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- PDB-7xyx: Crystal structure of ZYG11B bound to CFLH degron -

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Basic information

Entry
Database: PDB / ID: 7xyx
TitleCrystal structure of ZYG11B bound to CFLH degron
ComponentsProtein zyg-11 homolog B
KeywordsLIGASE / E3
Function / homology
Function and homology information


Cul2-RING ubiquitin ligase complex / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cytoplasm
Similarity search - Function
: / : / Protein zer-1 homolog-like, C-terminal domain / Zer-1-like, Leucine-rich repeats / : / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily ...: / : / Protein zer-1 homolog-like, C-terminal domain / Zer-1-like, Leucine-rich repeats / : / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Protein zyg-11 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsDong, C. / Yan, X. / Li, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900865 China
National Natural Science Foundation of China (NSFC)32071193 China
National Natural Science Foundation of China (NSFC)81874039 China
CitationJournal: Nat Commun / Year: 2022
Title: CRL2 ZER1/ZYG11B recognizes small N-terminal residues for degradation.
Authors: Li, Y. / Zhao, Y. / Yan, X. / Ye, C. / Weirich, S. / Zhang, B. / Wang, X. / Song, L. / Jiang, C. / Jeltsch, A. / Dong, C. / Mi, W.
History
DepositionJun 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Protein zyg-11 homolog B
A: Protein zyg-11 homolog B


Theoretical massNumber of molelcules
Total (without water)57,1912
Polymers57,1912
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-25 kcal/mol
Surface area20740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.777, 97.369, 122.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein zyg-11 homolog B


Mass: 28595.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZYG11B, KIAA1730 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9C0D3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES (pH 6.5), 1.6 M MgSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.87→48.48 Å / Num. obs: 15037 / % possible obs: 98.52 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.2594 / Net I/σ(I): 13.3
Reflection shellResolution: 2.87→2.97 Å / Rmerge(I) obs: 1.507 / Num. unique obs: 1466 / CC1/2: 0.0459

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EP1

7ep1


Resolution: 2.87→46.4 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2638 680 4.57 %
Rwork0.202 14188 -
obs0.2049 14868 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.29 Å2 / Biso mean: 74.2189 Å2 / Biso min: 40.2 Å2
Refinement stepCycle: final / Resolution: 2.87→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3899 0 0 5 3904
Biso mean---62.82 -
Num. residues----487
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.87-3.090.35591370.29032693283095
3.09-3.40.32451330.24312789292299
3.4-3.890.28631390.209928452984100
3.9-4.90.20641250.175729013026100
4.91-46.40.26261460.18692960310698
Refinement TLS params.Method: refined / Origin x: -37.6086 Å / Origin y: -39.7845 Å / Origin z: 10.1415 Å
111213212223313233
T0.4399 Å20.093 Å20.0582 Å2-0.5324 Å20.081 Å2--0.4222 Å2
L1.9162 °21.7141 °20.0342 °2-4.3852 °2-0.0127 °2--1.3876 °2
S0.0435 Å °-0.3859 Å °-0.1479 Å °-0.2668 Å °-0.4495 Å °-0.2995 Å °0.3495 Å °0.1181 Å °0.3266 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB479 - 723
2X-RAY DIFFRACTION1allA479 - 723
3X-RAY DIFFRACTION1allC1 - 5

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