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- PDB-6lbf: Crystal structure of FEM1B -

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Basic information

Entry
Database: PDB / ID: 6lbf
TitleCrystal structure of FEM1B
ComponentsProtein fem-1 homolog B
KeywordsPROTEIN BINDING / ubiquitination / E3 ligase
Function / homology
Function and homology information


regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / branching involved in prostate gland morphogenesis / regulation of DNA damage checkpoint / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / death receptor binding / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of non-canonical NF-kappaB signal transduction / Cul2-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity ...regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / branching involved in prostate gland morphogenesis / regulation of DNA damage checkpoint / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / death receptor binding / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of non-canonical NF-kappaB signal transduction / Cul2-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / apoptotic process / nucleoplasm / nucleus / metal ion binding / cytoplasm / 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
Similarity search - Domain/homology
Protein fem-1 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.252 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 14, 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 1.4Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 B
B: Protein fem-1 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1124
Polymers78,9202
Non-polymers1922
Water00
1
A: Protein fem-1 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6523
Polymers39,4601
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-12 kcal/mol
Surface area15370 Å2
MethodPISA
2
B: Protein fem-1 homolog B


Theoretical massNumber of molelcules
Total (without water)39,4601
Polymers39,4601
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.810, 127.810, 143.034
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Protein fem-1 homolog B / FEM1b / FEM1-beta / Fem-1-like death receptor-binding protein alpha / Fem-1-like in apoptotic ...FEM1b / FEM1-beta / Fem-1-like death receptor-binding protein alpha / Fem-1-like in apoptotic pathway protein alpha / F1A-alpha


Mass: 39459.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FEM1B, F1AA, KIAA0396 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UK73
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
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: 3.7 Å3/Da / Density % sol: 66.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris-HCl, pH 8.5, 0.1M Guanidine hydrochloride, 0.8M Potassium sodium tartrate tetrahydrate, 0.5% w/v Polyethylene glycol monomethyl ether 5000

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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 315r / Detector: CCD / Date: Oct 21, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 19211 / % possible obs: 100 % / Redundancy: 25.2 % / CC1/2: 1 / Rmerge(I) obs: 1.98 / Net I/σ(I): 12.3
Reflection shellResolution: 3.25→3.37 Å / Num. unique obs: 1893 / CC1/2: 0.606

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
CRANK2phasing
RefinementMethod to determine structure: MAD / Resolution: 3.252→47.678 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 1919 9.99 %
Rwork0.218 17292 -
obs0.2216 19211 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140 Å2 / Biso mean: 94.0095 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.252→47.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 10 0 5094
Biso mean--86.53 --
Num. residues----685
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2523-3.33360.3611330.33541196100
3.3336-3.42370.33451340.31551205100
3.4237-3.52450.32781340.2981205100
3.5245-3.63820.37671350.2811220100
3.6382-3.76820.28371370.24791234100
3.7682-3.9190.28951340.23121198100
3.919-4.09720.24471360.23151223100
4.0972-4.31310.27151360.21451223100
4.3131-4.58310.20231360.19471225100
4.5831-4.93670.25591370.20181237100
4.9367-5.43280.25861380.2061234100
5.4328-6.21750.27811400.22971267100
6.2175-7.82780.22951410.20621270100
7.8278-47.6780.19771480.1766135599

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