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- PDB-6uhi: Closed-form Crystal Structure of Chimera Bt-hRyR_12 from Bacteroi... -

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Basic information

Entry
Database: PDB / ID: 6uhi
TitleClosed-form Crystal Structure of Chimera Bt-hRyR_12 from Bacteroides thetaiotaomicron /human
ComponentsRyanodine receptor 1 chimera
KeywordsMETAL TRANSPORT / Chimera Ryanodine Receptor / Bacteroides thetaiotaomicron VPI-5482/human / Alpha Fold / PSI-BIOLOGY / MCSG / Structural Genomics / Midwest Center for Structural Genomics
Function / homology
Function and homology information


junctional sarcoplasmic reticulum membrane / calcium-induced calcium release activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / I band / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to caffeine / ossification involved in bone maturation / skin development ...junctional sarcoplasmic reticulum membrane / calcium-induced calcium release activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / I band / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to caffeine / ossification involved in bone maturation / skin development / cellular response to caffeine / outflow tract morphogenesis / intracellularly gated calcium channel activity / organelle membrane / smooth endoplasmic reticulum / voltage-gated calcium channel activity / skeletal muscle fiber development / release of sequestered calcium ion into cytosol / Ion homeostasis / sarcoplasmic reticulum membrane / calcium channel complex / regulation of cytosolic calcium ion concentration / cellular response to calcium ion / sarcoplasmic reticulum / muscle contraction / calcium channel activity / cytoplasmic vesicle membrane / Stimuli-sensing channels / sarcolemma / Z disc / calcium ion transport / cell cortex / protein homotetramerization / calmodulin binding / response to hypoxia / calcium ion binding / extracellular exosome / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Ryanodine receptor 1 / Ryanodine receptor, SPRY domain 2 / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain / RyR/IP3 receptor binding core, RIH domain superfamily ...Ryanodine receptor 1 / Ryanodine receptor, SPRY domain 2 / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain / RyR/IP3 receptor binding core, RIH domain superfamily / : / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Ryanodine receptor 1 / Ryanodine receptor
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsWu, R. / Jedrzejczak, R. / KIm, Y. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: to be published
Title: Closed-form Crystal Structure of Chimera Bt-hRyR_12 from Bacteroides thetaiotaomicron /human
Authors: Wu, R. / Kim, Y. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionSep 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ryanodine receptor 1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9182
Polymers25,8261
Non-polymers921
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.913, 51.913, 85.174
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32

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Components

#1: Protein Ryanodine receptor 1 chimera / RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / Skeletal ...RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / Skeletal muscle-type ryanodine receptor / Type 1 ryanodine receptor


Mass: 25825.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_2247, RYR1, RYDR / Plasmid: PMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: Q8A5J2, UniProt: P21817
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Sodium Citrate:citric Acid pH 5.5, 40% (v/v) PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.49
ReflectionResolution: 2.88→50 Å / Num. obs: 5563 / % possible obs: 95.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.036 / Rrim(I) all: 0.096 / Χ2: 0.875 / Net I/σ(I): 7.8 / Num. measured all: 37471
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.88-2.934.80.5552050.9640.2420.6081.23274
2.93-2.984.70.5972040.9480.2610.6550.8872.6
2.98-3.044.90.5732620.9390.2480.6280.96484.2
3.04-3.14.60.5712620.9180.2610.6320.96891.9
3.1-3.175.40.4792760.980.2150.5280.95796.2
3.17-3.245.50.7282990.8730.3260.8010.88698.7
3.24-3.326.70.4322820.980.1790.4680.94699.3
3.32-3.416.90.2912830.9960.1180.3150.912100
3.41-3.517.30.3212970.9870.1270.3460.967100
3.51-3.637.40.1522930.9970.060.1640.955100
3.63-3.767.50.1742990.9960.0680.1870.933100
3.76-3.917.60.1492870.9970.0580.160.946100
3.91-4.097.60.1082890.9960.0420.1160.947100
4.09-4.37.60.0883060.9960.0350.0950.885100
4.3-4.577.50.062870.9990.0240.0650.809100
4.57-4.927.60.0572830.9960.0220.0610.717100
4.92-5.427.50.0572960.9960.0220.0610.673100
5.42-6.27.60.0472990.9960.0180.0510.608100
6.2-7.817.60.0422900.9950.0170.0450.588100
7.81-506.90.042640.9930.0160.0431.13888.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ERV

4erv


Resolution: 2.88→44.96 Å / Cross valid method: FREE R-VALUE / σ(F): 6.83 / Phase error: 24.2845
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2727 181 4.76 %
Rwork0.2274 3624 -
obs0.235 3805 65.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.57 Å2
Refinement stepCycle: LAST / Resolution: 2.88→44.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1536 0 6 15 1557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00281574
X-RAY DIFFRACTIONf_angle_d0.53682123
X-RAY DIFFRACTIONf_chiral_restr0.0378225
X-RAY DIFFRACTIONf_plane_restr0.0034276
X-RAY DIFFRACTIONf_dihedral_angle_d26.6463624
LS refinement shellHighest resolution: 2.88 Å
RfactorNum. reflection% reflection
Rfree0.2828 181 -
Rwork0.2306 3449 -
obs--65.24 %
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)
12.62488674041-1.766336914171.990061169642.38136585087-1.490397313981.962565161840.111597724911-0.181756657978-0.2688678502510.2899388141690.0483835052549-0.1177158815430.3240692997280.1391731559540.2355227621350.7689023006530.3067970115770.1186105513330.2808023814850.1933047264980.3154699870586.15924927205-13.7722843075-11.5834911641
20.832019553424-0.1677195472640.5897671617470.7433587015050.1516704080010.524863106206-0.3049485821670.1325320072560.2147200260010.184434516319-0.194990033651-0.264253698854-0.2380707819910.0539213436174-0.2681536269070.152949975535-0.22714229813-0.0881650683230.293010094432-0.0143381258780.2061953639968.468737599547.58770852366-14.7963374379
30.07386514111660.0413050130265-0.04715337927670.1062364921370.02474175510820.0694054465204-0.109436572403-0.15136797499-0.09664513411320.03937946652730.19677953939-0.1008461233150.2052918783490.2438575608740.04137716359970.3993290089770.02183071035780.163701951890.826194997444-0.2193210695110.56316318273625.17828138199.423427757-13.3013420102
40.6036646823580.1269667644120.05872044669480.4735086662120.1227959708880.6553161136730.05235507410780.129352572882-0.1446185520390.04866951528540.0937820688445-0.2316450515780.06130655323610.3508880471890.309355444195-0.403558045257-0.0401340368866-0.175902450010.2782153381360.1368437805850.1572439085766.96250452092-2.67511832883-15.9463280774
50.2627388524660.202560179691-0.2404053455840.347228550082-0.1065417672410.4441827710950.07127075690910.02695590010720.324861208159-0.0124013846008-0.1844297193560.0442312207501-0.4223656666140.195329381943-0.06657664877520.313339616496-0.1026195053550.1239719093040.370451848240.01657101585820.424896895267-1.116393865347.55844800256-10.8618879433
60.4747458256410.369638201486-0.1001990029890.3402882055-0.04022660459820.99715477118-0.1744990305090.1091188033620.00828764468593-0.262499415932-0.0309646456947-0.2491832516420.2545724259610.567277705158-0.02740740427180.390907511610.01256455283740.0630695140490.2872832040620.08898968369520.16409413505712.7464415353-5.38403046159-5.7094495706
71.128902825070.457836837749-1.489593748870.196906788236-0.6325398107612.03415037528-0.06940888013030.324407751420.00515583537162-0.242465897225-0.1206636788610.018308116690.195314430313-0.01377969804450.0762034818250.43963614075-0.107941642444-0.03687044239870.8721975632240.1732786760680.50867197928423.0310054641-9.03773009261-3.96403581992
80.8509397345820.661733657241-0.5134907017861.57070694397-0.6987541475850.9756590463430.134889082757-0.252470604767-0.01037415827340.145864317974-0.0749047511366-0.0773971258892-0.06021780685010.1108625592050.07210074682760.176138630921-0.3557953943710.1103982679360.3205655426770.1549818141410.3773546386411.05404643270.485670330597-0.1520708223
90.2057152084920.06861803919580.3998275807720.511578941741-0.3736890127371.2903742533-0.0478569878133-0.02792763601240.2431487837090.01949225981720.00703915771982-0.189629473512-0.06798204313680.05294367649020.1015632757130.1090016785240.177886450695-0.1099719131610.151436609789-0.004131369260790.2685241218020.01385501570316.90699932798-9.46828606893
101.099535356520.560354741027-0.5065589469281.95947961594-1.172012672190.7370357110790.05651631995080.0130662166552-0.078684405682-0.04434545720370.121362826130.175915805028-0.00232733619326-0.163058017092-0.01883041009940.1699633166390.213365413955-0.2066346713230.498919761142-0.1833275519320.262582407261-10.0183241996-1.22865999639-7.84906726632
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 71 )
4X-RAY DIFFRACTION4chain 'A' and (resid 72 through 92 )
5X-RAY DIFFRACTION5chain 'A' and (resid 93 through 128 )
6X-RAY DIFFRACTION6chain 'A' and (resid 129 through 170 )
7X-RAY DIFFRACTION7chain 'A' and (resid 171 through 185 )
8X-RAY DIFFRACTION8chain 'A' and (resid 186 through 198 )
9X-RAY DIFFRACTION9chain 'A' and (resid 199 through 206 )
10X-RAY DIFFRACTION10chain 'A' and (resid 207 through 214 )

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