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- PDB-7el6: Structure of SMCR8 bound FEM1B -

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Basic information

Entry
Database: PDB / ID: 7el6
TitleStructure of SMCR8 bound FEM1B
ComponentsProtein fem-1 homolog B,Guanine nucleotide exchange protein SMCR8
KeywordsPEPTIDE BINDING PROTEIN / ubiquitination E3 ligase
Function / homology
Function and homology information


regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / Atg1/ULK1 kinase complex / regulation of TORC1 signaling / negative regulation of autophagosome assembly / branching involved in prostate gland morphogenesis / guanyl-nucleotide exchange factor complex / regulation of DNA damage checkpoint / negative regulation of immune response / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway ...regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / Atg1/ULK1 kinase complex / regulation of TORC1 signaling / negative regulation of autophagosome assembly / branching involved in prostate gland morphogenesis / guanyl-nucleotide exchange factor complex / regulation of DNA damage checkpoint / negative regulation of immune response / 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 exocytosis / positive regulation of autophagosome maturation / Cul2-RING ubiquitin ligase complex / negative regulation of macroautophagy / protein kinase inhibitor activity / ubiquitin-like ligase-substrate adaptor activity / positive regulation of TOR signaling / GTPase activator activity / guanyl-nucleotide exchange factor activity / regulation of autophagy / cell projection / negative regulation of protein kinase activity / autophagy / positive regulation of GTPase activity / presynapse / Neddylation / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / negative regulation of gene expression / apoptotic process / chromatin / protein kinase binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Folliculin/SMCR8, longin domain / Folliculin/SMCR8, tripartite DENN domain / Vesicle coat protein involved in Golgi to plasma membrane transport / Tripartite DENN FLCN/SMCR8-type domain profile. / 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
Guanine nucleotide exchange protein SMCR8 / Protein fem-1 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 Å
AuthorsZhao, S. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural insights into SMCR8 C-degron recognition by FEM1B.
Authors: Zhao, S. / Ru, W. / Chen, X. / Liao, S. / Zhu, Z. / Zhang, J. / Xu, C.
History
DepositionApr 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 B,Guanine nucleotide exchange protein SMCR8
B: Protein fem-1 homolog B,Guanine nucleotide exchange protein SMCR8


Theoretical massNumber of molelcules
Total (without water)78,6042
Polymers78,6042
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-8 kcal/mol
Surface area29680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.306, 91.497, 112.148
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Protein fem-1 homolog B,Guanine nucleotide exchange protein SMCR8 / 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 / Smith-Magenis syndrome chromosomal region candidate gene 8 protein


Mass: 39301.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues 1-337 from FEM1b, linker, residues 378-387 from SMCR8.
Source: (gene. exp.) Homo sapiens (human) / Gene: FEM1B, F1AA, KIAA0396, SMCR8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UK73, UniProt: Q8TEV9

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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: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris pH7.3 4% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.8→37.383 Å / Num. obs: 20988 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 1 / Net I/σ(I): 49.5
Reflection shellResolution: 2.8→2.85 Å / Num. unique obs: 1998 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LBF

6lbf


Resolution: 2.802→37.383 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 1998 9.52 %
Rwork0.2031 18990 -
obs0.2091 20988 96.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.36 Å2 / Biso mean: 63.6504 Å2 / Biso min: 28.26 Å2
Refinement stepCycle: final / Resolution: 2.802→37.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5202 0 0 0 5202
Num. residues----686
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8021-2.87210.3561430.2661373100
2.8721-2.94980.3621460.25921380100
2.9498-3.03650.34831440.24571364100
3.0365-3.13450.30681440.23621362100
3.1345-3.24650.32891460.26061394100
3.2465-3.37640.32561440.24371372100
3.3764-3.52990.31821470.23421390100
3.5299-3.71590.2542890.218285061
3.7159-3.94840.26111420.1988135297
3.9484-4.25290.22561470.18431400100
4.2529-4.68020.23151490.1621411100
4.6802-5.35570.23081500.17731421100
5.3557-6.74120.25231500.20771430100
6.7412-37.3830.2311570.1754149198
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)
10.9410.28440.99010.41090.48692.88070.03130.13820.0249-0.07310.00760.05630.1028-0.3273-0.07040.35780.0075-0.00450.4070.03250.375924.53825.31827.147
21.3263-0.2441-1.23210.30320.66993.68-0.0659-0.256-0.10820.0334-0.031-0.06690.05390.26690.12110.4159-0.01360.00470.28640.04440.414319.73517.50770.269
31.5872-0.4188-0.46753.0735-0.55441.3265-0.18770.3815-0.24790.63090.0126-0.24560.25850.1436-0.01110.5811-0.1392-0.11390.5813-0.12290.520528.22518.1427.413
43.04780.60661.10032.8155-1.30934.5789-0.03620.15820.3582-0.28380.36780.6204-0.63750.0129-0.13220.50540.0216-0.0760.23460.0310.46614.37322.91966.469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:337 )A1 - 337
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:337 )B1 - 337
3X-RAY DIFFRACTION3( CHAIN A AND RESID 347:357 )A347 - 357
4X-RAY DIFFRACTION4( CHAIN B AND RESID 347:357 )B347 - 357

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