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- PDB-8ei1: Crystal structure of the N-terminal domain of CUL4B in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8ei1
TitleCrystal structure of the N-terminal domain of CUL4B in complex with H316, a Helicon Polypeptide
Components
  • Cullin-4B
  • H316
KeywordsLIGASE / E3 ligase / complex / stapled peptide
Function / homology
Function and homology information


Cul4-RING E3 ubiquitin ligase complex / astrocyte differentiation / UV-damage excision repair / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / positive regulation of G1/S transition of mitotic cell cycle / proteasomal protein catabolic process / Recognition of DNA damage by PCNA-containing replication complex / G1/S transition of mitotic cell cycle / DNA Damage Recognition in GG-NER ...Cul4-RING E3 ubiquitin ligase complex / astrocyte differentiation / UV-damage excision repair / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / positive regulation of G1/S transition of mitotic cell cycle / proteasomal protein catabolic process / Recognition of DNA damage by PCNA-containing replication complex / G1/S transition of mitotic cell cycle / DNA Damage Recognition in GG-NER / 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 / positive regulation of protein catabolic process / cellular response to UV / neuron projection development / ribosome biogenesis / Neddylation / gene expression / ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / DNA damage response / extracellular exosome / nucleoplasm / 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-4B
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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

Downloads & links

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Assembly

Deposited unit
A: Cullin-4B
B: Cullin-4B
C: Cullin-4B
D: Cullin-4B
E: H316
F: H316
G: H316
H: H316
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,67812
Polymers175,9098
Non-polymers7694
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18970 Å2
ΔGint-98 kcal/mol
Surface area63870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.650, 99.650, 366.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 196 through 495 or (resid 496...
21(chain B and (resid 196 through 530 or (resid 531...
31(chain C and (resid 196 through 239 or (resid 240...
41(chain D and resid 196 through 532)
12chain E
22chain F
13(chain G and (resid 4 through 16 or resid 101))
23(chain H and (resid 4 or (resid 5 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 196 through 495 or (resid 496...A196 - 495
121(chain A and (resid 196 through 495 or (resid 496...A496
131(chain A and (resid 196 through 495 or (resid 496...A196 - 539
141(chain A and (resid 196 through 495 or (resid 496...A196 - 539
151(chain A and (resid 196 through 495 or (resid 496...A196 - 539
161(chain A and (resid 196 through 495 or (resid 496...A196 - 539
211(chain B and (resid 196 through 530 or (resid 531...B196 - 530
221(chain B and (resid 196 through 530 or (resid 531...B531
231(chain B and (resid 196 through 530 or (resid 531...B196 - 539
241(chain B and (resid 196 through 530 or (resid 531...B196 - 539
251(chain B and (resid 196 through 530 or (resid 531...B196 - 539
261(chain B and (resid 196 through 530 or (resid 531...B196 - 539
271(chain B and (resid 196 through 530 or (resid 531...B196 - 539
311(chain C and (resid 196 through 239 or (resid 240...C196 - 239
321(chain C and (resid 196 through 239 or (resid 240...C240
331(chain C and (resid 196 through 239 or (resid 240...C196 - 532
341(chain C and (resid 196 through 239 or (resid 240...C196 - 532
351(chain C and (resid 196 through 239 or (resid 240...C196 - 532
361(chain C and (resid 196 through 239 or (resid 240...C196 - 532
371(chain C and (resid 196 through 239 or (resid 240...C196 - 532
381(chain C and (resid 196 through 239 or (resid 240...C196 - 532
411(chain D and resid 196 through 532)D196 - 532
112chain EE0 - 17
212chain FF0 - 17
113(chain G and (resid 4 through 16 or resid 101))G0
213(chain H and (resid 4 or (resid 5 and (name...H4
223(chain H and (resid 4 or (resid 5 and (name...H5
233(chain H and (resid 4 or (resid 5 and (name...H4 - 16
243(chain H and (resid 4 or (resid 5 and (name...H4 - 16
253(chain H and (resid 4 or (resid 5 and (name...H4 - 16
263(chain H and (resid 4 or (resid 5 and (name...H4 - 16

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Cullin-4B / CUL-4B


Mass: 41952.062 Da / Num. of mol.: 4 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL4B, KIAA0695 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13620
#2: Protein/peptide
H316


Mass: 2025.224 Da / Num. of mol.: 4 / 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.: 4 / 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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 30% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.89→52.36 Å / Num. obs: 42685 / % possible obs: 100 % / Redundancy: 26.6 % / CC1/2: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 23.9
Reflection shellResolution: 2.89→3 Å / Redundancy: 27.6 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4410 / CC1/2: 0.882 / % possible all: 100

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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: 4A64

4a64


Resolution: 2.89→49.82 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 2101 4.94 %
Rwork0.2116 40438 -
obs0.2137 42539 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 223.17 Å2 / Biso mean: 90.347 Å2 / Biso min: 47.08 Å2
Refinement stepCycle: final / Resolution: 2.89→49.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11751 0 58 0 11809
Biso mean--125.96 --
Num. residues----1427
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6792X-RAY DIFFRACTION14.718TORSIONAL
12B6792X-RAY DIFFRACTION14.718TORSIONAL
13C6792X-RAY DIFFRACTION14.718TORSIONAL
14D6792X-RAY DIFFRACTION14.718TORSIONAL
21E149X-RAY DIFFRACTION14.718TORSIONAL
22F149X-RAY DIFFRACTION14.718TORSIONAL
31G102X-RAY DIFFRACTION14.718TORSIONAL
32H102X-RAY DIFFRACTION14.718TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.89-2.960.41441360.369926282764
2.96-3.030.44831550.335926162771
3.03-3.110.32721290.302426752804
3.11-3.20.37111240.280126482772
3.2-3.310.33041470.251626222769
3.31-3.430.29951420.239826692811
3.43-3.560.28361320.23926492781
3.56-3.730.28671470.225126602807
3.73-3.920.2621340.211126722806
3.92-4.170.23111340.197827052839
4.17-4.490.21691540.191526612815
4.49-4.940.24461420.178127232865
4.94-5.650.21911410.197827392880
5.65-7.120.27011350.229228082943
7.12-49.820.20611490.175229633112
Refinement TLS params.Method: refined / Origin x: 1.3941 Å / Origin y: -54.9675 Å / Origin z: -36.3881 Å
111213212223313233
T0.5275 Å2-0.0223 Å2-0.0354 Å2-0.4468 Å2-0.0356 Å2--0.5223 Å2
L0.4582 °2-0.0232 °2-0.1233 °2-0.1377 °2-0.0091 °2--0.2867 °2
S-0.0106 Å °-0.008 Å °0.0322 Å °0.0602 Å °0.0235 Å °0.0007 Å °-0.0593 Å °0.0919 Å °0.0014 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA196 - 539
2X-RAY DIFFRACTION1allB196 - 539
3X-RAY DIFFRACTION1allC196 - 532
4X-RAY DIFFRACTION1allD195 - 532
5X-RAY DIFFRACTION1allE0 - 17
6X-RAY DIFFRACTION1allE18 - 101
7X-RAY DIFFRACTION1allF0 - 17
8X-RAY DIFFRACTION1allF18 - 101
9X-RAY DIFFRACTION1allG2 - 16
10X-RAY DIFFRACTION1allG101
11X-RAY DIFFRACTION1allH4 - 16
12X-RAY DIFFRACTION1allH101

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