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- PDB-6uy9: Crystal structure of the STAC3 tandem SH3 domains - P269R, W284S -

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Basic information

Entry
Database: PDB / ID: 6uy9
TitleCrystal structure of the STAC3 tandem SH3 domains - P269R, W284S
ComponentsSH3 and cysteine-rich domain-containing protein 3
KeywordsPROTEIN BINDING / Protein Binding Domains
Function / homology
Function and homology information


positive regulation of voltage-gated calcium channel activity / neuromuscular synaptic transmission / voltage-gated calcium channel complex / skeletal muscle contraction / skeletal muscle fiber development / extrinsic component of cytoplasmic side of plasma membrane / T-tubule / positive regulation of protein localization to plasma membrane / cytoplasmic side of plasma membrane / synapse ...positive regulation of voltage-gated calcium channel activity / neuromuscular synaptic transmission / voltage-gated calcium channel complex / skeletal muscle contraction / skeletal muscle fiber development / extrinsic component of cytoplasmic side of plasma membrane / T-tubule / positive regulation of protein localization to plasma membrane / cytoplasmic side of plasma membrane / synapse / nucleoplasm / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Stac3, first SH3 domain / STAC1/2/3 / Unstructured on SH3 and cysteine-rich domain-containing protein 2 / Variant SH3 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily ...Stac3, first SH3 domain / STAC1/2/3 / Unstructured on SH3 and cysteine-rich domain-containing protein 2 / Variant SH3 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
SH3 and cysteine-rich domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRufenach, B. / Van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-159601 Canada
CitationJournal: Structure / Year: 2020
Title: Multiple Sequence Variants in STAC3 Affect Interactions with CaV1.1 and Excitation-Contraction Coupling.
Authors: Rufenach, B. / Christy, D. / Flucher, B.E. / Bui, J.M. / Gsponer, J. / Campiglio, M. / Van Petegem, F.
History
DepositionNov 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 11, 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

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Assembly

Deposited unit
A: SH3 and cysteine-rich domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2384
Polymers14,0911
Non-polymers1473
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.032, 29.331, 57.143
Angle α, β, γ (deg.)90.000, 129.620, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

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Components

#1: Protein SH3 and cysteine-rich domain-containing protein 3


Mass: 14090.955 Da / Num. of mol.: 1 / Mutation: P269R, W284S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96MF2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.92 Å3/Da / Density % sol: 36.1 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M NaOAc, 0.2M LiSO4, 24% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→41.683 Å / Num. obs: 12785 / % possible obs: 88.59 % / Redundancy: 2.6 % / Rpim(I) all: 0.046 / Net I/σ(I): 23.3
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 2 % / Num. unique obs: 762 / Rpim(I) all: 0.158 / % possible all: 53.51

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.1_3469refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B26, 6B29

6b26

6b29


Resolution: 1.6→41.683 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.5
RfactorNum. reflection% reflection
Rfree0.2092 635 4.97 %
Rwork0.1821 --
obs0.1835 12785 88.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.06 Å2 / Biso mean: 19.1255 Å2 / Biso min: 5.29 Å2
Refinement stepCycle: final / Resolution: 1.6→41.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 21 141 1119
Biso mean--29.82 27.79 -
Num. residues----123
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.72380.2983680.2388165660
1.7238-1.89730.20961180.1952241989
1.8973-2.17180.19021390.1689262096
2.1718-2.73620.21181550.1815268498
2.7362-41.6830.20721550.1777277199
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)
14.3443.22532.56552.31881.80921.549-0.0543-0.05460.75090.121-0.12890.0476-0.09530.01750.22010.124-0.02170.02660.13870.01860.202614.37533.326211.8016
25.2769-0.95070.80252.8769-1.36862.39640.0482-0.0494-0.45280.01370.13260.01110.2724-0.0034-0.1630.10370.0322-0.00690.1204-0.00660.09747.5011-12.634412.6192
37.69170.5595.95047.33471.72194.72960.42690.2573-0.25320.0746-0.0307-0.00170.58290.1943-0.38120.09010.00110.03830.08060.00830.06878.6238-13.063913.7109
42.62-0.2015-0.22545.21692.13641.6375-0.29030.12181.1518-0.24230.27260.1483-0.29340.2583-0.08930.04440.03080.05560.0171-0.03370.1057-1.69020.00310.5402
53.118-0.80852.11581.2226-1.27332.85520.04860.00690.11960.02290.01050.0679-0.010.0195-0.06920.07390.01420.03630.0469-0.01610.0866-14.7655-1.747.0545
64.832-6.3-3.60878.69143.94385.72130.00771.1839-0.0267-0.2901-0.09160.0629-0.07260.57130.01040.07790.03840.03660.1475-0.08180.0765-9.4591-1.97313.8543
71.92010.19930.75012.4551-0.79747.36770.08920.01420.11440.10910.0284-0.0289-0.13860.1514-0.13480.04920.01040.03080.0662-0.02170.0864-13.19760.438912.0518
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 242 through 251 )A242 - 251
2X-RAY DIFFRACTION2chain 'A' and (resid 252 through 289 )A252 - 289
3X-RAY DIFFRACTION3chain 'A' and (resid 290 through 300 )A290 - 300
4X-RAY DIFFRACTION4chain 'A' and (resid 301 through 313 )A301 - 313
5X-RAY DIFFRACTION5chain 'A' and (resid 314 through 343 )A314 - 343
6X-RAY DIFFRACTION6chain 'A' and (resid 344 through 352 )A344 - 352
7X-RAY DIFFRACTION7chain 'A' and (resid 353 through 364 )A353 - 364

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