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- PDB-7ep2: Crystal structure of ZYG11B bound to GGFN degron -

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Basic information

Entry
Database: PDB / ID: 7ep2
TitleCrystal structure of ZYG11B bound to GGFN degron
ComponentsProtein zyg-11 homolog B
KeywordsLIGASE / E3 ligase
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 / : / 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 ...: / Protein zer-1 homolog-like, C-terminal domain / : / 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: 2.38 Å
AuthorsYan, 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: Mol.Cell / Year: 2021
Title: Molecular basis for recognition of Gly/N-degrons by CRL2 ZYG11B and CRL2 ZER1 .
Authors: Yan, X. / Li, Y. / Wang, G. / Zhou, Z. / Song, G. / Feng, Q. / Zhao, Y. / Mi, W. / Ma, Z. / Dong, C.
History
DepositionApr 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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
A: Protein zyg-11 homolog B
C: Protein zyg-11 homolog B
D: Protein zyg-11 homolog B
B: Protein zyg-11 homolog B


Theoretical massNumber of molelcules
Total (without water)131,5634
Polymers131,5634
Non-polymers00
Water1,15364
1
A: Protein zyg-11 homolog B
B: Protein zyg-11 homolog B


Theoretical massNumber of molelcules
Total (without water)65,7812
Polymers65,7812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-12 kcal/mol
Surface area24620 Å2
MethodPISA
2
C: Protein zyg-11 homolog B
D: Protein zyg-11 homolog B


Theoretical massNumber of molelcules
Total (without water)65,7812
Polymers65,7812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-13 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.360, 102.320, 164.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Protein zyg-11 homolog B


Mass: 32890.637 Da / Num. of mol.: 4
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.: 64 / 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: 2.92 Å3/Da / Density % sol: 57.92 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 25% (wt/vol) Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978565 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.38→102.32 Å / Num. obs: 62538 / % possible obs: 99.9 % / Redundancy: 13 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.8
Reflection shellResolution: 2.38→2.44 Å / Rmerge(I) obs: 1.536 / Num. unique obs: 4544

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDS0.7.4data reduction
XDS0.7.4data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EP0

7ep0


Resolution: 2.38→82.28 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2539 2000 -
Rwork0.1969 --
obs-62440 99.81 %
Displacement parametersBiso mean: 64.43 Å2
Refinement stepCycle: LAST / Resolution: 2.38→82.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9119 0 0 64 9183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00849325
X-RAY DIFFRACTIONf_angle_d0.90412655
X-RAY DIFFRACTIONf_chiral_restr0.04881443
X-RAY DIFFRACTIONf_plane_restr0.00521609
X-RAY DIFFRACTIONf_dihedral_angle_d23.93913377
LS refinement shellResolution: 2.38→2.465 Å
RfactorNum. reflection% reflection
Rfree0.3193 197 -
Rwork0.2897 --
obs-6148 99.92 %

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