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- PDB-7xyt: Crystal structure of ZER1 bound to AFLH degron -

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Basic information

Entry
Database: PDB / ID: 7xyt
TitleCrystal structure of ZER1 bound to AFLH degron
ComponentsProtein zer-1 homolog
KeywordsLIGASE / E3
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: 1.5 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
Citation
Journal: 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.
#1: Journal: Nat Commun / Year: 2022
Title: CRL2ZER1/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 28, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.type
Revision 1.2Feb 14, 2024Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein zer-1 homolog
B: Protein zer-1 homolog
D: Protein zer-1 homolog
C: Protein zer-1 homolog


Theoretical massNumber of molelcules
Total (without water)117,2364
Polymers117,2364
Non-polymers00
Water19,0781059
1
A: Protein zer-1 homolog
D: Protein zer-1 homolog


Theoretical massNumber of molelcules
Total (without water)58,6182
Polymers58,6182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-6 kcal/mol
Surface area20580 Å2
MethodPISA
2
B: Protein zer-1 homolog
C: Protein zer-1 homolog


Theoretical massNumber of molelcules
Total (without water)58,6182
Polymers58,6182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-5 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.979, 138.273, 69.510
Angle α, β, γ (deg.)90.00, 117.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29308.936 Da / Num. of mol.: 4
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.: 1059 / 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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M NH4F, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 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: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→138.27 Å / Num. obs: 170861 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.97
Reflection shellResolution: 1.5→1.54 Å / Rmerge(I) obs: 1.568 / Num. unique obs: 12605

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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: 7EP3

7ep3


Resolution: 1.5→34.61 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 8515 4.99 %
Rwork0.1957 --
obs0.1972 170646 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7958 0 0 1059 9017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068163
X-RAY DIFFRACTIONf_angle_d0.81611031
X-RAY DIFFRACTIONf_dihedral_angle_d12.081046
X-RAY DIFFRACTIONf_chiral_restr0.0721197
X-RAY DIFFRACTIONf_plane_restr0.0061409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.29532750.28975439X-RAY DIFFRACTION100
1.52-1.530.32282570.2765354X-RAY DIFFRACTION99
1.53-1.550.27493360.25495346X-RAY DIFFRACTION100
1.55-1.570.29273010.25335364X-RAY DIFFRACTION100
1.57-1.590.26812650.24175385X-RAY DIFFRACTION100
1.59-1.620.28242760.23355429X-RAY DIFFRACTION100
1.62-1.640.26232370.23315409X-RAY DIFFRACTION100
1.64-1.660.24533330.22355379X-RAY DIFFRACTION100
1.66-1.690.253020.21225405X-RAY DIFFRACTION100
1.69-1.720.24532850.20945357X-RAY DIFFRACTION100
1.72-1.750.2412910.20595387X-RAY DIFFRACTION100
1.75-1.780.24732950.2115465X-RAY DIFFRACTION100
1.78-1.810.23933040.20875305X-RAY DIFFRACTION100
1.81-1.850.2483040.20135389X-RAY DIFFRACTION100
1.85-1.890.22442640.20615448X-RAY DIFFRACTION100
1.89-1.930.27822790.21725440X-RAY DIFFRACTION100
1.93-1.980.24212810.20795344X-RAY DIFFRACTION100
1.98-2.040.24762580.20725445X-RAY DIFFRACTION100
2.04-2.10.23392920.1985356X-RAY DIFFRACTION100
2.1-2.160.23092610.19485455X-RAY DIFFRACTION100
2.16-2.240.2322790.18885438X-RAY DIFFRACTION100
2.24-2.330.22473120.1945339X-RAY DIFFRACTION100
2.33-2.440.242710.19555394X-RAY DIFFRACTION100
2.44-2.560.2252770.19365478X-RAY DIFFRACTION100
2.56-2.730.22052350.19325440X-RAY DIFFRACTION100
2.73-2.940.22352880.19095444X-RAY DIFFRACTION100
2.94-3.230.20382550.1895431X-RAY DIFFRACTION100
3.23-3.70.20653010.18485442X-RAY DIFFRACTION100
3.7-4.660.20142980.17115419X-RAY DIFFRACTION100
4.66-34.610.19593030.17865405X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 16.0207 Å / Origin y: 13.2666 Å / Origin z: 0.7674 Å
111213212223313233
T0.0872 Å20.0061 Å2-0.0031 Å2-0.1444 Å20.0072 Å2--0.1202 Å2
L0.1349 °2-0.0263 °2-0.0256 °2-0.5787 °20.2211 °2--0.2811 °2
S-0.0483 Å °-0.0478 Å °-0.0044 Å °0.0396 Å °0.0574 Å °0.0041 Å °0.0257 Å °0.013 Å °-0.01 Å °
Refinement TLS groupSelection details: all

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