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- PDB-7xys: Crystal structure of ZER1 bound to SFLH degron -

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Basic information

Entry
Database: PDB / ID: 7xys
TitleCrystal structure of ZER1 bound to SFLH degron
ComponentsProtein zer-1 homolog
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
Similarity search - Function
: / Protein zer-1 homolog-like, C-terminal domain / : / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Leucine-rich repeat domain superfamily / Armadillo-like helical / Alpha Horseshoe ...: / Protein zer-1 homolog-like, C-terminal domain / : / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Leucine-rich repeat domain superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Protein zer-1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
A: Protein zer-1 homolog
B: Protein zer-1 homolog
C: Protein zer-1 homolog
D: Protein zer-1 homolog


Theoretical massNumber of molelcules
Total (without water)117,3004
Polymers117,3004
Non-polymers00
Water29,5451640
1
A: Protein zer-1 homolog
B: Protein zer-1 homolog


Theoretical massNumber of molelcules
Total (without water)58,6502
Polymers58,6502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-4 kcal/mol
Surface area20460 Å2
MethodPISA
2
C: Protein zer-1 homolog
D: Protein zer-1 homolog


Theoretical massNumber of molelcules
Total (without water)58,6502
Polymers58,6502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-3 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.137, 137.191, 69.484
Angle α, β, γ (deg.)90.000, 117.500, 90.000
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: 29324.936 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


Mass: 18.015 Da / Num. of mol.: 1640 / 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: 2.31 Å3/Da / Density % sol: 46.79 %
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: Photon Factory / Beamline: BL-1A / Wavelength: 1.07 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.42
ReflectionResolution: 1.7→48.53 Å / Num. obs: 116008 / % possible obs: 99.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.33
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.453 / Num. unique obs: 36520

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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: 1.7→36.72 Å / Cross valid method: THROUGHOUT / σ(F): 53.65 / Phase error: 30.38 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1834 1167 1.01 %
Rwork0.1466 114851 -
obs0.1626 116008 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.32 Å2 / Biso mean: 17.7899 Å2 / Biso min: 5.31 Å2
Refinement stepCycle: final / Resolution: 1.7→36.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7946 0 0 1640 9586
Biso mean---28.24 -
Num. residues----982
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.780.24111430.2376142131435698
1.78-1.870.22011460.2209142361438298
1.87-1.990.25081440.2051143001444498
1.99-2.140.23361450.1882143111445698
2.14-2.360.21751420.1742143391448199
2.36-2.70.19851440.1672144351457999
2.7-3.40.20171430.1447144331457699
3.4-36.720.15261500.1233145841473499

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