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- PDB-2hye: Crystal Structure of the DDB1-Cul4A-Rbx1-SV5V Complex -

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Basic information

Entry
Database: PDB / ID: 2hye
TitleCrystal Structure of the DDB1-Cul4A-Rbx1-SV5V Complex
Components
  • Cullin-4A
  • DNA damage-binding protein 1
  • Nonstructural protein V
  • RING-box protein 1
KeywordsPROTEIN BINDING / beta propeller / RING finger / zinc finger / propeller cluster / helical repeats / cullin repeats
Function / homology
Function and homology information


negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / negative regulation of mitophagy / cullin-RING ubiquitin ligase complex / regulation of xenophagy / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / regulation of cell cycle process ...negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / negative regulation of mitophagy / cullin-RING ubiquitin ligase complex / regulation of xenophagy / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / regulation of cell cycle process / neural crest cell differentiation / RNA polymerase II transcription initiation surveillance / positive regulation by virus of viral protein levels in host cell / positive regulation of protein autoubiquitination / protein neddylation / spindle assembly involved in female meiosis / regulation of BMP signaling pathway / NEDD8 ligase activity / epigenetic programming in the zygotic pronuclei / regulation of mitophagy / negative regulation of response to oxidative stress / regulation of centrosome duplication / protein K27-linked ubiquitination / UV-damage excision repair / VCB complex / Cul5-RING ubiquitin ligase complex / regulation of TOR signaling / ubiquitin-ubiquitin ligase activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / biological process involved in interaction with symbiont / negative regulation of DNA-templated DNA replication / regulation of mitotic cytokinesis / Cul3-RING ubiquitin ligase complex / regulation of DNA damage checkpoint / regulation of mitotic cell cycle phase transition / negative regulation of type I interferon production / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / WD40-repeat domain binding / Prolactin receptor signaling / regulation of cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of adipose tissue development / regulation of cellular response to stress / limb development / viral release from host cell / protein monoubiquitination / cullin family protein binding / centrosome duplication / regulation of DNA-templated DNA replication initiation / positive regulation of viral genome replication / positive regulation of gluconeogenesis / cilium assembly / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ubiquitin-like ligase-substrate adaptor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / intrinsic apoptotic signaling pathway / ribosome-associated ubiquitin-dependent protein catabolic process / signal transduction in response to DNA damage / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of insulin receptor signaling pathway / Nuclear events stimulated by ALK signaling in cancer / protein K48-linked ubiquitination / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / in utero embryonic development / transcription-coupled nucleotide-excision repair / post-translational protein modification / cellular response to amino acid stimulus / regulation of embryonic development / replication fork processing / negative regulation of canonical NF-kappaB signal transduction / regulation of mitotic cell cycle / Regulation of BACH1 activity / site of DNA damage / T cell activation / G1/S transition of mitotic cell cycle / proteasomal protein catabolic process / negative regulation of canonical Wnt signaling pathway / epigenetic regulation of gene expression / Degradation of DVL / Degradation of CRY and PER proteins / nucleotide-excision repair / Degradation of GLI1 by the proteasome / regulation of autophagy / Recognition of DNA damage by PCNA-containing replication complex / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / RING-type E3 ubiquitin transferase / Hedgehog 'on' state / Vif-mediated degradation of APOBEC3G / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome
Similarity search - Function
Paramyxovirinae protein V, zinc-binding domain / Zinc-binding domain of Paramyxoviridae V protein / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / DNA polymerase; domain 1 - #910 / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin protein neddylation domain / Cullin, conserved site ...Paramyxovirinae protein V, zinc-binding domain / Zinc-binding domain of Paramyxoviridae V protein / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / DNA polymerase; domain 1 - #910 / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin alpha solenoid domain / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / : / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Zinc finger RING-type profile. / DNA polymerase; domain 1 / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Non-structural protein V / E3 ubiquitin-protein ligase RBX1 / Cullin-4A / DNA damage-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Simian virus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsAngers, S. / Li, T. / Yi, X. / MacCoss, M.J. / Moon, R.T. / Zheng, N.
CitationJournal: Nature / Year: 2006
Title: Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery.
Authors: Angers, S. / Li, T. / Yi, X. / MacCoss, M.J. / Moon, R.T. / Zheng, N.
History
DepositionAug 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA damage-binding protein 1
B: Nonstructural protein V
C: Cullin-4A
D: RING-box protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,5149
Polymers251,1874
Non-polymers3275
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.452, 203.165, 424.875
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein DNA damage-binding protein 1 / Damage-specific DNA-binding protein 1 / UV-damaged DNA-binding factor / DDB p127 subunit / DDBa / ...Damage-specific DNA-binding protein 1 / UV-damaged DNA-binding factor / DDB p127 subunit / DDBa / UV-damaged DNA-binding protein 1 / UV-DDB 1 / Xeroderma pigmentosum group E- complementing protein / XPCe / XPE-binding factor / XPE-BF / X- associated protein 1 / XAP-1


Mass: 127117.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531
#2: Protein Nonstructural protein V


Mass: 23965.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 5 / Genus: Rubulavirus / Gene: P/V / Production host: Escherichia coli (E. coli) / References: UniProt: P11207
#3: Protein Cullin-4A / CUL-4A


Mass: 87814.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL4A / Production host: Escherichia coli (E. coli) / References: UniProt: Q13619
#4: Protein RING-box protein 1 / Rbx1 / Regulator of cullins 1 / RING finger protein 75 / ZYP protein


Mass: 12289.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBX1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62877
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / 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: 3.58 Å3/Da / Density % sol: 65.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM NaHEPES, 7-9% PEG4000, 10% iso-propanol, 5mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 62466 / % possible obs: 92 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.079 / Χ2: 1.985 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.1-3.214.40.40641590.54462
3.21-3.344.50.29653700.59880.1
3.34-3.494.80.22760760.74390.2
3.49-3.685.10.17763210.87994.5
3.68-3.915.30.14865221.25397
3.91-4.215.50.11566691.61298.5
4.21-4.635.60.0966942.38598.5
4.63-5.35.70.0867313.03498.9
5.3-6.676.10.08268313.14699.7
6.67-506.20.04770933.32599.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.3155 56809 RANDOM
Rwork0.2496 --
obs0.253 59833 -
all-66062 -
Displacement parametersBiso mean: 75.92 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16938 0 5 0 16943

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