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- PDB-5an3: Structure of an Sgt1-Skp1 Complex -

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Basic information

Entry
Database: PDB / ID: 5an3
TitleStructure of an Sgt1-Skp1 Complex
Components
  • SGT1
  • SUPPRESSOR OF KINETOCHORE PROTEIN 1
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / septin ring assembly / The NLRP3 inflammasome / regulation of exit from mitosis ...RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / septin ring assembly / The NLRP3 inflammasome / regulation of exit from mitosis / kinetochore assembly / vacuolar acidification / positive regulation of D-glucose transmembrane transport / protein neddylation / regulation of metabolic process / mitotic intra-S DNA damage checkpoint signaling / silent mating-type cassette heterochromatin formation / mitochondrial fusion / exit from mitosis / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / protein quality control for misfolded or incompletely synthesized proteins / Orc1 removal from chromatin / DNA replication origin binding / cullin family protein binding / Antigen processing: Ubiquitination & Proteasome degradation / regulation of protein-containing complex assembly / subtelomeric heterochromatin formation / endomembrane system / negative regulation of cytoplasmic translation / ubiquitin ligase complex / regulation of mitotic cell cycle / kinetochore / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / mitotic cell cycle / protein-folding chaperone binding / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / chromosome, telomeric region / protein ubiquitination / endoplasmic reticulum / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein Sgt1-like / SGS domain / SGS domain / SGS domain profile. / CS domain / CS domain / CS domain profile. / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily ...Protein Sgt1-like / SGS domain / SGS domain / SGS domain profile. / CS domain / CS domain / CS domain profile. / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / HSP20-like chaperone / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / 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 / Tetratricopeptide-like helical domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Suppressor of kinetochore protein 1 / Protein SGT1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.82 Å
AuthorsWillhoft, O. / Vaughan, C.K.
CitationJournal: Sci Rep / Year: 2017
Title: The crystal structure of the Sgt1-Skp1 complex: the link between Hsp90 and both SCF E3 ubiquitin ligases and kinetochores.
Authors: Willhoft, O. / Kerr, R. / Patel, D. / Zhang, W. / Al-Jassar, C. / Daviter, T. / Millson, S.H. / Thalassinos, K. / Vaughan, C.K.
History
DepositionSep 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SGT1
B: SGT1
C: SGT1
D: SUPPRESSOR OF KINETOCHORE PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)67,3634
Polymers67,3634
Non-polymers00
Water39622
1
A: SGT1
B: SGT1
C: SGT1


Theoretical massNumber of molelcules
Total (without water)52,4763
Polymers52,4763
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: SUPPRESSOR OF KINETOCHORE PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)14,8871
Polymers14,8871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.560, 94.560, 122.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein SGT1 / SUPPRESSOR OF G2 ALLELE OF SKP1


Mass: 17492.070 Da / Num. of mol.: 3 / Fragment: TPR DOMAIN, UNP RESIDUES 1-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): T7 EXPRESS LYSY/IQ / References: UniProt: Q08446
#2: Protein SUPPRESSOR OF KINETOCHORE PROTEIN 1 / CENTROMERE DNA-BINDING PROTEIN COMPLEX CBF3 SUBUNIT D / E3 UBIQUITIN LIGASE COMPLEX SCF SUBUNIT SKP1 / SKP1


Mass: 14886.524 Da / Num. of mol.: 1 / Fragment: BTBPOZ DOMAIN, UNP RESIDUES 1-35,65-158
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): T7 EXPRESS LYSY/IQ / References: UniProt: P52286
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.72 Å3/Da / Density % sol: 54.84 % / Description: NONE
Crystal growDetails: 0.325 M MGCL2, 22.5% PEG-6000, 0.1 M TRIS-HCL PH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979494
DetectorType: ADSC ADSC Q105 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979494 Å / Relative weight: 1
ReflectionResolution: 2.82→81.89 Å / Num. obs: 15826 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 21.5 % / Biso Wilson estimate: 86.92 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 29.2
Reflection shellResolution: 2.82→2.89 Å / Redundancy: 21.9 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
xia2data reduction
xia2data scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.82→19.88 Å / Cor.coef. Fo:Fc: 0.9337 / Cor.coef. Fo:Fc free: 0.8998 / SU R Cruickshank DPI: 1.211 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.105 / SU Rfree Blow DPI: 0.322 / SU Rfree Cruickshank DPI: 0.33
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 968 6.15 %RANDOM
Rwork0.202 ---
obs0.2043 15739 99.98 %-
Displacement parametersBiso mean: 70.85 Å2
Baniso -1Baniso -2Baniso -3
1--4.4323 Å20 Å20 Å2
2---4.4323 Å20 Å2
3---8.8646 Å2
Refine analyzeLuzzati coordinate error obs: 0.441 Å
Refinement stepCycle: LAST / Resolution: 2.82→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 0 22 3729
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013790HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.985166HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1658SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes68HARMONIC2
X-RAY DIFFRACTIONt_gen_planes576HARMONIC5
X-RAY DIFFRACTIONt_it3790HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.52
X-RAY DIFFRACTIONt_other_torsion2.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion515SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4425SEMIHARMONIC4
LS refinement shellResolution: 2.82→3.02 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2858 175 6.27 %
Rwork0.2421 2618 -
all0.245 2793 -
obs--99.98 %
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)
19.61232.3624-4.73535.4894-2.70797.7882-0.12690.0708-0.0052-0.6368-0.1398-0.9116-0.14340.77010.2667-0.1539-0.1309-0.0076-0.45650.0441-0.345327.82320.294226.5189
21.98620.6654-1.54756.5327-3.62896.214-0.0441-0.09510.20580.4242-0.11970.051-0.40520.32120.1638-0.2208-0.0157-0.0447-0.31770.0415-0.221620.75655.436948.8887
32.58230.53650.88274.65730.5272.66950.1367-0.10630.27490.266-0.1070.0358-0.0146-0.2883-0.0297-0.2394-0.03640.0032-0.20630.021-0.23494.897133.543229.2299
47.6982-5.8916-5.01486.08543.90686.0337-0.34120.2631-0.11850.5598-0.2410.30210.1492-0.58820.5822-0.1711-0.03890.0185-0.0876-0.2805-0.143-10.839348.276645.8423
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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