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- PDB-6ley: Structure of Sil1G bound FEM1C -

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Basic information

Entry
Database: PDB / ID: 6ley
TitleStructure of Sil1G bound FEM1C
ComponentsProtein fem-1 homolog C,Peptide from Nucleotide exchange factor SIL1
KeywordsPROTEIN BINDING / ubiquitination E3 ligase
Function / homology
Function and homology information


adenyl-nucleotide exchange factor activity / cotranslational protein targeting to membrane / 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 / intracellular protein transport / unfolded protein binding / protein folding / Neddylation ...adenyl-nucleotide exchange factor activity / cotranslational protein targeting to membrane / 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 / intracellular protein transport / unfolded protein binding / protein folding / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / endoplasmic reticulum lumen / endoplasmic reticulum / extracellular space / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
Nucleotide exchange factor Fes1 / : / Nucleotide exchange factor Fes1 / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily ...Nucleotide exchange factor Fes1 / : / Nucleotide exchange factor Fes1 / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Protein fem-1 homolog C / Nucleotide exchange factor SIL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsChen, X. / Liao, S. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) 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,Peptide from Nucleotide exchange factor SIL1
B: Protein fem-1 homolog C,Peptide from Nucleotide exchange factor SIL1


Theoretical massNumber of molelcules
Total (without water)91,2302
Polymers91,2302
Non-polymers00
Water2,900161
1
A: Protein fem-1 homolog C,Peptide from Nucleotide exchange factor SIL1


Theoretical massNumber of molelcules
Total (without water)45,6151
Polymers45,6151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein fem-1 homolog C,Peptide from Nucleotide exchange factor SIL1


Theoretical massNumber of molelcules
Total (without water)45,6151
Polymers45,6151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.497, 95.973, 147.478
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,Peptide from Nucleotide exchange factor SIL1 / FEM1c / FEM1-gamma / BiP-associated protein / BAP


Mass: 45615.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FEM1C fused with SIL1G peptide, linked with linker residues GGGSGGGSGGGSGGGS.
Source: (gene. exp.) Homo sapiens (human) / Gene: FEM1C, KIAA1785, SIL1, UNQ545/PRO836 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96JP0, UniProt: Q9H173
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 4.01 Å3/Da / Density % sol: 69.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.0M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic pH 6.9

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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: 2.39→147.48 Å / Num. obs: 54296 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 12.9
Reflection shellResolution: 2.39→2.45 Å / Num. unique obs: 5321 / CC1/2: 0.826

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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: 2.39→80.44 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 2767 5.1 %
Rwork0.1976 51529 -
obs0.1992 54296 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.83 Å2 / Biso mean: 73.4135 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.39→80.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5587 0 0 161 5748
Biso mean---58.82 -
Num. residues----759
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.39-2.43080.30781380.2713250499
2.4308-2.4750.30241330.25942546100
2.475-2.52260.27311220.2562564100
2.5226-2.57410.29581690.24572504100
2.5741-2.630.31271300.24212542100
2.63-2.69120.24041100.22372557100
2.6912-2.75850.27881460.22362552100
2.7585-2.83310.23921310.22052575100
2.8331-2.91650.2591500.22482519100
2.9165-3.01060.271190.23362600100
3.0106-3.11820.25331530.22682523100
3.1182-3.24310.26661510.22312562100
3.2431-3.39070.29281510.22782572100
3.3907-3.56950.20531310.20152591100
3.5695-3.79310.22521320.17552582100
3.7931-4.08590.20861380.16812597100
4.0859-4.49710.1751310.15562615100
4.4971-5.14770.21261410.17382620100
5.1477-6.48520.21351290.20432672100
6.4852-80.440.20871620.1907273299
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)
11.34370.7433-0.04122.2006-0.0671.24530.03210.2461-0.0081-0.2212-0.0849-0.22290.050.03720.0650.29450.09230.02880.4139-0.00770.373613.9770.14932.948
22.23530.4808-0.48231.3516-0.52491.0793-0.0637-0.29240.10820.3794-0.0014-0.0914-0.0179-0.01590.06130.6160.05940.04170.3817-0.03350.394727.046-10.6644.246
35.3550.8913-4.76440.1864-0.79944.24-0.79790.6015-0.6408-0.891-0.4659-0.01970.9187-0.11961.08481.0150.07750.03221.1560.07380.979716.0524.5927.223
41.59130.31362.81480.12760.5574.9792-0.0847-0.4136-0.19120.0006-0.32430.19270.0159-0.34730.36991.5388-0.186-0.20240.9015-0.00020.853133.539-8.3939.941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:390 )A2 - 390
2X-RAY DIFFRACTION2( CHAIN B AND RESID 5:390 )B5 - 390
3X-RAY DIFFRACTION3( CHAIN A AND RESID 411:417 )A411 - 417
4X-RAY DIFFRACTION4( CHAIN B AND RESID 412:417 )B412 - 417

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