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- PDB-5b26: Crystal structure of mouse SEL1L -

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Basic information

Entry
Database: PDB / ID: 5b26
TitleCrystal structure of mouse SEL1L
ComponentsProtein sel-1 homolog 1
KeywordsSIGNALING PROTEIN / SEL1L / SLR motif / ERAD
Function / homology
Function and homology information


Hrd1p ubiquitin ligase ERAD-L complex / : / Hedgehog ligand biogenesis / ABC-family proteins mediated transport / Derlin-1 retrotranslocation complex / retrograde protein transport, ER to cytosol / triglyceride metabolic process / protein secretion / ERAD pathway / Notch signaling pathway ...Hrd1p ubiquitin ligase ERAD-L complex / : / Hedgehog ligand biogenesis / ABC-family proteins mediated transport / Derlin-1 retrotranslocation complex / retrograde protein transport, ER to cytosol / triglyceride metabolic process / protein secretion / ERAD pathway / Notch signaling pathway / response to endoplasmic reticulum stress / membrane => GO:0016020 / endoplasmic reticulum
Similarity search - Function
Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Protein sel-1 homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsJeong, H. / Lee, C.
Funding support Korea, Republic Of, 5items
OrganizationGrant numberCountry
Ministry of Health & WelfareHI12C1744 Korea, Republic Of
Ulsan National Institute of Science and Technology1.150024.01 Korea, Republic Of
National Research Foundation of KoreaNRF-2011-0024241 Korea, Republic Of
National Research Foundation of Korea2012R1A1A1011604 Korea, Republic Of
National Research Foundation of KoreaNRF-2014H1A2A1020322 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structure of SEL1L: Insight into the roles of SLR motifs in ERAD pathway
Authors: Jeong, H. / Sim, H.J. / Song, E.K. / Lee, H. / Ha, S.C. / Jun, Y. / Park, T.J. / Lee, C.
History
DepositionJan 9, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein sel-1 homolog 1
B: Protein sel-1 homolog 1
C: Protein sel-1 homolog 1
D: Protein sel-1 homolog 1


Theoretical massNumber of molelcules
Total (without water)82,0444
Polymers82,0444
Non-polymers00
Water84747
1
A: Protein sel-1 homolog 1
B: Protein sel-1 homolog 1


Theoretical massNumber of molelcules
Total (without water)41,0222
Polymers41,0222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-19 kcal/mol
Surface area16890 Å2
MethodPISA
2
C: Protein sel-1 homolog 1
D: Protein sel-1 homolog 1


Theoretical massNumber of molelcules
Total (without water)41,0222
Polymers41,0222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-21 kcal/mol
Surface area17080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.128, 110.523, 109.810
Angle α, β, γ (deg.)90.00, 90.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein sel-1 homolog 1 / Suppressor of lin-12-like protein 1 / Sel-1L


Mass: 20510.990 Da / Num. of mol.: 4 / Fragment: UNP residues 348-533
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sel1l, Sel1h / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z2G6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% Isopropanol, 100 mM Sodium chloride, 100 mM Tris, 5 mM DTT, 20 mM Phenol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 21479 / % possible obs: 99.5 % / Redundancy: 4.1 % / Net I/σ(I): 29.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
PHENIXphasing
Cootmodel building
RefinementResolution: 2.6→30 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / Phase error: 31.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2817 1085 5.06 %
Rwork0.2067 --
obs0.2105 21446 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5402 0 0 47 5449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015525
X-RAY DIFFRACTIONf_angle_d1.3657435
X-RAY DIFFRACTIONf_dihedral_angle_d14.6371971
X-RAY DIFFRACTIONf_chiral_restr0.059732
X-RAY DIFFRACTIONf_plane_restr0.007991
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5937-2.71170.35861370.27392498X-RAY DIFFRACTION99
2.7117-2.85460.34111330.27862534X-RAY DIFFRACTION99
2.8546-3.03330.38651400.28512516X-RAY DIFFRACTION100
3.0333-3.26730.34541430.26092594X-RAY DIFFRACTION100
3.2673-3.59560.34021380.23422517X-RAY DIFFRACTION100
3.5956-4.11480.25281320.19982572X-RAY DIFFRACTION100
4.1148-5.18010.26541270.16612560X-RAY DIFFRACTION100
5.1801-30.59390.19511350.15832570X-RAY DIFFRACTION99

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