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- PDB-6uha: Open-form Crystal Structure of Human RYR Receptor 3 ( 848-1055) -

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Basic information

Entry
Database: PDB / ID: 6uha
TitleOpen-form Crystal Structure of Human RYR Receptor 3 ( 848-1055)
ComponentsRyanodine receptor 3
KeywordsMETAL TRANSPORT / Type 3 Ryanodine Receptor / Alpha Fold / MCSG / Structural Genomics / Midwest Center for Structural Genomics / PSI-Biology
Function / homology
Function and homology information


calcium-induced calcium release activity / cellular response to magnesium ion / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cellular response to ATP / cellular response to caffeine / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / striated muscle contraction / release of sequestered calcium ion into cytosol ...calcium-induced calcium release activity / cellular response to magnesium ion / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cellular response to ATP / cellular response to caffeine / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / striated muscle contraction / release of sequestered calcium ion into cytosol / Ion homeostasis / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to calcium ion / calcium ion transmembrane transport / Stimuli-sensing channels / sarcolemma / Z disc / intracellular calcium ion homeostasis / calcium ion transport / protein homotetramerization / calmodulin binding / calcium ion binding / membrane
Similarity search - Function
: / Ryanodine receptor junctional solenoid repeat / 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 ...: / Ryanodine receptor junctional solenoid repeat / 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. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Ryanodine receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.855 Å
AuthorsWu, R. / Kim, Y. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Open-form Crystal Structure of Human RYR Receptor 3 ( 848-1055)
Authors: Wu, R. / Kim, Y. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionSep 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 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
B: Ryanodine receptor 3
A: Ryanodine receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4943
Polymers48,3882
Non-polymers1061
Water54030
1
B: Ryanodine receptor 3


Theoretical massNumber of molelcules
Total (without water)24,1941
Polymers24,1941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Ryanodine receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3002
Polymers24,1941
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.495, 94.495, 116.895
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Ryanodine receptor 3 / RyR3 / Brain ryanodine receptor-calcium release channel / Brain-type ryanodine receptor / Type 3 ...RyR3 / Brain ryanodine receptor-calcium release channel / Brain-type ryanodine receptor / Type 3 ryanodine receptor


Mass: 24194.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RYR3, HBRR / Plasmid: PLASMID / Details (production host): pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: Q15413
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG3350 15%, protein in co-crystallization with 30mM Caffeine and 10mM ATP

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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: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 11458 / % possible obs: 96 % / Redundancy: 2.8 % / Biso Wilson estimate: 50.43 Å2 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.042 / Rrim(I) all: 0.075 / Χ2: 0.737 / Net I/σ(I): 7.2 / Num. measured all: 31797
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.85-2.92.60.6685700.4980.4910.8340.9198.8
2.9-2.952.70.5196050.5930.3780.6460.91298.1
2.95-3.012.70.4445640.7110.3190.550.79998.1
3.01-3.072.60.3455930.7170.2560.4330.80697.9
3.07-3.142.60.3145660.7660.2310.3920.77796.3
3.14-3.212.70.2285640.8490.1660.2840.63496.9
3.21-3.292.80.2125980.8970.1490.2610.70798.2
3.29-3.382.80.1535830.9250.1070.1880.73498
3.38-3.482.80.1145790.950.0780.1390.58598.5
3.48-3.592.80.0865910.9630.060.1060.55797.7
3.59-3.722.70.0735760.9640.0510.0890.46997.8
3.72-3.872.60.0655680.9740.0460.080.5195.6
3.87-4.042.80.0535780.9820.0350.0640.4495.7
4.04-4.262.90.0465740.9820.0290.0550.43896.5
4.26-4.522.90.0465630.9750.0310.0560.45296.2
4.52-4.872.80.045690.9880.0270.0480.38895
4.87-5.362.80.0375650.9850.0250.0450.39793.1
5.36-6.1430.0385550.9780.0240.0460.6693.1
6.14-7.732.80.0375490.9830.0230.0440.38890.9
7.73-5030.0445480.970.0290.0533.05387.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575_1309refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4REV

4rev


Resolution: 2.855→47.248 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2678 520 4.82 %
Rwork0.2226 10264 -
obs0.2248 10784 90.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.95 Å2 / Biso mean: 51.3049 Å2 / Biso min: 10.02 Å2
Refinement stepCycle: final / Resolution: 2.855→47.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3343 0 7 30 3380
Biso mean--58.9 36.95 -
Num. residues----412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053426
X-RAY DIFFRACTIONf_angle_d0.9014638
X-RAY DIFFRACTIONf_chiral_restr0.044506
X-RAY DIFFRACTIONf_plane_restr0.006600
X-RAY DIFFRACTIONf_dihedral_angle_d23.9571338
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.855-3.14220.4171320.296216977
3.1422-3.59670.31861110.2505274996
3.5967-4.53090.23881320.2083272896
4.5309-47.2480.22411450.1976261891
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)
1-0.0005-0.00730.02180.0285-0.03920.0110.18090.0066-0.0933-0.13570.00570.06050.118-0.040400.30940.1226-0.2295-0.10690.3963-0.125170.737-1.99128.941
20.00850.0190.00720.00980.0050.00620.06090.0708-0.06490.0584-0.05540.10320.1348-0.1684-00.2041-0.0988-0.00060.09240.09020.335359.2524.31529.324
3-0.0023-0.0088-0.00310.0077-0.01730.00870.0474-0.01890.011-0.01170.0331-0.0391-0.01420.031300.36520.0068-0.15570.24350.07230.174881.8274.26837.414
40.0008-0.0016-0.00130.0020.0023-0.0008-0.0041-0.0055-0.0180.0230.02310.0085-0.001-0.007600.25540.07720.11820.226-0.01060.490859.39919.94736.309
50.0006-0.00610.006-0.00330.00370.00460.0322-0.00820.01280.06480.03060.02890.012-0.001-00.3007-0.1334-0.05830.13940.10840.11774.06513.41233.213
6-0.00150.00480.0005-0.0012-0.00860.00570.0493-0.01440.0090.0010.01490.0144-0.00080.040800.0907-0.1114-0.23720.0414-0.2062-0.187277.2740.0117.665
7-0.00090.00120.0026-0.0014-0.0034-0.0008-0.0086-0.0123-0.04330.06770.0196-0.00320.0257-0.01060-0.028-0.0046-0.46330.11460.0699-0.318860.844-7.18410.584
8-0.0001-0.00090.00130.0019-0.00020.00140.01230.03580.03250.016-0.0176-0.0028-0.00560.0333-00.27160.00860.09720.3350.09540.455.7981.0384.893
90.0007-0.00040.00230.0003-0.00230.00060.0367-0.00620.01490.01530.07010.0317-0.0289-0.0043-00.05720.206-0.10490.06340.04860.038768.7571.7597.152
10-0.0031-0.00270.00130.00720.00990.0048-0.11490.0325-0.1146-0.0117-0.0851-0.005-0.0450.0212-00.47810.0778-0.4786-0.01170.24480.030677.7075.50424.618
110.03140.0252-0.03340.0091-0.02290.01290.3179-0.09690.22220.05280.0198-0.0005-0.06910.011800.25960.02030.04610.21680.07190.248969.99547.51730.499
120.0057-0.0077-0.0030.0032-0.0062-0.0038-0.0009-0.0320.00440.0101-0.04260.03920.022-0.046-00.53010.1362-0.06370.50210.09160.815452.38337.41530.068
130.0012-0.0006-0.0033-0.0049-0.00270.00630.0437-0.0381-0.0015-0.0511-0.0230.0787-0.0010.0001-00.33030.06250.43880.04110.17670.157867.7951.80630.914
14-0.0150.0245-0.0027-0.0013-0.0178-0.00460.10610.0454-0.029-0.05960.0459-0.0025-0.04530.0695-00.3609-0.01330.25090.13260.2836-0.010378.58139.7322.591
150.000300.00220.00080.00010.0001-0.01480.0032-0.0022-0.0047-0.00130.01170.0154-0.013700.23570.0847-0.16810.19140.00550.313457.93929.88523.796
16-0.00040.00280.0022-0.00450.00180.00220.03350.027-0.0311-0.02570.02360.02640.015-0.027600.27450.08350.12830.13270.06990.118879.29134.37728.638
17-0.0066-0.0206-0.0065-0.0283-0.02570.01380.1089-0.05720.0167-0.063-0.08520.0070.043-0.00520-0.3903-0.07660.88420.21670.1185-0.873171.10649.94445.069
180.00020.0007-0.00370.0022-0.00050.0020.0491-0.0281-0.02-0.03330.01160.0040.00970.0339-00.1519-0.0529-0.10430.12290.08980.296155.90846.23855.113
19-0.0081-0.0041-0.0079-0.01030.02340.00860.1837-0.2571-0.0495-0.1409-0.04290.01060.1589-0.0621-0-0.020.24190.4597-0.0596-0.2591-0.277975.6743.10540.251
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 849:884 )B849 - 884
2X-RAY DIFFRACTION2( CHAIN B AND RESID 885:932 )B885 - 932
3X-RAY DIFFRACTION3( CHAIN B AND RESID 933:951 )B933 - 951
4X-RAY DIFFRACTION4( CHAIN B AND RESID 952:961 )B952 - 961
5X-RAY DIFFRACTION5( CHAIN B AND RESID 962:976 )B962 - 976
6X-RAY DIFFRACTION6( CHAIN B AND RESID 977:995 )B977 - 995
7X-RAY DIFFRACTION7( CHAIN B AND RESID 996:1005 )B996 - 1005
8X-RAY DIFFRACTION8( CHAIN B AND RESID 1006:1015 )B1006 - 1015
9X-RAY DIFFRACTION9( CHAIN B AND RESID 1016:1026 )B1016 - 1026
10X-RAY DIFFRACTION10( CHAIN B AND RESID 1027:1054 )B1027 - 1054
11X-RAY DIFFRACTION11( CHAIN A AND RESID 850:887 )A850 - 887
12X-RAY DIFFRACTION12( CHAIN A AND RESID 888:912 )A888 - 912
13X-RAY DIFFRACTION13( CHAIN A AND RESID 913:932 )A913 - 932
14X-RAY DIFFRACTION14( CHAIN A AND RESID 933:955 )A933 - 955
15X-RAY DIFFRACTION15( CHAIN A AND RESID 956:965 )A956 - 965
16X-RAY DIFFRACTION16( CHAIN A AND RESID 966:976 )A966 - 976
17X-RAY DIFFRACTION17( CHAIN A AND RESID 977:1005 )A977 - 1005
18X-RAY DIFFRACTION18( CHAIN A AND RESID 1006:1015 )A1006 - 1015
19X-RAY DIFFRACTION19( CHAIN A AND RESID 1016:1055 )A1016 - 1055

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