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

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Basic information

Entry
Database: PDB / ID: 3dqv
TitleStructural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation
Components
  • Cullin-5
  • NEDD8
  • Rbx1
KeywordsLIGASE / ubiquitin / nedd8 / scf / cullin-ring ligase / cullin / Nucleus / Ubl conjugation pathway / Host-virus interaction / Receptor / Ubl conjugation / Acetylation / Cytoplasm / DNA damage / DNA repair / Metal-binding / Zinc / Zinc-finger / SIGNALING PROTEIN
Function / homology
Function and homology information


ERBB2 signaling pathway / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / reelin-mediated signaling pathway / 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 / regulation of neuron migration ...ERBB2 signaling pathway / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / reelin-mediated signaling pathway / 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 / regulation of neuron migration / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / protein neddylation / protein K11-linked ubiquitination / 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 / Cul2-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / 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 / TGF-beta receptor signaling activates SMADs / cullin family protein binding / regulation of proteolysis / site of DNA damage / regulation of postsynapse assembly / anatomical structure morphogenesis / 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 / T cell activation / Degradation of DVL / cellular response to amino acid stimulus / 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 / Inactivation of CSF3 (G-CSF) signaling / 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 / modification-dependent protein catabolic process / NOTCH1 Intracellular Domain Regulates Transcription / protein modification process / Dual Incision in GG-NER / calcium channel activity / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Regulation of expression of SLITs and ROBOs / Downregulation of ERBB2 signaling / Formation of Incision Complex in GG-NER / protein tag activity / 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 / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / cellular response to UV / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / UCH proteinases / intracellular protein localization / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Cargo recognition for clathrin-mediated endocytosis / MAPK cascade / signaling receptor activity / Neddylation
Similarity search - Function
Cullin; Chain C, Domain 2 / Cullin Repeats / 5 helical Cullin repeat like / Nedd8-like ubiquitin / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin family signature. ...Cullin; Chain C, Domain 2 / Cullin Repeats / 5 helical Cullin repeat like / Nedd8-like ubiquitin / 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 / Ribosomal Protein S5; domain 2 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Arc Repressor Mutant, subunit A / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Roll / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / Ubiquitin-like protein NEDD8 / Cullin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsDuda, D.M. / Borg, L.A. / Scott, D.C. / Hunt, H.W. / Hammel, 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 9, 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 30, 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 / struct_conn / 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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _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: NEDD8
C: Cullin-5
R: Rbx1
B: NEDD8
D: Cullin-5
Y: Rbx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,11912
Polymers133,7276
Non-polymers3926
Water00
1
A: NEDD8
C: Cullin-5
R: Rbx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0606
Polymers66,8633
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NEDD8
D: Cullin-5
Y: Rbx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0606
Polymers66,8633
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: NEDD8
D: Cullin-5
Y: Rbx1
hetero molecules

A: NEDD8
C: Cullin-5
R: Rbx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,11912
Polymers133,7276
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
Buried area17590 Å2
ΔGint-103 kcal/mol
Surface area52140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.315, 122.442, 128.647
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 NEDD8 / Ubiquitin-like protein Nedd8 / Neddylin


Mass: 9078.012 Da / Num. of mol.: 2 / Fragment: NEDD8 C-terminus covalently linked to Cul5 Lys724 / Mutation: L162M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15843
#2: Protein Cullin-5 / CUL-5 / Vasopressin-activated calcium-mobilizing receptor / VACM-1


Mass: 45601.828 Da / Num. of mol.: 2 / Fragment: Cullin-5 residues 401-780 / Mutation: L407E, L439K, V440K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL5, VACM1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93034
#3: Protein Rbx1 / Rbx1 / Regulator of cullins 1 / RING finger protein 75 / Protein ZYP


Mass: 12183.467 Da / Num. of mol.: 2 / Fragment: Rbx1 residues 5-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBX1, RNF75, ROC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62877
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 277 K
Details: with ~19% PEG3350, 275mM (NH4)2PO4, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 28564 / Biso Wilson estimate: 92.18 Å2 / Rsym value: 0.125
Reflection shellResolution: 3→3.11 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.678 / % possible all: 96.7

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3→50 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1634466.22 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1415 5 %RANDOM
Rwork0.249 ---
obs0.249 28357 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.636 Å2 / ksol: 0.273459 e/Å3
Displacement parametersBiso mean: 74.4 Å2
Baniso -1Baniso -2Baniso -3
1-23.09 Å20 Å20 Å2
2---21.75 Å20 Å2
3----1.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8833 0 6 0 8839
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.455 211 4.7 %
Rwork0.406 4270 -
obs--95.5 %

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