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- PDB-1ldk: Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex -

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Basic information

Entry
Database: PDB / ID: 1ldk
TitleStructure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex
Components
  • (CULLIN HOMOLOG) x 2
  • CYCLIN A/CDK2-ASSOCIATED PROTEIN P19
  • SKP2-like protein type gamma
  • ring-box protein 1
KeywordsLIGASE / SCF / cullin / rbx1 / roc1 / hrt1 / skp1 / skp2 / F-box / fbox / ubiquitin / ubiquitination / E3 ligase
Function / homology
Function and homology information


positive regulation of protein polyubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects / PcG protein complex / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex ...positive regulation of protein polyubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects / PcG protein complex / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / positive regulation of ubiquitin protein ligase activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / positive regulation of protein autoubiquitination / protein neddylation / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / negative regulation of response to oxidative stress / positive regulation of intracellular estrogen receptor signaling pathway / ubiquitin-ubiquitin ligase activity / Cul4A-RING E3 ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / negative regulation of type I interferon production / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / Prolactin receptor signaling / protein monoubiquitination / cullin family protein binding / protein K63-linked ubiquitination / ubiquitin-like ligase-substrate adaptor activity / positive regulation of double-strand break repair via homologous recombination / Nuclear events stimulated by ALK signaling in cancer / protein K48-linked ubiquitination / positive regulation of TORC1 signaling / T cell activation / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / intrinsic apoptotic signaling pathway / post-translational protein modification / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / molecular function activator activity / Vpu mediated degradation of CD4 / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Recognition of DNA damage by PCNA-containing replication complex / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / animal organ morphogenesis / cellular response to amino acid stimulus / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / DNA Damage Recognition in GG-NER / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / RING-type E3 ubiquitin transferase / Degradation of beta-catenin by the destruction complex / negative regulation of canonical Wnt signaling pathway / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Dual Incision in GG-NER / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / beta-catenin binding / Regulation of expression of SLITs and ROBOs / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Formation of Incision Complex in GG-NER / FCERI mediated NF-kB activation / Interleukin-1 signaling / Orc1 removal from chromatin / Dual incision in TC-NER / G1/S transition of mitotic cell cycle / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of RAS by GAPs / protein polyubiquitination / positive regulation of protein catabolic process / Regulation of RUNX2 expression and activity / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / cellular response to UV / Regulation of PLK1 Activity at G2/M Transition / KEAP1-NFE2L2 pathway / MAPK cascade / ubiquitin protein ligase activity / Circadian Clock / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process
Similarity search - Function
Cullin; Chain C, Domain 2 / Cullin Repeats / Monooxygenase - #50 / 5 helical Cullin repeat like / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like ...Cullin; Chain C, Domain 2 / Cullin Repeats / Monooxygenase - #50 / 5 helical Cullin repeat like / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / 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 / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Cullin / Monooxygenase / 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 / Ribosomal Protein S5; domain 2 / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / SKP1/BTB/POZ domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Leucine-rich repeat domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Arc Repressor Mutant, subunit A / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / S-phase kinase-associated protein 1 / S-phase kinase-associated protein 2 / Cullin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsZheng, N. / Schulman, B.A. / Song, L. / Miller, J.J. / Jeffrey, P.D. / Wang, P. / Chu, C. / Koepp, D.M. / Elledge, S.J. / Pagano, M. ...Zheng, N. / Schulman, B.A. / Song, L. / Miller, J.J. / Jeffrey, P.D. / Wang, P. / Chu, C. / Koepp, D.M. / Elledge, S.J. / Pagano, M. / Conaway, R.C. / Conaway, J.W. / Harper, J.W. / Pavletich, N.P.
CitationJournal: Nature / Year: 2002
Title: Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF ubiquitin ligase complex.
Authors: Zheng, N. / Schulman, B.A. / Song, L. / Miller, J.J. / Jeffrey, P.D. / Wang, P. / Chu, C. / Koepp, D.M. / Elledge, S.J. / Pagano, M. / Conaway, R.C. / Conaway, J.W. / Harper, J.W. / Pavletich, N.P.
History
DepositionApr 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Database references / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CULLIN HOMOLOG
B: CULLIN HOMOLOG
C: ring-box protein 1
D: CYCLIN A/CDK2-ASSOCIATED PROTEIN P19
E: SKP2-like protein type gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9078
Polymers118,7115
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9970 Å2
ΔGint-65 kcal/mol
Surface area51510 Å2
MethodPISA
2
A: CULLIN HOMOLOG
B: CULLIN HOMOLOG
C: ring-box protein 1
D: CYCLIN A/CDK2-ASSOCIATED PROTEIN P19
E: SKP2-like protein type gamma
hetero molecules

A: CULLIN HOMOLOG
B: CULLIN HOMOLOG
C: ring-box protein 1
D: CYCLIN A/CDK2-ASSOCIATED PROTEIN P19
E: SKP2-like protein type gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,81416
Polymers237,42110
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area23160 Å2
ΔGint-148 kcal/mol
Surface area99800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.378, 50.529, 158.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein CULLIN HOMOLOG / cul1


Mass: 45754.766 Da / Num. of mol.: 1 / Fragment: RESIDUES 15-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13616
#2: Protein CULLIN HOMOLOG / cul1


Mass: 42507.910 Da / Num. of mol.: 1 / Fragment: RESIDUES 411-776
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13616
#3: Protein ring-box protein 1 / Rbx1


Mass: 10655.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62877
#4: Protein CYCLIN A/CDK2-ASSOCIATED PROTEIN P19 / Skp1 / RNA POLYMERASE II ELONGATION FACTOR-LIKE PROTEIN / ORGAN OF CORTI PROTEIN 2 / OCP-II PROTEIN ...Skp1 / RNA POLYMERASE II ELONGATION FACTOR-LIKE PROTEIN / ORGAN OF CORTI PROTEIN 2 / OCP-II PROTEIN / TRANSCRIPTION ELONGATION FACTOR B / SIII


Mass: 15033.173 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: P63208

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Protein/peptide / Non-polymers , 2 types, 4 molecules E

#5: Protein/peptide SKP2-like protein type gamma / Skp2-Fbox


Mass: 4759.569 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13309
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: peg4k, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1100 mMBTP1reservoir
27-9 %PEG40001reservoir
3200-400 mM1reservoirNaCl
45 mMdithiothreitol1reservoirpH7.0
510-20 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11701
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.928
SYNCHROTRONCHESS F120.943
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9281
20.9431
ReflectionResolution: 3.1→20 Å / Num. obs: 30847 / Observed criterion σ(I): 0
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 88.8 % / Num. measured all: 123884 / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 63.5 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→20 Å / σ(F): 0 /
RfactorNum. reflection
Rfree0.331 -
Rwork0.289 -
obs-24828
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7919 0 3 0 7922
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.289
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.513 / Rfactor Rwork: 0.473

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