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- PDB-8y1u: Crystal structure of ASB7-Elongin B/C bound to the LZTS1-degron -

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Basic information

Entry
Database: PDB / ID: 8y1u
TitleCrystal structure of ASB7-Elongin B/C bound to the LZTS1-degron
Components
  • Ankyrin repeat and SOCS box protein 7
  • Elongin-B
  • Elongin-C
  • Peptide from Leucine zipper putative tumor suppressor 1
KeywordsCYTOSOLIC PROTEIN / ubiquitin ligase
Function / homology
Function and homology information


target-directed miRNA degradation / VCB complex / elongin complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / regulation of dendrite morphogenesis / negative regulation of macroautophagy / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / regulation of postsynapse assembly ...target-directed miRNA degradation / VCB complex / elongin complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / regulation of dendrite morphogenesis / negative regulation of macroautophagy / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / regulation of postsynapse assembly / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / regulation of synaptic plasticity / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Regulation of expression of SLITs and ROBOs / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / dendritic spine / postsynaptic density / intracellular signal transduction / protein ubiquitination / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / glutamatergic synapse / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ankyrin repeat and SOCS box protein 7, SOCS box domain / Leucine zipper putative tumor suppressor / : / Fez1 / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box ...Ankyrin repeat and SOCS box protein 7, SOCS box domain / Leucine zipper putative tumor suppressor / : / Fez1 / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Elongin-C / Elongin B / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Elongin-C / Elongin-B / Ankyrin repeat and SOCS box protein 7 / Leucine zipper putative tumor suppressor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsDong, C. / Yan, X. / Zhou, M.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900865 China
National Natural Science Foundation of China (NSFC)32271265 China
National Natural Science Foundation of China (NSFC)32071193 China
CitationJournal: Nat Commun / Year: 2024
Title: Molecular insights into degron recognition by CRL5 ASB7 ubiquitin ligase.
Authors: Zhou, M. / Wang, X. / Li, J. / Ma, J. / Bao, Z. / Yan, X. / Zhang, B. / Liu, T. / Yu, Y. / Mi, W. / Dong, C.
History
DepositionJan 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ankyrin repeat and SOCS box protein 7
B: Peptide from Leucine zipper putative tumor suppressor 1
C: Elongin-B
D: Elongin-C


Theoretical massNumber of molelcules
Total (without water)60,3284
Polymers60,3284
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-41 kcal/mol
Surface area22120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.145, 43.724, 159.233
Angle α, β, γ (deg.)90.00, 92.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ankyrin repeat and SOCS box protein 7 / ASB-7


Mass: 34835.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASB7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H672
#2: Protein/peptide Peptide from Leucine zipper putative tumor suppressor 1 / F37/esophageal cancer-related gene-coding leucine-zipper motif / Fez1


Mass: 2900.288 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y250
#3: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 11748.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15370
#4: Protein Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 10843.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15369
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M DL-Malic acid pH7.0, 10% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.41→48.21 Å / Num. obs: 49898 / % possible obs: 99.95 % / Redundancy: 2 % / Rmerge(I) obs: 0.09333 / Net I/σ(I): 14.47
Reflection shellResolution: 2.41→2.496 Å / Rmerge(I) obs: 0.846 / Num. unique obs: 4433

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→48.12 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 3829 7.68 %
Rwork0.2148 --
obs0.217 49860 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.41→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3106 0 0 85 3191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083287
X-RAY DIFFRACTIONf_angle_d0.964442
X-RAY DIFFRACTIONf_dihedral_angle_d6.109466
X-RAY DIFFRACTIONf_chiral_restr0.052508
X-RAY DIFFRACTIONf_plane_restr0.006588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.440.34091250.31261519X-RAY DIFFRACTION92
2.44-2.470.28141350.28511697X-RAY DIFFRACTION100
2.47-2.50.3081590.28071742X-RAY DIFFRACTION100
2.5-2.540.27081440.27431699X-RAY DIFFRACTION99
2.54-2.580.28591310.25861728X-RAY DIFFRACTION100
2.58-2.620.32841340.26081693X-RAY DIFFRACTION100
2.62-2.660.29321440.25261711X-RAY DIFFRACTION100
2.66-2.710.26011600.23511786X-RAY DIFFRACTION100
2.71-2.760.27941150.25711649X-RAY DIFFRACTION100
2.76-2.810.28791640.2631708X-RAY DIFFRACTION100
2.81-2.870.3441280.25211719X-RAY DIFFRACTION100
2.87-2.930.30741580.26511730X-RAY DIFFRACTION100
2.93-30.29211320.23041731X-RAY DIFFRACTION100
3-3.070.28551490.20591709X-RAY DIFFRACTION100
3.07-3.160.20671370.1931687X-RAY DIFFRACTION100
3.16-3.250.21781470.19131736X-RAY DIFFRACTION100
3.25-3.350.23821390.20231700X-RAY DIFFRACTION100
3.35-3.470.19311490.18651704X-RAY DIFFRACTION100
3.47-3.610.18831440.17861742X-RAY DIFFRACTION99
3.61-3.780.23791270.17821704X-RAY DIFFRACTION99
3.78-3.970.23941530.19081723X-RAY DIFFRACTION100
3.98-4.220.21081260.17261701X-RAY DIFFRACTION100
4.22-4.550.18791500.18341694X-RAY DIFFRACTION100
4.55-5.010.22021430.19361741X-RAY DIFFRACTION100
5.01-5.730.27721430.23261666X-RAY DIFFRACTION100
5.73-7.210.25781510.2461748X-RAY DIFFRACTION100
7.22-48.120.23861420.23111664X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -26.2241 Å / Origin y: -9.0188 Å / Origin z: 53.5838 Å
111213212223313233
T0.4725 Å20.142 Å20.0313 Å2-0.5545 Å20.0763 Å2--0.3872 Å2
L1.265 °20.2372 °2-0.2279 °2-1.5334 °2-0.0364 °2--2.1377 °2
S0.1509 Å °0.6584 Å °0.1134 Å °-0.577 Å °-0.1104 Å °-0.2133 Å °0.0756 Å °0.0737 Å °-0.0256 Å °
Refinement TLS groupSelection details: all

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