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- PDB-6akl: Crystal structure of Striatin3 in complex with SIKE1 Coiled-coil ... -

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Basic information

Entry
Database: PDB / ID: 6akl
TitleCrystal structure of Striatin3 in complex with SIKE1 Coiled-coil domain
Components
  • Striatin-3
  • Suppressor of IKBKE 1
KeywordsPROTEIN BINDING / Coiled-coil domain / heterotrimer
Function / homology
Function and homology information


FAR/SIN/STRIPAK complex / armadillo repeat domain binding / negative regulation of intracellular estrogen receptor signaling pathway / TRAF6 mediated IRF7 activation / protein phosphatase 2A binding / small GTPase binding / SARS-CoV-1 activates/modulates innate immune responses / response to estradiol / TRAF3-dependent IRF activation pathway / calmodulin binding ...FAR/SIN/STRIPAK complex / armadillo repeat domain binding / negative regulation of intracellular estrogen receptor signaling pathway / TRAF6 mediated IRF7 activation / protein phosphatase 2A binding / small GTPase binding / SARS-CoV-1 activates/modulates innate immune responses / response to estradiol / TRAF3-dependent IRF activation pathway / calmodulin binding / negative regulation of DNA-templated transcription / dendrite / neuronal cell body / protein-containing complex binding / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SIKE family / SIKE family / Striatin, N-terminal / Striatin family / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat ...SIKE family / SIKE family / Striatin, N-terminal / Striatin family / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Striatin-3 / Suppressor of IKBKE 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsZhou, L. / Chen, M. / Zhou, Z.C.
CitationJournal: Cell Discov / Year: 2019
Title: Architecture, substructures, and dynamic assembly of STRIPAK complexes in Hippo signaling.
Authors: Tang, Y. / Chen, M. / Zhou, L. / Ma, J. / Li, Y. / Zhang, H. / Shi, Z. / Xu, Q. / Zhang, X. / Gao, Z. / Zhao, Y. / Cheng, Y. / Jiao, S. / Zhou, Z.
History
DepositionSep 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Suppressor of IKBKE 1
B: Suppressor of IKBKE 1
C: Striatin-3


Theoretical massNumber of molelcules
Total (without water)16,0343
Polymers16,0343
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-32 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.282, 42.382, 91.228
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Suppressor of IKBKE 1 / Suppressor of IKK-epsilon


Mass: 6440.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIKE1, SIKE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Variant (production host): CodonPlus / References: UniProt: Q9BRV8
#2: Protein/peptide Striatin-3 / Cell cycle autoantigen SG2NA / S/G2 antigen


Mass: 3153.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13033
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 35% (v/v) MPD; 0.1 M imidazole pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 16205 / % possible obs: 99.8 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.02 / Rrim(I) all: 0.07 / Net I/σ(I): 28
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 798 / CC1/2: 0.828 / Rpim(I) all: 0.376 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AKK

6akk


Resolution: 1.75→31.048 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.48
RfactorNum. reflection% reflection
Rfree0.2133 1536 9.98 %
Rwork0.1866 --
obs0.1893 15392 96.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→31.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 0 121 1097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071070
X-RAY DIFFRACTIONf_angle_d0.7741445
X-RAY DIFFRACTIONf_dihedral_angle_d8.799878
X-RAY DIFFRACTIONf_chiral_restr0.043158
X-RAY DIFFRACTIONf_plane_restr0.004190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.80660.2542950.2258847X-RAY DIFFRACTION67
1.8066-1.87110.29531350.22211226X-RAY DIFFRACTION95
1.8711-1.9460.28111470.21661273X-RAY DIFFRACTION100
1.946-2.03460.2451370.19281287X-RAY DIFFRACTION100
2.0346-2.14180.18971390.16931290X-RAY DIFFRACTION100
2.1418-2.2760.20391420.17351290X-RAY DIFFRACTION100
2.276-2.45160.19661470.17971313X-RAY DIFFRACTION100
2.4516-2.69820.19621430.17311282X-RAY DIFFRACTION100
2.6982-3.08840.22921490.18481320X-RAY DIFFRACTION100
3.0884-3.88980.18631470.16971348X-RAY DIFFRACTION100
3.8898-31.05330.21461550.20251380X-RAY DIFFRACTION98
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)
11.966-0.79230.56761.002-2.21886.5432-0.0551-0.2230.13130.19640.0225-0.0489-0.1554-0.01410.02880.43-0.0501-0.00260.3033-0.01620.25839.80694.069743.289
20.96-0.0427-0.45020.6993-0.02793.40610.04160.3311-0.20540.1663-0.0189-0.14130.14320.09720.06990.08140.04680.04660.06480.00990.142343.48288.7269.877
31.06410.06190.06911.12630.49524.78370.03540.1839-0.0880.1280.0263-0.1496-0.04280.0149-0.05470.0471-0.0055-0.00830.0727-0.0220.108339.148315.243810.9009
40.6931-0.6617-1.02871.70841.86412.26410.0018-0.15950.14520.12850.1419-0.2775-0.01220.5044-0.11810.1384-0.04120.04950.3026-0.0230.224847.306120.73665.718
56.5277-0.193-0.05880.8169-1.77674.0118-0.0313-0.36930.68730.1847-0.0505-0.0358-0.64840.12150.05960.33670.02510.03430.25950.00670.160341.414723.7255-4.0314
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 68 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 119 )
3X-RAY DIFFRACTION3chain 'B' and (resid 73 through 119 )
4X-RAY DIFFRACTION4chain 'C' and (resid 172 through 185 )
5X-RAY DIFFRACTION5chain 'C' and (resid 186 through 190 )

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