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- PDB-6lbg: Structure of OR51B2 bound FEM1C -

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Basic information

Entry
Database: PDB / ID: 6lbg
TitleStructure of OR51B2 bound FEM1C
ComponentsProtein fem-1 homolog C,Peptide from Olfactory receptor 51B2
KeywordsPROTEIN BINDING / ubiquitination / E3 ligase
Function / homology
Function and homology information


olfactory receptor activity / 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 / G protein-coupled receptor activity / Olfactory Signaling Pathway / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process ...olfactory receptor activity / 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 / G protein-coupled receptor activity / Olfactory Signaling Pathway / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / membrane => GO:0016020 / protein ubiquitination / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Olfactory receptor / Olfactory receptor / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / G protein-coupled receptor, rhodopsin-like ...Olfactory receptor / Olfactory receptor / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Protein fem-1 homolog C / Olfactory receptor 51B2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 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 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation
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 13, 2021Group: Database references / Category: citation_author
Revision 1.3Jan 20, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Mar 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Nov 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
B: Protein fem-1 homolog C,Peptide from Olfactory receptor 51B2
A: Protein fem-1 homolog C,Peptide from Olfactory receptor 51B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9818
Polymers91,4052
Non-polymers5766
Water1,49583
1
B: Protein fem-1 homolog C,Peptide from Olfactory receptor 51B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9904
Polymers45,7021
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-33 kcal/mol
Surface area17130 Å2
MethodPISA
2
A: Protein fem-1 homolog C,Peptide from Olfactory receptor 51B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9904
Polymers45,7021
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-35 kcal/mol
Surface area16700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.918, 97.690, 146.197
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 Olfactory receptor 51B2 / FEM1c / FEM1-gamma / OR51B2 peptide


Mass: 45702.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FEM1C fused with OR51B2 peptide, linked with linker residues GGGSGGGSGGGSGGGS.
Source: (gene. exp.) Homo sapiens (human) / Gene: FEM1C, KIAA1785, OR51B2, OR51B1P / Production host: Escherichia coli (E. coli) / References: UniProt: Q96JP0, UniProt: Q9Y5P1
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.53 Å3/Da / Density % sol: 65.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris-HCl, pH 7.0, 0.8M Lithium sulfate

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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 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.51→87.89 Å / Num. obs: 43610 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.998 / Net I/σ(I): 9.4
Reflection shellResolution: 2.51→2.58 Å / Num. unique obs: 4267 / CC1/2: 0.886

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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: 2.51→19.555 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.51
RfactorNum. reflection% reflection
Rfree0.2311 2196 5.04 %
Rwork0.1959 --
obs0.1977 43610 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.39 Å2 / Biso mean: 64.5883 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.51→19.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5687 0 30 83 5800
Biso mean--96.04 54.98 -
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 (%)
2.51-2.580.32111150.2776255199
2.5644-2.62390.32681230.25662569100
2.6239-2.68940.29321330.25242544100
2.6894-2.76190.30551160.24242592100
2.7619-2.84290.28661320.23712553100
2.8429-2.93440.28321350.23862583100
2.9344-3.03890.2561410.22852527100
3.0389-3.16010.28681510.22282568100
3.1601-3.30320.24651260.22832576100
3.3032-3.47650.31631570.2172567100
3.4765-3.69290.21591270.18342585100
3.6929-3.97590.21141400.17312588100
3.9759-4.37190.17471440.15822620100
4.3719-4.99530.23211560.15982585100
4.9953-6.25910.21391500.19962656100
6.2591-19.5550.18011500.17552750100
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)
11.01110.412-0.06031.89980.40751.00970.0620.09980.0764-0.2015-0.0003-0.1904-0.0266-0.0653-0.0750.48220.0631-0.00590.3253-0.01560.329814.53-0.25732.336
21.70780.7783-0.12861.24140.12051.14860.0363-0.15730.10910.137-0.0048-0.04520.0947-0.0285-0.04130.43290.0820.0110.33250.00380.313925.627-10.64.956
31.9786-0.8285-1.83628.35822.61912.2519-0.4283-0.1108-0.1756-0.3956-0.03060.2971-0.29370.0350.33661.0349-0.0262-0.0270.8134-0.08680.736130.768-9.7588.46
41.2535-0.15451.05413.10970.28870.9657-0.1224-0.0554-0.27430.1056-0.37630.2860.1092-0.23750.39611.2585-0.06760.2770.8260.03970.679515.4014.41527.972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 2:390 )B2 - 390
2X-RAY DIFFRACTION2( CHAIN A AND RESID 3:390 )A3 - 390
3X-RAY DIFFRACTION3( CHAIN A AND RESID 412:416 )A412 - 416
4X-RAY DIFFRACTION4( CHAIN B AND RESID 413:416 )B413 - 416

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