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- PDB-6len: Structure of NS11 bound FEM1C -

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Basic information

Entry
Database: PDB / ID: 6len
TitleStructure of NS11 bound FEM1C
ComponentsProtein fem-1 homolog C,NS11 peptide
KeywordsPROTEIN BINDING / ubiquitination E3 ligase
Function / homology
Function and homology information


ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / nucleoplasm / cytosol
Similarity search - Function
Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Protein fem-1 homolog C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.383 Å
AuthorsChen, x. / Liao, S. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Molecular basis for arginine C-terminal degron recognition by Cul2 FEM1 E3 ligase.
Authors: Chen, X. / Liao, S. / Makaros, Y. / Guo, Q. / Zhu, Z. / Krizelman, R. / Dahan, K. / Tu, X. / Yao, X. / Koren, I. / Xu, C.
History
DepositionNov 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 20, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein fem-1 homolog C,NS11 peptide
B: Protein fem-1 homolog C,NS11 peptide


Theoretical massNumber of molelcules
Total (without water)91,8012
Polymers91,8012
Non-polymers00
Water3,873215
1
A: Protein fem-1 homolog C,NS11 peptide


Theoretical massNumber of molelcules
Total (without water)45,9001
Polymers45,9001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein fem-1 homolog C,NS11 peptide


Theoretical massNumber of molelcules
Total (without water)45,9001
Polymers45,9001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.727, 96.508, 146.860
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 fem-1 homolog C,NS11 peptide / FEM1c / FEM1-gamma


Mass: 45900.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FEM1C fused with NS11 peptide, linked with linker residues GGGSGGGSGGGSGGGS.
Source: (gene. exp.) Homo sapiens (human) / Gene: FEM1C, KIAA1785 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96JP0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 3.79 Å3/Da / Density % sol: 67.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium citrate tribasic dihydrate, 0.1M Tris pH 8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.38→80.652 Å / Num. obs: 54996 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.998 / Net I/σ(I): 16.8
Reflection shellResolution: 2.38→2.51 Å / Num. unique obs: 5405 / CC1/2: 0.823

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LBF

6lbf


Resolution: 2.383→80.652 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.81
RfactorNum. reflection% reflection
Rfree0.2346 2718 4.94 %
Rwork0.1989 --
obs0.2006 54996 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.47 Å2 / Biso mean: 63.4071 Å2 / Biso min: 33.89 Å2
Refinement stepCycle: final / Resolution: 2.383→80.652 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5722 0 0 215 5937
Biso mean---54.7 -
Num. residues----765
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.383-2.42610.34981470.29742686100
2.4261-2.47280.35921490.27272750100
2.4728-2.52330.26631670.26692653100
2.5233-2.57810.28941540.25742709100
2.5781-2.63810.28231420.23662710100
2.6381-2.70410.28591490.23522731100
2.7041-2.77720.29341260.23672746100
2.7772-2.85890.28781490.22712709100
2.8589-2.95120.28081460.21342727100
2.9512-3.05670.27251540.22182721100
3.0567-3.17910.26551200.21432762100
3.1791-3.32380.28941730.22122721100
3.3238-3.4990.2371280.21242759100
3.499-3.71820.21021180.18582788100
3.7182-4.00530.21661530.17982762100
4.0053-4.40840.20891300.16872780100
4.4084-5.04620.21831200.17462824100
5.0462-6.35730.19961350.20312833100
6.3573-80.6520.1891580.1743290798

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