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- PDB-7rxq: Crystal structure of junctophilin-2 in complex with a CaV1.1 peptide -

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Basic information

Entry
Database: PDB / ID: 7rxq
TitleCrystal structure of junctophilin-2 in complex with a CaV1.1 peptide
Components
  • Junctophilin-2 N-terminal fragment
  • Voltage-dependent L-type calcium channel subunit alpha-1S
KeywordsSTRUCTURAL PROTEIN / complex / membrane / ion channel
Function / homology
Function and homology information


regulation of cardiac muscle tissue development / junctional membrane complex / positive regulation of muscle contraction / junctional sarcoplasmic reticulum membrane / phosphatidylinositol-5-phosphate binding / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / phosphatidic acid binding / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-4-phosphate binding ...regulation of cardiac muscle tissue development / junctional membrane complex / positive regulation of muscle contraction / junctional sarcoplasmic reticulum membrane / phosphatidylinositol-5-phosphate binding / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / phosphatidic acid binding / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / calcium ion transport into cytosol / positive regulation of ryanodine-sensitive calcium-release channel activity / phosphatidylserine binding / cellular response to caffeine / phosphatidylinositol-3,4,5-trisphosphate binding / calcium ion import across plasma membrane / voltage-gated calcium channel activity / calcium ion homeostasis / core promoter sequence-specific DNA binding / release of sequestered calcium ion into cytosol / regulation of ryanodine-sensitive calcium-release channel activity / T-tubule / phosphatidylinositol-4,5-bisphosphate binding / sarcoplasmic reticulum / muscle contraction / calcium ion transmembrane transport / DNA-binding transcription repressor activity, RNA polymerase II-specific / Z disc / transmembrane transporter binding / membrane => GO:0016020 / calmodulin binding / negative regulation of DNA-templated transcription / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding / plasma membrane
Similarity search - Function
Junctophilin / Voltage-dependent calcium channel, L-type, alpha-1S subunit / Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / MORN motif / MORN repeat / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain ...Junctophilin / Voltage-dependent calcium channel, L-type, alpha-1S subunit / Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / MORN motif / MORN repeat / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / 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 / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
ETHANOL / Voltage-dependent L-type calcium channel subunit alpha-1S / Junctophilin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 23, 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 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Junctophilin-2 N-terminal fragment
B: Voltage-dependent L-type calcium channel subunit alpha-1S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3406
Polymers38,0062
Non-polymers3344
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-36 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.394, 30.381, 96.679
Angle α, β, γ (deg.)90.000, 115.960, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Junctophilin-2 N-terminal fragment / JP2NT


Mass: 36122.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JPH2, JP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BR39
#2: Protein/peptide Voltage-dependent L-type calcium channel subunit alpha-1S / Calcium channel / L type / alpha-1 polypeptide / isoform 3 / skeletal muscle / Dihydropyridine ...Calcium channel / L type / alpha-1 polypeptide / isoform 3 / skeletal muscle / Dihydropyridine receptor alpha-1S subunit / DHPR / Voltage-gated calcium channel subunit alpha Cav1.1


Mass: 1883.094 Da / Num. of mol.: 1
Fragment: EERIFRRTGGLFGQVD correspond to UNP residues 1594-1609
Source method: obtained synthetically / Source: (synth.) Oryctolagus cuniculus (rabbit) / References: UniProt: P07293
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.02 Å3/Da / Density % sol: 39.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG3350, potassium sulphate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.03→44.34 Å / Num. obs: 19608 / % possible obs: 97.1 % / Redundancy: 3.18 % / Biso Wilson estimate: 30.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.034 / Rrim(I) all: 0.062 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.03-2.073.210.2251.89390.950.1490.27197.71
2.07-2.13.220.2082.19560.9390.1360.2597.15
2.1-2.143.130.22.39810.9460.1340.24296.37
2.14-2.192.930.1682.89540.9530.1150.20594.83
2.19-2.233.160.1563.39710.9720.1050.1996.91
2.23-2.293.30.1364.19670.9730.0890.16398.77
2.29-2.343.340.1433.99820.9730.0920.17198.59
2.34-2.413.30.1214.99820.9810.0790.14598.79
2.41-2.483.220.1125.39940.980.0730.13497.26
2.48-2.563.130.1065.89430.9790.070.12894.21
2.56-2.652.950.096.89620.9880.0610.10995.82
2.65-2.763.170.0868.29860.9870.0580.10496.57
2.76-2.883.310.07311.49670.9910.0470.08898.27
2.88-3.033.290.0631410050.9940.040.07598.24
3.03-3.223.230.05420.69880.9950.0350.06498.5
3.22-3.473.010.04823.89560.9960.0320.05894
3.47-3.823.30.04133.510140.9960.0260.04998.35
3.82-4.373.260.03934.79970.9960.0260.04798.13
4.37-5.5130.03333.710020.9990.0220.0496.53
5.51-44.353.110.03337.810620.9980.0220.0497.16

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RW4

7rw4


Resolution: 2.03→38.07 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2517 993 5.07 %0
Rwork0.2024 18593 --
obs0.2048 19586 96.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.75 Å2 / Biso mean: 44.0478 Å2 / Biso min: 13.33 Å2
Refinement stepCycle: final / Resolution: 2.03→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 18 127 2283
Biso mean--57.39 38.08 -
Num. residues----290
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.130.30361340.2542557269195
2.13-2.270.26751490.21472600274996
2.27-2.440.25491480.21452657280598
2.44-2.690.32141380.22732607274595
2.69-3.080.27971480.21932713286198
3.08-3.880.20641410.18152666280797
3.88-38.070.23951350.19012793292897
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)
13.56520.68280.64241.84280.9155.53290.0784-0.29230.28640.0996-0.09380.0504-0.0899-0.2120.0210.2225-0.0720.01810.1421-0.02650.206-2.480610.194260.5703
21.8773-0.5978-0.13242.42791.11524.17680.28980.79880.1468-0.3962-0.57030.396-0.3718-1.15980.24570.24990.1344-0.0410.6337-0.04540.2991-9.15992.251927.31
32.99990.42820.29343.44811.38533.3211-0.53881.1059-0.0409-0.3501-0.30460.2389-0.5923-0.94530.11481.0660.3058-0.36881.8313-0.00030.4529-16.04943.46512.6053
42.0166-0.37340.2331.03091.16911.86990.15470.1149-0.05680.064-0.29760.10.1435-0.47680.03610.2323-0.05430.00390.15050.04840.2333-6.5314-0.263843.3092
55.38271.57065.41842.43361.57937.6962-0.76010.3961.3528-0.5706-0.15980.1568-0.56360.03770.82810.4562-0.0267-0.0140.34240.06790.3611-0.466217.072756.0155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 70 )A1 - 70
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 319 )A71 - 319
3X-RAY DIFFRACTION3chain 'A' and (resid 320 through 364 )A320 - 364
4X-RAY DIFFRACTION4chain 'A' and (resid 365 through 437 )A365 - 437
5X-RAY DIFFRACTION5chain 'B' and (resid 1595 through 1609 )B0

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