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- PDB-7rw4: Crystal structure of junctophilin-1 -

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Basic information

Entry
Database: PDB / ID: 7rw4
TitleCrystal structure of junctophilin-1
ComponentsJunctophilin-1
KeywordsSTRUCTURAL PROTEIN / Muscle / membrane / ion channel
Function / homology
Function and homology information


junctional membrane complex / junctional sarcoplasmic reticulum membrane / calcium ion transport into cytosol / muscle organ development / structural constituent of muscle / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum / Z disc / membrane => GO:0016020 / endoplasmic reticulum membrane ...junctional membrane complex / junctional sarcoplasmic reticulum membrane / calcium ion transport into cytosol / muscle organ development / structural constituent of muscle / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum / Z disc / membrane => GO:0016020 / endoplasmic reticulum membrane / nucleoplasm / plasma membrane
Similarity search - Function
Junctophilin / Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / MORN motif / MORN repeat
Similarity search - Domain/homology
ACETATE ION / Junctophilin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.31 Å
AuthorsYang, Z. / Panwar, P. / Van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structures of the junctophilin/voltage-gated calcium channel interface reveal hot spot for cardiomyopathy mutations.
Authors: Yang, Z.F. / Panwar, P. / McFarlane, C.R. / Tuinte, W.E. / Campiglio, M. / Van Petegem, F.
History
DepositionAug 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: 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 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Junctophilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4157
Polymers37,9291
Non-polymers4866
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.076, 55.203, 142.447
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 Junctophilin-1 / JP-1 / Junctophilin type 1


Mass: 37928.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JPH1, JP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HDC5
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Sodium Acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.31→40 Å / Num. obs: 84406 / % possible obs: 99.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 14.45 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.031 / Rrim(I) all: 0.079 / Χ2: 0.901 / Net I/σ(I): 8.5 / Num. measured all: 528933
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.31-1.3451.09754550.5020.5421.2280.97697.6
1.34-1.375.70.93454950.6390.4241.0280.97899.3
1.37-1.416.40.71755970.7970.3030.780.97100
1.41-1.456.40.5555480.8750.2320.5980.962100
1.45-1.56.20.4255760.9160.1810.4590.95199.9
1.5-1.556.40.31955800.9450.1360.3470.962100
1.55-1.626.40.22855840.9710.0960.2480.92499.9
1.62-1.696.50.18156040.9790.0760.1970.92599.9
1.69-1.786.30.12556270.9870.0540.1360.89399.9
1.78-1.896.30.09556010.9910.040.1030.87599.7
1.89-2.046.70.0756050.9940.0290.0760.84799.7
2.04-2.246.40.05756570.9950.0240.0630.81599.8
2.24-2.566.50.05356940.9950.0220.0580.815100
2.56-3.236.40.04857750.9960.0210.0520.8100
3.23-406.10.04860080.9960.0210.0520.86499.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.31→37.48 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 14.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.168 3924 5.03 %
Rwork0.1366 74052 -
obs0.1381 77976 92.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.94 Å2 / Biso mean: 20.5321 Å2 / Biso min: 9.32 Å2
Refinement stepCycle: final / Resolution: 1.31→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2460 0 40 327 2827
Biso mean--45.1 33.72 -
Num. residues----321
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.31-1.330.2932160.232231833411
1.33-1.340.2705570.212690696333
1.34-1.360.25321150.19781800191564
1.36-1.380.22981340.18572446258085
1.38-1.40.19221250.17852652277795
1.4-1.420.2291550.16872815297098
1.42-1.440.22361330.17552803293699
1.44-1.470.23521340.15382840297499
1.47-1.490.21271490.129127892938100
1.49-1.520.16461480.117928492997100
1.52-1.550.13981620.112427962958100
1.55-1.580.15331610.11228773038100
1.58-1.610.15641510.105827932944100
1.61-1.650.15191790.103728273006100
1.65-1.690.16471610.107228372998100
1.69-1.740.13771310.110928562987100
1.74-1.790.14581570.106628443001100
1.79-1.850.15791520.119328483000100
1.85-1.910.17681660.120128713037100
1.91-1.990.13941430.11182828297199
1.99-2.080.14581730.110828513024100
2.08-2.190.14091480.120628683016100
2.19-2.330.15221330.124929133046100
2.33-2.510.1781480.138228983046100
2.51-2.760.1671520.153329143066100
2.76-3.160.18781380.164129353073100
3.16-3.980.18471480.140429783126100
3.98-37.480.15581550.153931003255100

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