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- PDB-6lf0: Structure of FEM1C -

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Basic information

Entry
Database: PDB / ID: 6lf0
TitleStructure of FEM1C
ComponentsProtein fem-1 homolog C
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: 2.11 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 27, 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

Downloads & links

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Assembly

Deposited unit
A: Protein fem-1 homolog C
B: Protein fem-1 homolog C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3113
Polymers89,2152
Non-polymers961
Water4,936274
1
A: Protein fem-1 homolog C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7032
Polymers44,6071
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area19120 Å2
MethodPISA
2
B: Protein fem-1 homolog C


Theoretical massNumber of molelcules
Total (without water)44,6071
Polymers44,6071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.720, 98.480, 146.570
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 / FEM1c / FEM1-gamma


Mass: 44607.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FEM1C, KIAA1785 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96JP0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 3.59 Å3/Da / Density % sol: 65.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M Lithium sulfate, 0.1M Tris-HCl pH 7.3

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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: Jan 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.11→81.74 Å / Num. obs: 74445 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 19.7
Reflection shellResolution: 2.11→2.16 Å / Num. unique obs: 7352 / CC1/2: 0.82

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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: 2.11→56.502 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.47
RfactorNum. reflection% reflection
Rfree0.2291 3550 4.77 %
Rwork0.195 --
obs0.1966 74445 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 172.21 Å2 / Biso mean: 58.7608 Å2 / Biso min: 33.19 Å2
Refinement stepCycle: final / Resolution: 2.11→56.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5784 0 5 274 6063
Biso mean--100.63 54.2 -
Num. residues----773
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.11-2.13890.32941400.29732840100
2.1389-2.16950.32181480.27622779100
2.1695-2.20180.25661230.25242811100
2.2018-2.23630.27341490.23072795100
2.2363-2.27290.22481580.222783100
2.2729-2.31210.25181360.21622781100
2.3121-2.35420.24831540.20792815100
2.3542-2.39940.23111600.20332802100
2.3994-2.44840.28141490.19712791100
2.4484-2.50170.23491230.20282804100
2.5017-2.55980.21921380.19952822100
2.5598-2.62390.24291340.19562799100
2.6239-2.69480.22881330.19662832100
2.6948-2.77410.26951290.21112848100
2.7741-2.86360.28441460.21732822100
2.8636-2.9660.21291340.22422820100
2.966-3.08470.25251380.22692852100
3.0847-3.22510.25261820.21782795100
3.2251-3.39510.25671310.21062853100
3.3951-3.60780.21671360.18052834100
3.6078-3.88630.20351460.17422868100
3.8863-4.27730.17731460.16392877100
4.2773-4.89590.17911320.16162910100
4.8959-6.16710.23851360.20332922100
6.1671-56.5020.24411490.1888304099
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)
11.17380.0084-0.60160.4321-0.2110.80650.14560.27730.108-0.34440.0836-0.1701-0.4703-0.05200.7139-0.01880.14710.5028-0.00250.556129.504220.336913.1525
20.55650.2324-1.49340.9465-0.69011.33680.09860.0203-0.0436-0.0916-0.0273-0.0405-0.1655-0.05760.00020.40610.0173-0.0220.4139-0.03410.428215.9098.689537.1407
31.43790.44750.23861.09370.68491.2336-0.0068-0.0999-0.04260.2137-0.0415-0.03220.4167-0.0697-0.00010.5194-0.0305-0.02030.3933-0.01630.41644.8839-20.353641.7872
40.00980.048-0.0486-0.0672-0.17310.0667-0.20510.0556-0.1727-0.1259-0.0213-0.2647-0.08850.23460.00020.6378-0.1874-0.03670.5719-0.00570.580914.5608-12.18717.9722
5-0.03120.01380.22270.122-0.16540.7090.17-0.3593-0.01651.50590.2822-0.0425-0.06850.08080.02051.16210.1049-0.14090.7696-0.12090.541345.10594.077723.8635
61.23050.3180.41011.18520.92940.75240.0026-0.15490.00540.16880.0914-0.01440.08260.05250.00010.40450.04290.04060.44230.02620.445635.4155-6.2742-0.3721
70.45210.6374-0.56671.6306-0.45340.9989-0.01620.13240.1228-0.20080.01360.01280.1007-0.25300.4006-0.05580.01050.52250.0130.45119.3029-20.8943-4.7618
81.0073-0.26830.01340.2491-0.58551.44490.0355-0.15830.09370.06-0.3218-0.1969-0.2043-0.03270.00010.446-0.135-0.00930.48410.04740.417412.354-22.739517.7133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 104 )A2 - 104
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 226 )A105 - 226
3X-RAY DIFFRACTION3chain 'A' and (resid 227 through 370 )A227 - 370
4X-RAY DIFFRACTION4chain 'A' and (resid 371 through 403 )A371 - 403
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 104 )B5 - 104
6X-RAY DIFFRACTION6chain 'B' and (resid 105 through 226 )B105 - 226
7X-RAY DIFFRACTION7chain 'B' and (resid 227 through 350 )B227 - 350
8X-RAY DIFFRACTION8chain 'B' and (resid 351 through 403 )B351 - 403

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