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- PDB-8zuh: Crystal structure of bovine Fbs2/Skp1/Man3GlcNAc2 complex -

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Basic information

Entry
Database: PDB / ID: 8zuh
TitleCrystal structure of bovine Fbs2/Skp1/Man3GlcNAc2 complex
Components
  • F-box only protein 6
  • S-phase kinase-associated protein 1
KeywordsLIGASE / UBIQUITIN / SCF / FBS2 / LIGASE COMPLEX
Function / homology
Function and homology information


SCF-beta-TrCP mediated degradation of Emi1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Cyclin D associated events in G1 / Regulation of BACH1 activity / Iron uptake and transport / Activation of NF-kappaB in B cells / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling ...SCF-beta-TrCP mediated degradation of Emi1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Cyclin D associated events in G1 / Regulation of BACH1 activity / Iron uptake and transport / Activation of NF-kappaB in B cells / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / NIK-->noncanonical NF-kB signaling / Orc1 removal from chromatin / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Regulation of RUNX2 expression and activity / Interleukin-1 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Degradation of beta-catenin by the destruction complex / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / glycoprotein catabolic process / endoplasmic reticulum quality control compartment / Downstream TCR signaling / GLI3 is processed to GLI3R by the proteasome / Regulation of PLK1 Activity at G2/M Transition / Cul7-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / cullin family protein binding / response to unfolded protein / ERAD pathway / protein ubiquitination / DNA repair / nucleus / cytosol / cytoplasm
Similarity search - Function
F-box associated (FBA) domain / F-box only protein / F-box associated region / F-box-associated (FBA) domain profile. / F-box associated region / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation ...F-box associated (FBA) domain / F-box only protein / F-box associated region / F-box-associated (FBA) domain profile. / F-box associated region / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
F-box only protein 6 / S-phase kinase-associated protein 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSatoh, T. / Mizushima, T. / Yagi, H. / Kato, R. / Kato, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP24gm1410003 Japan
CitationJournal: Febs Lett. / Year: 2024
Title: Structural basis of sugar recognition by SCF FBS2 ubiquitin ligase involved in NGLY1 deficiency.
Authors: Satoh, T. / Yagi-Utsumi, M. / Ishii, N. / Mizushima, T. / Yagi, H. / Kato, R. / Tachida, Y. / Tateno, H. / Matsuo, I. / Kato, K. / Suzuki, T. / Yoshida, Y.
History
DepositionJun 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F-box only protein 6
B: S-phase kinase-associated protein 1
C: F-box only protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4065
Polymers80,5853
Non-polymers1,8222
Water25214
1
A: F-box only protein 6
B: S-phase kinase-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6893
Polymers49,7792
Non-polymers9111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: F-box only protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7172
Polymers30,8061
Non-polymers9111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.720, 115.720, 110.384
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein F-box only protein 6 / F-box protein that recognizes sugar chains 2


Mass: 30806.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: FBXO6, FBS2, FBX6 / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3SX24
#2: Protein S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / S-phase kinase-associated protein 1A / p19A / p19skp1


Mass: 18972.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: SKP1, SKP1A / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3ZCF3
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 4.59 Å3/Da / Density % sol: 73.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.9 M Sodium citrate/0.1 M Tris-HCl (pH 8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 24111 / % possible obs: 99.6 % / Redundancy: 7 % / Biso Wilson estimate: 88.03 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.174 / Net I/σ(I): 10.4
Reflection shellResolution: 3.2→3.39 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.244 / Mean I/σ(I) obs: 2 / Num. unique obs: 3869 / CC1/2: 0.673 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF-Q3SX24-F1,2E31

2e31


Resolution: 3.2→40.91 Å / SU ML: 0.4447 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.6669
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2468 1269 5.27 %
Rwork0.2061 22825 -
obs0.2084 24094 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.05 Å2
Refinement stepCycle: LAST / Resolution: 3.2→40.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5187 0 124 14 5325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01025459
X-RAY DIFFRACTIONf_angle_d1.16687420
X-RAY DIFFRACTIONf_chiral_restr0.0596821
X-RAY DIFFRACTIONf_plane_restr0.0088929
X-RAY DIFFRACTIONf_dihedral_angle_d17.56872084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.330.35771060.28892570X-RAY DIFFRACTION99.63
3.33-3.480.36221260.25312536X-RAY DIFFRACTION99.96
3.48-3.660.26071230.23092527X-RAY DIFFRACTION100
3.66-3.890.21941850.19672483X-RAY DIFFRACTION99.96
3.89-4.190.2191440.17562530X-RAY DIFFRACTION99.96
4.19-4.610.19541420.17112537X-RAY DIFFRACTION99.93
4.61-5.280.22561550.16662522X-RAY DIFFRACTION100
5.28-6.650.23721240.22282554X-RAY DIFFRACTION99.85
6.65-40.910.2731640.2242566X-RAY DIFFRACTION99.6
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)
10.02232872131861.224639040290.5605322538251.205411830820.5727540217340.1157445773930.2712370930450.115879466848-0.2231480932170.151482930028-0.1436542409970.0627827381373-0.5304539396740.00307183500717-3.13903684216E-50.767422044487-0.123975680118-0.03579193765230.7755554873790.01516407326850.79769855146120.739481309918.65898210913.8935387724
21.610269459740.2748545346020.7610662184011.182156889130.4230829772482.141579653860.06529737458890.0008652033517760.0861249631643-0.157539167240.05918940246570.0219963634538-0.1450641457610.1447971636943.89898891033E-60.6686107270030.0005750924159210.01404371675550.571660818264-0.001532377262350.6861174545028.768613119138.75168910377-14.9932046724
30.1935335116520.05284541047190.1083902424330.2122054947860.1530795247560.08045201795970.303200654655-1.254172615880.146294043420.359939671357-0.454252069859-0.00720939242143-0.1383699022110.6459716255610.0005287794346730.8807400473070.006739312973840.1256681262130.914345179523-0.2310883432241.01736442634.160111873953.039064970427.8414913324
40.0411023910694-0.0353461905424-0.03822841248230.133182502733-0.1183651585210.1074311491140.1744748192770.1007224924320.0105012750582-0.0712410062158-0.1511644631890.183099610745-0.735023602580.348248291497-0.0002938145615920.8508544744860.156415206822-0.0159190980130.8797702036810.005807308377510.79148715026828.480910034952.934361334620.565101536
50.05405302280060.03514068665120.1013262588930.01327067935830.06436106759970.0555676031824-0.732255725736-0.870140763088-0.2226300083620.4755586847860.851801957496-0.09318902296070.07826004679290.2868567423620.0007820978711620.954929374012-0.07450842200610.1067686274331.0938715356-0.1946365950540.89389748746825.898518897748.914103344329.621581688
60.0977608683072-0.129219688825-0.02402453966470.1419354515040.05052318002980.0274267754375-0.5690638212750.3623321348130.545859125339-0.674538683993-0.404939272657-0.5015307876090.3108929088220.4777829295787.30055710745E-50.6766022518670.03190721116380.04193748179450.802579772646-0.0529440769490.9305148680434.584664633245.451932694218.0312179657
70.0700178840621-0.13845970549-0.1283753932630.3639138688560.2449862838450.145278207641-0.113181221699-0.5379560784320.0998653339947-0.455419186924-0.01722522352740.5066695575240.5192840459940.370153356724-0.0002722070338350.754478497743-0.0733904871293-0.003379658886430.8121859411140.02385544265080.8582867103833.386549844839.02946273899.48110544776
80.0468119901040.163461722081-0.009090837993680.267882375961-0.05386137411070.09486773417150.19376958738-0.2108272992770.5806855275640.07100477230590.152973213389-0.26003447237-0.1277930456480.1457616654380.0007824097130950.63509494981-0.05814440365970.05179731387360.7353663081180.008225072134770.83536517037432.656320015936.17905773623.6783384591
9-0.0130291363642-0.02638279498620.0252593351144-0.00384964917655-0.0098456806177-0.00391052958045-0.1710374542240.162979438861-0.740184879346-0.5000458483090.03953932533970.444736916710.7682213502920.425502219074-0.0005761467106630.764111778361-0.090260314938-0.07831369965890.8462519668190.08932630973920.80196937551830.728390379130.73308379315.2985970385
100.06260857704050.0114773483649-0.1133021940240.0332708706491-0.03044533607110.1201406710460.7204299078520.9145633133140.116409399431-0.907978552416-0.0202616112838-0.6536116060490.254230704444-0.114378223133-0.0002786374082410.8769620442210.035251952201-0.2180616134560.849166252231-0.1331156310290.9818316246339.847728216816.990711688217.0676347837
110.03927448072080.01302957364650.001640302729830.00919648415211-0.01821132296110.0692194925651-0.0142146399565-0.1715581673680.5256209331670.01881037080870.127974826689-0.3638458561180.2955062575930.5429660749350.0004212899911961.62119921435-0.00887678575319-0.3296427388141.34750785664-0.03783202598361.1959784404338.029184120310.885405324227.6621117504
12-0.02057928607930.0174594305731-0.01429076818770.0346465572622-0.08137050047830.0891889033247-0.4381687819770.4531702992140.3075047354750.2640555623850.2371603208890.2509490431960.324326459316-0.1693815592280.0009671671398041.03963279360.155464788199-0.3005023095180.991728355625-0.08705672453911.5368442870628.94216721884.6737402858917.2971407033
13-0.02262742516370.0996182023414-0.04485023414370.270967428054-0.1012060052910.170459289258-0.1205126993571.27275843604-0.974541189428-0.583401928612-0.092413874177-0.2613194149180.927032750181.3080611240.001190682820541.566421445960.5018987803490.09775436376721.28757333885-0.2644641828791.1960159644967.30382851828.8391091432-29.5176498708
14-0.2094813498040.01879777013420.105609729980.60014540449-0.124228766928-0.01550583358850.09102016768640.23297612820.1428975748920.00295122608289-0.114789635728-0.1607989246780.7483399187370.453660230124.7346557129E-50.9485521008690.0760407882780.08000914733741.0125293035-0.007898628518860.81498417203359.401891773436.4675767411-16.7472467151
151.15651892975-0.700318163141-0.3053665182790.8626331577140.4158142722812.394855170530.0527399231453-0.032667235059-0.188809986803-0.0657045682872-0.1014506838730.0273510902728-0.006948622442020.2128482247-7.0226342897E-60.6374023131730.01071739443450.0140197226450.5974940573940.02603680119810.62627299830560.501104333345.71075698243.83164898946
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 87 )AA6 - 871 - 82
22chain 'A' and (resid 88 through 259 )AA88 - 25983 - 254
33chain 'B' and (resid 2 through 12 )BB2 - 121 - 11
44chain 'B' and (resid 13 through 23 )BB13 - 2312 - 22
55chain 'B' and (resid 24 through 51 )BB24 - 5123 - 42
66chain 'B' and (resid 52 through 64 )BB52 - 6443 - 55
77chain 'B' and (resid 65 through 96 )BB65 - 9656 - 73
88chain 'B' and (resid 97 through 112 )BB97 - 11274 - 89
99chain 'B' and (resid 113 through 127 )BB113 - 12790 - 104
1010chain 'B' and (resid 128 through 139 )BB128 - 139105 - 116
1111chain 'B' and (resid 140 through 147 )BB140 - 147117 - 124
1212chain 'B' and (resid 148 through 160 )BB148 - 160125 - 137
1313chain 'C' and (resid 12 through 54 )CC12 - 541 - 38
1414chain 'C' and (resid 55 through 87 )CC55 - 8739 - 71
1515chain 'C' and (resid 88 through 258 )CC88 - 25872 - 242

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