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- PDB-4a0c: Structure of the CAND1-CUL4B-RBX1 complex -

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Basic information

Entry
Database: PDB / ID: 4a0c
TitleStructure of the CAND1-CUL4B-RBX1 complex
Components
  • CULLIN-4B
  • CULLIN-ASSOCIATED NEDD8-DISSOCIATED PROTEIN 1
  • E3 UBIQUITIN-PROTEIN LIGASE RBX1
KeywordsCELL CYCLE / TRANSCRIPTION / LIGASE / UBIQUITIN / DNA DAMAGE REPAIR
Function / homology
Function and homology information


Prolactin receptor signaling / SCF complex assembly / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / Formation of TC-NER Pre-Incision Complex / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of Incision Complex in GG-NER ...Prolactin receptor signaling / SCF complex assembly / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / Formation of TC-NER Pre-Incision Complex / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of Incision Complex in GG-NER / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of DVL / Orc1 removal from chromatin / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Hedgehog 'on' state / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Degradation of beta-catenin by the destruction complex / eukaryotic initiation factor 4E binding / negative regulation of catalytic activity / Interleukin-1 signaling / anaphase-promoting complex / GLI3 is processed to GLI3R by the proteasome / Neddylation / cullin-RING-type E3 NEDD8 transferase / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / KEAP1-NFE2L2 pathway / astrocyte differentiation / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / protein neddylation / Antigen processing: Ubiquitination & Proteasome degradation / UV-damage excision repair / NEDD8 ligase activity / 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 / cullin family protein binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / protein monoubiquitination / ubiquitin ligase complex / positive regulation of G1/S transition of mitotic cell cycle / protein K48-linked ubiquitination / proteasomal protein catabolic process / transcription-coupled nucleotide-excision repair / positive regulation of TORC1 signaling / negative regulation of insulin receptor signaling pathway / TBP-class protein binding / T cell activation / cellular response to amino acid stimulus / protein catabolic process / Iron uptake and transport / Recognition of DNA damage by PCNA-containing replication complex / G1/S transition of mitotic cell cycle / DNA Damage Recognition in GG-NER / RING-type E3 ubiquitin transferase / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / protein polyubiquitination / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / cellular response to UV / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ribosome biogenesis / Neddylation / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / secretory granule lumen / spermatogenesis / gene expression / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / cell differentiation / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / Golgi apparatus / extracellular exosome / extracellular region / zinc ion binding
Similarity search - Function
TATA-binding protein interacting (TIP20) / Cullin-associated NEDD8-dissociated protein 1/2 / TATA-binding protein interacting (TIP20) / HEAT-like repeat / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin family signature. ...TATA-binding protein interacting (TIP20) / Cullin-associated NEDD8-dissociated protein 1/2 / TATA-binding protein interacting (TIP20) / HEAT-like repeat / 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. / Leucine-rich Repeat Variant / Zinc/RING finger domain, C3HC4 (zinc finger) / Leucine-rich Repeat Variant / Herpes Virus-1 / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / Cullin-4B / Cullin-associated NEDD8-dissociated protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsScrima, A. / Fischer, E.S. / Faty, M. / Gut, H. / Thoma, N.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation
Authors: Scrima, A. / Fischer, E.S. / Iwai, S. / Gut, H. / Thoma, N.H.
History
DepositionSep 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / pdbx_seq_map_depositor_info
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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-ASSOCIATED NEDD8-DISSOCIATED PROTEIN 1
B: CULLIN-ASSOCIATED NEDD8-DISSOCIATED PROTEIN 1
C: CULLIN-4B
D: E3 UBIQUITIN-PROTEIN LIGASE RBX1
E: CULLIN-4B
F: E3 UBIQUITIN-PROTEIN LIGASE RBX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)475,43012
Polymers475,0376
Non-polymers3926
Water00
1
A: CULLIN-ASSOCIATED NEDD8-DISSOCIATED PROTEIN 1
E: CULLIN-4B
F: E3 UBIQUITIN-PROTEIN LIGASE RBX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,7156
Polymers237,5193
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12430 Å2
ΔGint-39.5 kcal/mol
Surface area85930 Å2
MethodPISA
2
B: CULLIN-ASSOCIATED NEDD8-DISSOCIATED PROTEIN 1
C: CULLIN-4B
D: E3 UBIQUITIN-PROTEIN LIGASE RBX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,7156
Polymers237,5193
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12350 Å2
ΔGint-30.3 kcal/mol
Surface area86780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.090, 152.360, 263.010
Angle α, β, γ (deg.)90.00, 89.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CULLIN-ASSOCIATED NEDD8-DISSOCIATED PROTEIN 1 / CULLIN-ASSOCIATED AND NEDDYLATION-DISSOCIATED PROTEIN 1 / TBP-INTERACTING PROTEIN OF 120 KDA A / ...CULLIN-ASSOCIATED AND NEDDYLATION-DISSOCIATED PROTEIN 1 / TBP-INTERACTING PROTEIN OF 120 KDA A / TBP-INTERACTING PROTEIN 120A / P120 CAND1


Mass: 139226.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q86VP6
#2: Protein CULLIN-4B / CUL-4B


Mass: 86961.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q13620
#3: Protein E3 UBIQUITIN-PROTEIN LIGASE RBX1 / RING FINGER PROTEIN 75 / RING-BOX PROTEIN 1 / RBX1


Mass: 11330.942 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PFASTBAC DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper)
References: UniProt: P62878, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
Sequence detailsCHAINS A AND B CONTAINS NATURAL VARIANT A952V

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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: 3.52 Å3/Da / Density % sol: 65.08 %
Description: CAND1 USED AS MODEL FROM 1U6G, CUL4B MODEL GENERATED USING MODELLER BASED ON CUL4A FROM 2HYE
Crystal growpH: 6.3 / Details: 100 MM MES PH 6.3, 30% PEG 200, 2% PEG 8000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 59850 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2
Reflection shellResolution: 3.8→3.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1U6G, 2HYE

1u6g

2hye


Resolution: 3.8→47.76 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.882 / SU B: 56.264 / SU ML: 0.797 / Cross valid method: THROUGHOUT / ESU R Free: 0.906 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.31856 2993 5 %RANDOM
Rwork0.23805 ---
obs0.24206 56857 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 128.578 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20.73 Å2
2---0.61 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 3.8→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30798 0 6 0 30804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02231305
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.98142261
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78953846
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.15124.7031363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.222156034
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.62515182
X-RAY DIFFRACTIONr_chiral_restr0.0810.24945
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02122755
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2911.519308
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.532231334
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.362311997
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.6694.510927
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.8→3.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 218 -
Rwork0.325 4140 -
obs--100 %

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