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- PDB-6b29: Crystal structure of the second SH3 domain of STAC3 (309-364) -

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Basic information

Entry
Database: PDB / ID: 6b29
TitleCrystal structure of the second SH3 domain of STAC3 (309-364)
ComponentsSH3 and cysteine-rich domain-containing protein 3
KeywordsPROTEIN BINDING / excitation-contraction coupling / ion channel adaptor protein
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 / T-tubule / extrinsic component of cytoplasmic side of plasma membrane / 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 / T-tubule / extrinsic component of cytoplasmic side of plasma membrane / 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: 1.3 Å
AuthorsWong King Yuen, S.M. / Van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-119608 Canada
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural insights into binding of STAC proteins to voltage-gated calcium channels.
Authors: Wong King Yuen, S.M. / Campiglio, M. / Tung, C.C. / Flucher, B.E. / Van Petegem, F.
History
DepositionSep 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: SH3 and cysteine-rich domain-containing protein 3
B: SH3 and cysteine-rich domain-containing protein 3
C: SH3 and cysteine-rich domain-containing protein 3
D: SH3 and cysteine-rich domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)26,5304
Polymers26,5304
Non-polymers00
Water5,495305
1
A: SH3 and cysteine-rich domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)6,6331
Polymers6,6331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SH3 and cysteine-rich domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)6,6331
Polymers6,6331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SH3 and cysteine-rich domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)6,6331
Polymers6,6331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SH3 and cysteine-rich domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)6,6331
Polymers6,6331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.540, 57.960, 156.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 6632.563 Da / Num. of mol.: 4 / Fragment: residues 309-364
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M Bis-Tris, 22.5% PEG3350 and 0.2M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.3→39.205 Å / Num. obs: 55375 / % possible obs: 98.97 % / Redundancy: 6.7 % / Biso Wilson estimate: 14.57 Å2 / Rmerge(I) obs: 0.05199 / Net I/σ(I): 20.96
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 3.41 / % possible all: 91.63

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→39.205 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.55
RfactorNum. reflection% reflection
Rfree0.1887 2769 5 %
Rwork0.1568 --
obs0.1584 55372 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.9 Å2 / Biso mean: 21.7583 Å2 / Biso min: 8.09 Å2
Refinement stepCycle: final / Resolution: 1.3→39.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 0 305 2102
Biso mean---35.32 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131860
X-RAY DIFFRACTIONf_angle_d1.2232509
X-RAY DIFFRACTIONf_chiral_restr0.111289
X-RAY DIFFRACTIONf_plane_restr0.008322
X-RAY DIFFRACTIONf_dihedral_angle_d12.9821008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.32240.2161240.1732352247689
1.3224-1.34650.2531290.16772461259095
1.3465-1.37240.20351360.15782589272598
1.3724-1.40040.20771380.146326252763100
1.4004-1.43090.18111380.136726182756100
1.4309-1.46410.21721400.140526582798100
1.4641-1.50080.20121370.13725962733100
1.5008-1.54130.18851390.133926442783100
1.5413-1.58670.17261390.132626492788100
1.5867-1.63790.19651380.13326142752100
1.6379-1.69640.18981390.140226482787100
1.6964-1.76440.19411390.148626412780100
1.7644-1.84470.17341390.142826372776100
1.8447-1.94190.19551400.14726512791100
1.9419-2.06360.17211400.138326622802100
2.0636-2.22290.171400.147526562796100
2.2229-2.44660.181400.163826642804100
2.4466-2.80050.20871410.181326852826100
2.8005-3.5280.19591440.169627252869100
3.528-39.22280.18171490.163828282977100

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