule #7: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.289977 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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Macromolecule #8: Cyclin-dependent kinase inhibitor 1B

MacromoleculeName: Cyclin-dependent kinase inhibitor 1B / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.185262 KDa
Recombinant expressionOrganism: synthetic construct (others)
SequenceString: MSNVRVSNGS PSLERMDARQ AEHPKPSACR NLFGPVDHEE LTRDLEKHCR DMEEASQRKW NFDFQNHKPL EGKYEWQEVE KGSLPEFYY RPPRPPKGAC KVPAQESQDV SGSRPAAPLI GAPANSEDTH LVDPKTDPSD SQTGLAEQCA GIRKRPATDD S ST(DHA)NKRAN ...String:
MSNVRVSNGS PSLERMDARQ AEHPKPSACR NLFGPVDHEE LTRDLEKHCR DMEEASQRKW NFDFQNHKPL EGKYEWQEVE KGSLPEFYY RPPRPPKGAC KVPAQESQDV SGSRPAAPLI GAPANSEDTH LVDPKTDPSD SQTGLAEQCA GIRKRPATDD S ST(DHA)NKRAN RTEENVSDGS PNAGSVEQ(TPO)P RRPGLRRRQT

UniProtKB: Cyclin-dependent kinase inhibitor 1B

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 5 / 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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 759489
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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