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- PDB-7ep3: Crystal structure of ZER1 bound to GAGN degron -

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Basic information

Entry
Database: PDB / ID: 7ep3
TitleCrystal structure of ZER1 bound to GAGN degron
ComponentsProtein zer-1 homolog
KeywordsLIGASE / E3 ligase
Function / homologyCul2-RING ubiquitin ligase complex / protein quality control for misfolded or incompletely synthesized proteins / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich repeat domain superfamily / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Armadillo-like helical / Armadillo-type fold / Protein zer-1 homolog
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.513 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 zer-1 homolog


Theoretical massNumber of molelcules
Total (without water)28,9821
Polymers28,9821
Non-polymers00
Water1,71195
1
A: Protein zer-1 homolog

A: Protein zer-1 homolog


Theoretical massNumber of molelcules
Total (without water)57,9652
Polymers57,9652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area1900 Å2
ΔGint-4 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.970, 120.420, 68.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Protein zer-1 homolog / Hzyg / Zyg-11 homolog B-like protein / Zyg11b-like protein


Mass: 28982.477 Da / Num. of mol.: 1 / Fragment: UNP residues 520-766
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZER1, C9orf60, ZYG, ZYG11BL / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z7L7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.48 Å3/Da / Density % sol: 50.34 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium formate, 23% (wt/vol) Polyethylene glycol 3,350, 0.033% (wt/vol) Anthrone, 0.033% (wt/vol) Congo Red, 0.033% (wt/vol) N-(2-Acetamido)-2-aminoethanesulfonic acid, 0.002 M HEPES sodium pH 6.8

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979191 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979191 Å / Relative weight: 1
ReflectionResolution: 1.51→59.19 Å / Num. obs: 43366 / % possible obs: 98.8 % / Redundancy: 11 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 30.6
Reflection shellResolution: 1.51→1.55 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2864

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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: 1.513→22.323 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2555 1983 -
Rwork0.2189 --
obs-43322 97.94 %
Displacement parametersBiso mean: 28.5 Å2
Refinement stepCycle: LAST / Resolution: 1.513→22.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 0 95 2059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572008
X-RAY DIFFRACTIONf_angle_d0.75212712
X-RAY DIFFRACTIONf_chiral_restr0.0465294
X-RAY DIFFRACTIONf_plane_restr0.0051347
X-RAY DIFFRACTIONf_dihedral_angle_d23.2076757
LS refinement shellResolution: 1.513→1.567 Å
RfactorNum. reflection% reflection
Rfree0.288 192 -
Rwork0.2845 --
obs-3920 90.57 %

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