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- PDB-8ei2: Crystal structure of the N-terminal domain of CUL5 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8ei2
TitleCrystal structure of the N-terminal domain of CUL5 in complex with H314, a Helicon Polypeptide
Components
  • Cullin-5
  • H314
KeywordsLIGASE / E3 ligase / complex / stapled peptide
Function / homology
Function and homology information


ERBB2 signaling pathway / Cul5-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / site of DNA damage / intrinsic apoptotic signaling pathway / Vif-mediated degradation of APOBEC3G / G1/S transition of mitotic cell cycle / calcium channel activity / Inactivation of CSF3 (G-CSF) signaling ...ERBB2 signaling pathway / Cul5-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / site of DNA damage / intrinsic apoptotic signaling pathway / Vif-mediated degradation of APOBEC3G / G1/S transition of mitotic cell cycle / calcium channel activity / Inactivation of CSF3 (G-CSF) signaling / Downregulation of ERBB2 signaling / ubiquitin-protein transferase activity / protein-macromolecule adaptor activity / Antigen processing: Ubiquitination & Proteasome degradation / signaling receptor activity / Neddylation / protein ubiquitination / ubiquitin protein ligase binding / nucleus / cytosol
Similarity search - Function
Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain ...Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
N,N'-(1,4-phenylene)diacetamide / Cullin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLi, K. / Tokareva, O.S. / Thomson, T.M. / Verdine, G.L. / McGee, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2023
Title: Recognition and reprogramming of E3 ubiquitin ligase surfaces by alpha-helical peptides.
Authors: Tokareva, O.S. / Li, K. / Travaline, T.L. / Thomson, T.M. / Swiecicki, J.M. / Moussa, M. / Ramirez, J.D. / Litchman, S. / Verdine, G.L. / McGee, J.H.
History
DepositionSep 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cullin-5
C: H314
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0373
Polymers46,8452
Non-polymers1921
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-11 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.030, 173.030, 57.480
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Space group name HallP6

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Components

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


Mass: 44972.461 Da / Num. of mol.: 1 / Fragment: N-terminal domain
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
#2: Protein/peptide H314


Mass: 1872.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide


Mass: 192.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O2
Has ligand of interestN

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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: 5.3 Å3/Da / Density % sol: 76.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% w/v PEG 8000, 0.1M MES Sodium Salt pH6.5, 0.2M Ammonium Sulfate, 4% v/v 1,3-Propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.85
ReflectionResolution: 2.8→47.88 Å / Num. obs: 24154 / % possible obs: 98.2 % / Redundancy: 13.2 % / Biso Wilson estimate: -4.64 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.322 / Net I/σ(I): 5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3518 / CC1/2: 0.888 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WZK

2wzk


Resolution: 2.8→47.88 Å / SU ML: 0.4852 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.6178
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3575 845 5.11 %
Rwork0.3389 15697 -
obs0.3398 16542 67.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.32 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3053 0 14 0 3067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00893125
X-RAY DIFFRACTIONf_angle_d1.00874212
X-RAY DIFFRACTIONf_chiral_restr0.0538462
X-RAY DIFFRACTIONf_plane_restr0.0063540
X-RAY DIFFRACTIONf_dihedral_angle_d17.34661174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.980.507490.3976886X-RAY DIFFRACTION23.14
2.98-3.210.42421310.35911618X-RAY DIFFRACTION43.11
3.21-3.530.37521370.33892338X-RAY DIFFRACTION61.14
3.53-4.040.34642000.33363116X-RAY DIFFRACTION81.31
4.04-5.090.2971610.32443839X-RAY DIFFRACTION97.21
5.09-47.880.34641670.34133900X-RAY DIFFRACTION96.72

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