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- PDB-6le6: Structure of LNLPTQGRAR bound FEM1C -

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Basic information

Entry
Database: PDB / ID: 6le6
TitleStructure of LNLPTQGRAR bound FEM1C
ComponentsProtein fem-1 homolog C,10-mer 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-like ligase-substrate adaptor activity / ubiquitin ligase complex / Neddylation / ubiquitin-dependent protein catabolic process / 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: 2.33 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 24, 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,10-mer peptide
B: Protein fem-1 homolog C,10-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3385
Polymers91,0502
Non-polymers2883
Water2,108117
1
A: Protein fem-1 homolog C,10-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6212
Polymers45,5251
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18400 Å2
MethodPISA
2
B: Protein fem-1 homolog C,10-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7173
Polymers45,5251
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-15 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.515, 96.334, 146.498
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,10-mer peptide / FEM1c / FEM1-gamma


Mass: 45524.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FEM1C fused with a 10-mer peptide LNLPTQGRAR, linked with linker residues GGGSGGGSGGGSGGGS.
Source: (gene. exp.) Homo sapiens (human) / Gene: FEM1C, KIAA1785 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96JP0
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.76 Å3/Da / Density % sol: 67.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.6M Lithium sulfate, 0.1M BIS-TRIS propane Ph 6.4

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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: Oct 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.33→94.52 Å / Num. obs: 57097 / % possible obs: 99.3 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 17.9
Reflection shellResolution: 2.33→2.39 Å / Num. unique obs: 5517 / CC1/2: 0.931

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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: 2.33→79.421 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.47
RfactorNum. reflection% reflection
Rfree0.2505 2762 4.84 %
Rwork0.2036 --
obs0.2059 57097 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 176.89 Å2 / Biso mean: 71.357 Å2 / Biso min: 33.53 Å2
Refinement stepCycle: final / Resolution: 2.33→79.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5745 0 15 117 5877
Biso mean--90.06 57.44 -
Num. residues----770
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.33-2.36990.31011320.2844262596
2.3699-2.4130.33831160.281264497
2.413-2.45940.30361340.2569264998
2.4594-2.50960.331380.2523265999
2.5096-2.56420.30681610.2496267098
2.5642-2.62380.29951090.2296273298
2.6238-2.68950.26291360.2246267398
2.6895-2.76220.27361560.2339265899
2.7622-2.84350.28661530.2328266198
2.8435-2.93530.2971400.249271699
2.9353-3.04020.29621520.2424267899
3.0402-3.16190.28261370.2323272899
3.1619-3.30580.28681250.2408274299
3.3058-3.48010.30931150.2384275199
3.4801-3.69810.23171280.1905273299
3.6981-3.98370.22941670.18262753100
3.9837-4.38450.21291360.1623275899
4.3845-5.01890.20531580.1697275299
5.0189-6.32290.22851220.20852849100
6.3229-79.4210.23751470.1794290598
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0114-0.0102-0.00190.01550.01080.0135-0.1538-0.09210.0530.0208-0.0337-0.05490.04560.0350.00110.8532-0.0999-0.01321.0170.04180.640632.031-8.9179.398
20.0148-0.0070.01080.0128-0.00780.0088-0.01-0.0219-0.0051-0.0353-0.13660.03040.0499-0.0552-0.00121.1144-0.06020.03790.6988-0.15640.651315.0854.71427.012
30.64880.3537-0.15410.96910.36440.37580.1320.0618-0.0026-0.1804-0.0962-0.12420.0363-0.041700.41010.06750.00010.39360.01620.419814.1470.34132.2
40.84380.1947-0.11140.407-0.21990.6725-0.1017-0.08380.11330.20760.0621-0.0103-0.0538-0.002300.44970.05780.01040.4116-0.02040.417626.52-10.2454.954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 412:416 )B412 - 416
2X-RAY DIFFRACTION2( CHAIN A AND RESID 411:416 )A411 - 416
3X-RAY DIFFRACTION3( CHAIN A AND RESID 2:390 )A2 - 390
4X-RAY DIFFRACTION4( CHAIN B AND RESID 2:390 )B2 - 390

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