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- PDB-5v89: Structure of DCN4 PONY domain bound to CUL1 WHB -

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Basic information

Entry
Database: PDB / ID: 5v89
TitleStructure of DCN4 PONY domain bound to CUL1 WHB
Components
  • Cullin-1
  • DCN1-like protein 4
KeywordsLigase / protein binding / E3 Ligase / Ligase - protein binding complex
Function / homology
Function and homology information


positive regulation of protein neddylation / ubiquitin-like protein binding / Parkin-FBXW7-Cul1 ubiquitin ligase complex / cullin-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / protein neddylation / ubiquitin conjugating enzyme binding / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling ...positive regulation of protein neddylation / ubiquitin-like protein binding / Parkin-FBXW7-Cul1 ubiquitin ligase complex / cullin-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / protein neddylation / ubiquitin conjugating enzyme binding / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / ubiquitin ligase complex scaffold activity / cullin family protein binding / protein monoubiquitination / ubiquitin ligase complex / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / intrinsic apoptotic signaling pathway / Regulation of BACH1 activity / animal organ morphogenesis / MAP3K8 (TPL2)-dependent MAPK1/3 activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Iron uptake and transport / G1/S transition of mitotic cell cycle / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / 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 / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / : / Regulation of PLK1 Activity at G2/M Transition / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / cell population proliferation / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / ubiquitin protein ligase binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cullin, PONY binding domain / Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily ...Cullin, PONY binding domain / Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / 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. / EF-hand / Recoverin; domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cullin-1 / DCN1-like protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsGuy, R.K. / Schulman, B.A. / Scott, D.C. / Hammill, J.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37GM069530 United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Blocking an N-terminal acetylation-dependent protein interaction inhibits an E3 ligase.
Authors: Scott, D.C. / Hammill, J.T. / Min, J. / Rhee, D.Y. / Connelly, M. / Sviderskiy, V.O. / Bhasin, D. / Chen, Y. / Ong, S.S. / Chai, S.C. / Goktug, A.N. / Huang, G. / Monda, J.K. / Low, J. / ...Authors: Scott, D.C. / Hammill, J.T. / Min, J. / Rhee, D.Y. / Connelly, M. / Sviderskiy, V.O. / Bhasin, D. / Chen, Y. / Ong, S.S. / Chai, S.C. / Goktug, A.N. / Huang, G. / Monda, J.K. / Low, J. / Kim, H.S. / Paulo, J.A. / Cannon, J.R. / Shelat, A.A. / Chen, T. / Kelsall, I.R. / Alpi, A.F. / Pagala, V. / Wang, X. / Peng, J. / Singh, B. / Harper, J.W. / Schulman, B.A. / Guy, R.K.
History
DepositionMar 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DCN1-like protein 4
C: Cullin-1


Theoretical massNumber of molelcules
Total (without water)31,7732
Polymers31,7732
Non-polymers00
Water5,621312
1
A: DCN1-like protein 4


Theoretical massNumber of molelcules
Total (without water)22,7571
Polymers22,7571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cullin-1


Theoretical massNumber of molelcules
Total (without water)9,0161
Polymers9,0161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.930, 62.476, 38.580
Angle α, β, γ (deg.)90.000, 105.480, 90.000
Int Tables number5
Space group name H-MC121
DetailsMonomer as determined by gel filtration

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Components

#1: Protein DCN1-like protein 4 / DCUN1 domain-containing protein 4 / Defective in cullin neddylation protein 1-like protein 4


Mass: 22756.834 Da / Num. of mol.: 1 / Fragment: residues 102-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCUN1D4, KIAA0276 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92564
#2: Protein Cullin-1 / CUL-1


Mass: 9015.699 Da / Num. of mol.: 1 / Fragment: WHB subdomain residues 702-776
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL1 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13616
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.42 %
Description: The authors state that the density surrounding the CUL1WHB subdomain in this structure was relatively weak, presumably due to its lack of participation in forming crystal contacts. ...Description: The authors state that the density surrounding the CUL1WHB subdomain in this structure was relatively weak, presumably due to its lack of participation in forming crystal contacts. Therefore we modeled and built this chain largely from a previous high resolution and high quality structure of CUL1WHB, 3TDU.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG3350, 0.2M LiSO4, 10mM TCEP, 10mM Bis-Tris Propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 36927 / % possible obs: 93.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.072 / Χ2: 1.061 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.6120.43224030.805160.9
1.61-1.672.50.3630.785180.5
1.67-1.7530.320.755193.2
1.75-1.843.50.2630.814199.3
1.84-1.953.70.190.8391100
1.95-2.13.80.1230.8841100
2.1-2.323.80.0921.0271100
2.32-2.653.80.0851.3061100
2.65-3.343.80.0641.4781100
3.34-503.80.041.404199.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TDU.pdb

3tdu


Resolution: 1.55→23.917 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.42
RfactorNum. reflection% reflection
Rfree0.1939 1868 5.06 %
Rwork0.151 --
obs0.1533 36917 93.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.85 Å2 / Biso mean: 28.4826 Å2 / Biso min: 7.28 Å2
Refinement stepCycle: final / Resolution: 1.55→23.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 0 312 2407
Biso mean---34.6 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092168
X-RAY DIFFRACTIONf_angle_d1.1312940
X-RAY DIFFRACTIONf_chiral_restr0.044329
X-RAY DIFFRACTIONf_plane_restr0.006369
X-RAY DIFFRACTIONf_dihedral_angle_d12.728805
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5503-1.59220.2427740.20061679175358
1.5922-1.6390.20241260.18382121224774
1.639-1.69190.25511430.16552471261487
1.6919-1.75240.20481470.1632771291895
1.7524-1.82250.18731400.15472846298699
1.8225-1.90540.2221130.142729043017100
1.9054-2.00580.1921490.139428703019100
2.0058-2.13140.18081580.133928993057100
2.1314-2.29590.19271720.131228883060100
2.2959-2.52670.17841510.138828623013100
2.5267-2.89180.17621610.147528843045100
2.8918-3.64130.19541520.148529193071100
3.6413-23.920.19681820.167129353117100

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