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- PDB-7rxe: Crystal structure of junctophilin-2 -

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Basic information

Entry
Database: PDB / ID: 7rxe
TitleCrystal structure of junctophilin-2
ComponentsJunctophilin-2 N-terminal fragment
KeywordsSTRUCTURAL PROTEIN / muscle / membrane / ion channel
Function / homology
Function and homology information


regulation of cardiac muscle tissue development / junctional membrane complex / junctional sarcoplasmic reticulum membrane / phosphatidylinositol-5-phosphate binding / 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 ...regulation of cardiac muscle tissue development / junctional membrane complex / junctional sarcoplasmic reticulum membrane / phosphatidylinositol-5-phosphate binding / 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 / phosphatidylinositol-3,4,5-trisphosphate binding / calcium ion homeostasis / core promoter sequence-specific DNA binding / regulation of ryanodine-sensitive calcium-release channel activity / phosphatidylinositol-4,5-bisphosphate binding / sarcoplasmic reticulum / DNA-binding transcription repressor activity, RNA polymerase II-specific / Z disc / membrane => GO:0016020 / negative regulation of DNA-templated transcription / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / 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
CITRATE ANION / ISOPROPYL ALCOHOL / Junctophilin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 22, 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

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Assembly

Deposited unit
A: Junctophilin-2 N-terminal fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4925
Polymers36,1231
Non-polymers3694
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.121, 63.121, 149.677
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-633-

HOH

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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: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG4000, sodium citrate, isopropanol

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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: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.35→54.664 Å / Num. all: 15049 / Num. obs: 15049 / % possible obs: 100 % / Redundancy: 8.7 % / Biso Wilson estimate: 33.42 Å2 / Rpim(I) all: 0.105 / Rrim(I) all: 0.314 / Rsym value: 0.295 / Net I/av σ(I): 2.1 / Net I/σ(I): 5.4 / Num. measured all: 131028
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.35-2.489.21.4350.41961821380.4961.521.4351.5100
2.48-2.638.91.1520.51829920480.4061.2231.1521.8100
2.63-2.818.30.7990.81578019110.2920.8520.7992.499.9
2.81-3.038.90.5011.31607617980.1760.5320.5013.8100
3.03-3.3290.3252.11498216700.1130.3440.3255.6100
3.32-3.728.20.2083.21240915110.0770.2220.2087.6100
3.72-4.299.10.15941221513430.0550.1680.15910.4100
4.29-5.258.50.1364.4989611580.0480.1440.13610.7100
5.25-7.438.30.1314.876009170.0480.140.1319.3100
7.43-37.4197.50.1065.441535550.0410.1140.10611.899.1

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Processing

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

7rw4


Resolution: 2.35→36.85 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2606 679 4.53 %0
Rwork0.2175 14314 --
obs0.2196 14993 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.32 Å2 / Biso mean: 38.0939 Å2 / Biso min: 17.87 Å2
Refinement stepCycle: final / Resolution: 2.35→36.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 38 93 2512
Biso mean--43.44 36.78 -
Num. residues----312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062497
X-RAY DIFFRACTIONf_angle_d0.843371
X-RAY DIFFRACTIONf_chiral_restr0.044320
X-RAY DIFFRACTIONf_plane_restr0.006452
X-RAY DIFFRACTIONf_dihedral_angle_d18.053899
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.35-2.530.2951400.256227862926
2.53-2.790.34941300.258828042934
2.79-3.190.30871400.255628352975
3.19-4.020.27471260.200628813007
4.02-36.850.19631430.191230083151
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)
10.8703-0.669-0.18381.73690.63131.054-0.1134-0.33160.17650.29560.2176-0.23390.11460.1895-0.09910.27790.0631-0.02670.2416-0.01250.24464.9462-8.72420.3586
20.1031-0.2427-0.07930.63080.27280.5854-0.04440.08710.0382-0.0390.1795-0.15930.29090.1021-0.09660.4209-0.05620.12590.7352-0.12440.529-42.76686.575619.4456
30.66150.1780.04860.9395-0.060.8254-0.0169-0.0717-0.0037-0.07080.00080.343-0.0985-0.11710.00820.33040.09480.00190.2585-0.00940.3638-25.089217.93346.502
41.1145-0.74030.14411.52210.24420.38910.0991-0.0588-0.1041-0.0237-0.0202-0.00430.32370.0296-0.05120.2627-0.01410.02910.27260.00060.1913-2.4864-8.444914.0628
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 147 )A1 - 147
2X-RAY DIFFRACTION2chain 'A' and (resid 148 through 287 )A148 - 287
3X-RAY DIFFRACTION3chain 'A' and (resid 288 through 361 )A288 - 361
4X-RAY DIFFRACTION4chain 'A' and (resid 362 through 436 )A362 - 436

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