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

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Basic information

Entry
Database: PDB / ID: 1ldj
TitleStructure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex
Components
  • Cullin homolog 1
  • ring-box protein 1
KeywordsLIGASE / cullin / rbx1 / roc1 / hrt1 / zinc ring finger / ubiquitin / ubiquitination / SCF
Function / homology
Function and homology information


Parkin-FBXW7-Cul1 ubiquitin ligase complex / cullin-RING-type E3 NEDD8 transferase / 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 / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance ...Parkin-FBXW7-Cul1 ubiquitin ligase complex / cullin-RING-type E3 NEDD8 transferase / 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 / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / protein neddylation / NEDD8 ligase activity / VCB complex / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / negative regulation of type I interferon production / ubiquitin-ubiquitin ligase activity / Cul2-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of mitophagy / Prolactin receptor signaling / cullin family protein binding / protein monoubiquitination / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / transcription-coupled nucleotide-excision repair / positive regulation of TORC1 signaling / regulation of cellular response to insulin stimulus / intrinsic apoptotic signaling pathway / negative regulation of insulin receptor signaling pathway / post-translational protein modification / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / T cell activation / animal organ morphogenesis / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Degradation of DVL / cellular response to amino acid stimulus / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / G1/S transition of mitotic cell cycle / negative regulation of canonical Wnt signaling pathway / 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 / DNA Damage Recognition in GG-NER / Degradation of beta-catenin by the destruction complex / RING-type E3 ubiquitin transferase / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / Dual Incision in GG-NER / CLEC7A (Dectin-1) signaling / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / Interleukin-1 signaling / Orc1 removal from chromatin / protein polyubiquitination / Dual incision in TC-NER / Regulation of RAS by GAPs / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of RUNX2 expression and activity / positive regulation of protein catabolic process / Cyclin D associated events in G1 / cellular response to UV / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / : / Regulation of PLK1 Activity at G2/M Transition / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / MAPK cascade / Neddylation / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / spermatogenesis / protein-macromolecule adaptor activity / molecular adaptor activity / Potential therapeutics for SARS
Similarity search - Function
Ring Box Chain A; domain 5 / Ring Box Chain A; domain 5 / Cullin Repeats / 5 helical Cullin repeat like / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin family signature. ...Ring Box Chain A; domain 5 / Ring Box Chain A; domain 5 / Cullin Repeats / 5 helical Cullin repeat like / 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 alpha solenoid domain / Cullin family profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Few Secondary Structures / Irregular / 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 / Cullin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 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 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cullin homolog 1
B: ring-box protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9265
Polymers98,7302
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-22 kcal/mol
Surface area40840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.974, 49.968, 135.883
Angle α, β, γ (deg.)90.00, 107.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cullin homolog 1 / CUL-1


Mass: 88074.430 Da / Num. of mol.: 1 / Fragment: Residues 17-776
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13616
#2: Protein ring-box protein 1 / Rbx1


Mass: 10655.229 Da / Num. of mol.: 1 / Fragment: Residues 19-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62877
#3: Chemical ChemComp-ZN / ZINC ION


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.73 Å3/Da / Density % sol: 67.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% Ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1100 mMTris-HCl1reservoir
212-18 %ethanol1reservoir
3200-500 mM1reservoirNaCl
45 mMdithiothreitol1reservoirpH8.0
510-20 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11701
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F110.943
SYNCHROTRONCHESS A120.928
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9431
20.9281
ReflectionResolution: 3→15 Å / Num. obs: 28766 / Observed criterion σ(I): 0
Reflection
*PLUS
Lowest resolution: 15 Å / % possible obs: 97.6 % / Num. measured all: 92525 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 97 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 3→15 Å / σ(F): 0
RfactorNum. reflection
Rfree0.288 23647
Rwork0.247 -
obs-25004
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6665 0 3 0 6668
Refinement
*PLUS
Lowest resolution: 15 Å / Num. reflection obs: 23647 / % reflection Rfree: 5 % / Rfactor obs: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.322 / Rfactor Rwork: 0.41 / Rfactor obs: 0.41

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