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- PDB-4n6j: Crystal structure of human Striatin-3 coiled coil domain -

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Basic information

Entry
Database: PDB / ID: 4n6j
TitleCrystal structure of human Striatin-3 coiled coil domain
ComponentsStriatin-3
KeywordsSIGNALING PROTEIN / WD40 / scaffolding protein / PP2A / CCM3 / CaM / CaV / Rassf.
Function / homology
Function and homology information


FAR/SIN/STRIPAK complex / armadillo repeat domain binding / negative regulation of intracellular estrogen receptor signaling pathway / negative regulation of hippo signaling / protein phosphatase 2A binding / small GTPase binding / response to estradiol / protein-macromolecule adaptor activity / calmodulin binding / negative regulation of DNA-templated transcription ...FAR/SIN/STRIPAK complex / armadillo repeat domain binding / negative regulation of intracellular estrogen receptor signaling pathway / negative regulation of hippo signaling / protein phosphatase 2A binding / small GTPase binding / response to estradiol / protein-macromolecule adaptor activity / calmodulin binding / negative regulation of DNA-templated transcription / neuronal cell body / dendrite / protein-containing complex binding / 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 / cytoplasm
Similarity search - Function
Striatin, N-terminal / : / Striatin family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...Striatin, N-terminal / : / Striatin family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.001 Å
AuthorsChen, C. / Shi, Z. / Zhou, Z.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Striatins contain a noncanonical coiled coil that binds protein phosphatase 2A A subunit to form a 2:2 heterotetrameric core of striatin-interacting phosphatase and kinase (STRIPAK) complex.
Authors: Chen, C. / Shi, Z. / Zhang, W. / Chen, M. / He, F. / Zhang, Z. / Wang, Y. / Feng, M. / Wang, W. / Zhao, Y. / Brown, J.H. / Jiao, S. / Zhou, Z.
History
DepositionOct 13, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Striatin-3
B: Striatin-3


Theoretical massNumber of molelcules
Total (without water)12,3132
Polymers12,3132
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-19 kcal/mol
Surface area7590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.064, 34.064, 161.388
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/peptide Striatin-3 / Cell cycle autoantigen SG2NA / S/G2 antigen


Mass: 6156.616 Da / Num. of mol.: 2 / Fragment: UNP residues 86-131 / Mutation: F99M, Y123M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GS2NA, SG2NA, STRN3 / Plasmid: HST-pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codonplus / References: UniProt: Q13033
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.2 Å3/Da / Density % sol: 43.97 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 0.2M MgCl2, 23% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9793 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 17, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 8009 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 16.2 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 43.11
Reflection shellResolution: 2→2.03 Å / Redundancy: 10 % / Rmerge(I) obs: 0.083 / Mean I/σ(I) obs: 24.19 / Num. unique all: 8009 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
AutoSolphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.001→29.5 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 25.95 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2521 1404 9.99 %RANDOM
Rwork0.2035 ---
obs0.2085 7949 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.001→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms790 0 0 114 904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008791
X-RAY DIFFRACTIONf_angle_d0.9241046
X-RAY DIFFRACTIONf_dihedral_angle_d14.063332
X-RAY DIFFRACTIONf_chiral_restr0.056113
X-RAY DIFFRACTIONf_plane_restr0.003136
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.001-2.07260.30641330.2151118897
2.0726-2.15560.27591450.19381296100
2.1556-2.25360.34691380.221290100
2.2536-2.37240.25841330.2104124599
2.3724-2.5210.29771480.22061254100
2.521-2.71550.24541420.20831261100
2.7155-2.98850.29391320.19961292100
2.9885-3.42040.21691520.20831296100
3.4204-4.30720.1781420.16931265100
4.3072-29.50350.26881390.22291266100

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