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- PDB-3dpl: Structural Insights into NEDD8 Activation of Cullin-RING Ligases:... -

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Basic information

Entry
Database: PDB / ID: 3dpl
TitleStructural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation.
Components
  • Cullin-5
  • RING-box protein 1
KeywordsLIGASE / ubiquitin / NEDD8 / cullin / Host-virus interaction / Receptor / Ubl conjugation / Ubl conjugation pathway / Acetylation / Cytoplasm / DNA damage / DNA repair / Metal-binding / Nucleus / Zinc / Zinc-finger
Function / homology
Function and homology information


ERBB2 signaling pathway / regulation of neuron migration / reelin-mediated signaling pathway / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling ...ERBB2 signaling pathway / regulation of neuron migration / reelin-mediated signaling pathway / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / protein K11-linked ubiquitination / protein neddylation / NEDD8 ligase activity / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / 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 / site of DNA damage / protein monoubiquitination / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / negative regulation of insulin receptor signaling pathway / post-translational protein modification / intrinsic apoptotic signaling pathway / T cell activation / Regulation of BACH1 activity / cellular response to amino acid stimulus / Degradation of DVL / Degradation of GLI1 by the proteasome / Recognition of DNA damage by PCNA-containing replication complex / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of canonical Wnt signaling pathway / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / 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 / Inactivation of CSF3 (G-CSF) signaling / DNA Damage Recognition in GG-NER / RING-type E3 ubiquitin transferase / Degradation of beta-catenin by the destruction complex / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / calcium channel activity / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / NOTCH1 Intracellular Domain Regulates Transcription / Formation of TC-NER Pre-Incision Complex / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / G1/S transition of mitotic cell cycle / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / Downregulation of ERBB2 signaling / Interleukin-1 signaling / Orc1 removal from chromatin / Dual incision in TC-NER / Regulation of RAS by GAPs / protein polyubiquitination / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / cellular response to UV / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity / MAPK cascade / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / signaling receptor activity / Neddylation / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / spermatogenesis / molecular adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / DNA repair / ubiquitin protein ligase binding / DNA damage response / zinc ion binding / nucleoplasm
Similarity search - Function
Cullin; Chain C, Domain 2 / 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; Chain C, Domain 2 / 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 family / Cullin family profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ribosomal Protein S5; domain 2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / 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 / Cullin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDuda, D.M. / Schulman, B.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Structural insights into NEDD8 activation of cullin-RING ligases: conformational control of conjugation.
Authors: Duda, D.M. / Borg, L.A. / Scott, D.C. / Hunt, H.W. / Hammel, M. / Schulman, B.A.
History
DepositionJul 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Cullin-5
R: RING-box protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2785
Polymers57,0822
Non-polymers1963
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-20.3 kcal/mol
Surface area24610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.965, 65.510, 141.116
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cullin-5 / CUL-5 / Vasopressin-activated calcium-mobilizing receptor / VACM-1


Mass: 44992.199 Da / Num. of mol.: 1 / Fragment: Residues 401-780 / Mutation: L407E, L439K, V440K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL5, VACM1 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: Q93034
#2: Protein RING-box protein 1 / Rbx1 / Regulator of cullin-1 / RING finger protein 75 / Protein ZYP


Mass: 12089.677 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBX1, RNF75, ROC1 / Plasmid: pRSF-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: P62877
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 277 K / pH: 8
Details: 2% PEG 3350, 0.1M HEPES, 0.2M L-proline, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2006
Details: CRYOGENICALLY COOLED FIRST CRYSTAL AND SAGITALLY BENT SECOND CRYSTAL HORIZONTALLY FOCUSING
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 18719 / % possible obs: 95.5 % / Redundancy: 5.2 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 16.1
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1323701.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.277 915 5.2 %RANDOM
Rwork0.244 ---
obs0.244 17724 95.3 %-
all-17724 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.9498 Å2 / ksol: 0.312432 e/Å3
Displacement parametersBiso mean: 47.7 Å2
Baniso -1Baniso -2Baniso -3
1-12.148 Å20 Å20 Å2
2---5.814 Å20 Å2
3----6.334 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.38 Å
Luzzati sigma a0.51 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3856 0 3 73 3932
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.382
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5511.5
X-RAY DIFFRACTIONc_mcangle_it2.7562
X-RAY DIFFRACTIONc_scbond_it2.1292
X-RAY DIFFRACTIONc_scangle_it3.4262.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.403 128 5.5 %
Rwork0.352 2186 -
obs--76.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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