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- PDB-6b27: Crystal structure of human STAC2 Tandem SH3 Domains (296-411) in ... -

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Basic information

Entry
Database: PDB / ID: 6b27
TitleCrystal structure of human STAC2 Tandem SH3 Domains (296-411) in complex with a CaV1.1 II-III loop peptide
Components
  • SH3 and cysteine-rich domain-containing protein 2
  • Voltage-dependent L-type calcium channel subunit alpha-1S
KeywordsPROTEIN BINDING / Excitation-contraction coupling / ion channel adaptor protein
Function / homology
Function and homology information


skeletal muscle adaptation / positive regulation of voltage-gated calcium channel activity / extraocular skeletal muscle development / positive regulation of muscle contraction / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / myoblast fusion / endoplasmic reticulum organization / NCAM1 interactions / I band ...skeletal muscle adaptation / positive regulation of voltage-gated calcium channel activity / extraocular skeletal muscle development / positive regulation of muscle contraction / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / myoblast fusion / endoplasmic reticulum organization / NCAM1 interactions / I band / voltage-gated calcium channel complex / neuromuscular junction development / cellular response to caffeine / skeletal muscle contraction / calcium ion import across plasma membrane / voltage-gated calcium channel activity / small molecule binding / skeletal muscle fiber development / striated muscle contraction / release of sequestered calcium ion into cytosol / extrinsic component of cytoplasmic side of plasma membrane / T-tubule / skeletal system development / sarcoplasmic reticulum / molecular function activator activity / muscle contraction / calcium ion transmembrane transport / positive regulation of protein localization to plasma membrane / cytoplasmic side of plasma membrane / sarcolemma / calcium ion transport / calmodulin binding / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Stac2, SH3 domain / STAC1/2/3 / Unstructured on SH3 and cysteine-rich domain-containing protein 2 / Voltage-dependent calcium channel, L-type, alpha-1S subunit / Voltage-dependent calcium channel, L-type, alpha-1 subunit / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-dependent L-type calcium channel, IQ-associated domain ...Stac2, SH3 domain / STAC1/2/3 / Unstructured on SH3 and cysteine-rich domain-containing protein 2 / Voltage-dependent calcium channel, L-type, alpha-1S subunit / Voltage-dependent calcium channel, L-type, alpha-1 subunit / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / Variant SH3 domain / 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 Domains / Voltage-dependent channel domain superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Ion transport domain / Ion transport protein / Roll / Mainly Beta
Similarity search - Domain/homology
Voltage-dependent L-type calcium channel subunit alpha-1S / SH3 and cysteine-rich domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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.title / _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 2
B: SH3 and cysteine-rich domain-containing protein 2
C: SH3 and cysteine-rich domain-containing protein 2
D: SH3 and cysteine-rich domain-containing protein 2
E: SH3 and cysteine-rich domain-containing protein 2
F: SH3 and cysteine-rich domain-containing protein 2
G: Voltage-dependent L-type calcium channel subunit alpha-1S
H: Voltage-dependent L-type calcium channel subunit alpha-1S
I: Voltage-dependent L-type calcium channel subunit alpha-1S
J: Voltage-dependent L-type calcium channel subunit alpha-1S
K: Voltage-dependent L-type calcium channel subunit alpha-1S
L: Voltage-dependent L-type calcium channel subunit alpha-1S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,46922
Polymers90,63012
Non-polymers83910
Water11,169620
1
A: SH3 and cysteine-rich domain-containing protein 2
G: Voltage-dependent L-type calcium channel subunit alpha-1S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3935
Polymers15,1052
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-42 kcal/mol
Surface area7640 Å2
MethodPISA
2
B: SH3 and cysteine-rich domain-containing protein 2
H: Voltage-dependent L-type calcium channel subunit alpha-1S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2013
Polymers15,1052
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-15 kcal/mol
Surface area7780 Å2
MethodPISA
3
C: SH3 and cysteine-rich domain-containing protein 2
I: Voltage-dependent L-type calcium channel subunit alpha-1S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2013
Polymers15,1052
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-18 kcal/mol
Surface area7710 Å2
MethodPISA
4
D: SH3 and cysteine-rich domain-containing protein 2
J: Voltage-dependent L-type calcium channel subunit alpha-1S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2013
Polymers15,1052
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-23 kcal/mol
Surface area7800 Å2
MethodPISA
5
E: SH3 and cysteine-rich domain-containing protein 2
K: Voltage-dependent L-type calcium channel subunit alpha-1S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2725
Polymers15,1052
Non-polymers1673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-30 kcal/mol
Surface area7420 Å2
MethodPISA
6
F: SH3 and cysteine-rich domain-containing protein 2
L: Voltage-dependent L-type calcium channel subunit alpha-1S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2013
Polymers15,1052
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-12 kcal/mol
Surface area7310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.920, 114.650, 144.678
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SH3 and cysteine-rich domain-containing protein 2 / 24b2/STAC2 / Src homology 3 and cysteine-rich domain-containing protein 2


Mass: 13471.185 Da / Num. of mol.: 6 / Fragment: residues 296-411
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAC2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZMT1
#2: Protein/peptide
Voltage-dependent L-type calcium channel subunit alpha-1S / Calcium channel / L type / alpha-1 polypeptide / isoform 3 / skeletal muscle / Voltage-gated ...Calcium channel / L type / alpha-1 polypeptide / isoform 3 / skeletal muscle / Voltage-gated calcium channel subunit alpha Cav1.1


Mass: 1633.799 Da / Num. of mol.: 6 / Fragment: residues 747-760 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13698
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 5.5 / Details: 2.24M ammonium sulfate, 0.1M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.73→35 Å / Num. obs: 83341 / % possible obs: 99.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.035 / Rrim(I) all: 0.068 / Χ2: 1.033 / Net I/σ(I): 7.8 / Num. measured all: 301764
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.73-1.783.60.49368660.7660.2940.5770.91899.6
1.78-1.843.60.36868640.8490.2210.4320.95599.2
1.84-1.93.50.27268170.8640.1660.321.06398.3
1.9-1.983.80.23168930.9080.1350.2691.09799.6
1.98-2.073.70.17468900.9430.1020.2031.04299.4
2.07-2.183.60.12568960.9760.0740.1461.08799.4
2.18-2.323.50.14268210.8240.0860.1671.06298.4
2.32-2.493.80.08469740.9910.0490.0981.08699.6
2.49-2.753.70.07369460.9860.0430.0851.09999.5
2.75-3.143.60.04669770.9970.0270.0531.03198.8
3.14-3.963.70.03670930.8840.0210.0421.01599.6
3.96-353.50.02373040.9980.0140.0270.93298.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
DENZOdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→35 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.358 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.11
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 4075 4.9 %RANDOM
Rwork0.1786 ---
obs0.1804 79187 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 85.63 Å2 / Biso mean: 24.436 Å2 / Biso min: 12.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å2-0 Å2
2---0.92 Å20 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 1.73→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5797 0 42 620 6459
Biso mean--55.94 32.25 -
Num. residues----744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.026135
X-RAY DIFFRACTIONr_bond_other_d0.0020.025567
X-RAY DIFFRACTIONr_angle_refined_deg1.9351.9688352
X-RAY DIFFRACTIONr_angle_other_deg1.045312970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0095779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99824.3300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.237151000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6941549
X-RAY DIFFRACTIONr_chiral_restr0.1190.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216914
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021259
LS refinement shellResolution: 1.731→1.776 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 270 -
Rwork0.255 5842 -
all-6112 -
obs--99.25 %

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