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

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Basic information

Entry
Database: PDB / ID: 6uhe
TitleClosed-form Crystal Structure of Human RYR Receptor 3 ( 848-1055)
ComponentsRyanodine receptor 3
KeywordsMETAL TRANSPORT / Type 3 Ryanodine Receptor / Alpha Fold / PSI-BIOLOGY / MCSG / Structural Genomics / Midwest Center for Structural Genomics
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 caffeine / cellular response to ATP / smooth endoplasmic reticulum / intracellularly gated calcium channel activity / Ion homeostasis / 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 caffeine / cellular response to ATP / smooth endoplasmic reticulum / intracellularly gated calcium channel activity / Ion homeostasis / release of sequestered calcium ion into cytosol / calcium channel complex / sarcoplasmic reticulum membrane / cellular response to calcium ion / Stimuli-sensing channels / sarcolemma / calcium ion transmembrane transport / Z disc / intracellular calcium ion homeostasis / calcium ion transport / protein homotetramerization / calmodulin binding / calcium ion binding / membrane
Similarity search - Function
Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / 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, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / 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. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / 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
Ryanodine receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.892 Å
AuthorsWu, R. / Kim, Y. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Closed-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 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ryanodine receptor 3
B: Ryanodine receptor 3
C: Ryanodine receptor 3
D: Ryanodine receptor 3


Theoretical massNumber of molelcules
Total (without water)97,1154
Polymers97,1154
Non-polymers00
Water37821
1
A: Ryanodine receptor 3


Theoretical massNumber of molelcules
Total (without water)24,2791
Polymers24,2791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ryanodine receptor 3


Theoretical massNumber of molelcules
Total (without water)24,2791
Polymers24,2791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ryanodine receptor 3


Theoretical massNumber of molelcules
Total (without water)24,2791
Polymers24,2791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ryanodine receptor 3


Theoretical massNumber of molelcules
Total (without water)24,2791
Polymers24,2791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.673, 64.673, 469.779
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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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: 24278.863 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 8.4
Details: 0.1 M Tris:HCl pH 8.5, 1.2 M Sodium Citrate Tribasic

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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: Jul 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 24385 / % possible obs: 98.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 84.13 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.038 / Rrim(I) all: 0.079 / Χ2: 0.7 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.95-33.80.69411110.840.3910.80.76599.2
3-3.063.80.54911360.8980.3110.6330.77997.3
3.06-3.114.20.56611770.90.3050.6440.75199.5
3.11-3.184.20.4311400.9230.2290.4880.73199.5
3.18-3.254.30.38612160.9440.2050.4380.72599.5
3.25-3.324.10.28211040.9540.1530.3220.76599.5
3.32-3.414.20.23512200.9740.1260.2670.7199.2
3.41-3.54.10.1711130.9780.0920.1940.73898.7
3.5-3.64.10.13611770.9860.0740.1550.75198
3.6-3.723.80.10411160.9860.0590.120.73797.8
3.72-3.8540.0911540.9870.0490.1030.73797.9
3.85-44.20.07911630.9890.0420.090.72999
4-4.194.20.06711450.9920.0360.0760.69998.9
4.19-4.414.10.05411760.9920.0290.0620.71398.9
4.41-4.6840.04711700.9920.0260.0540.64798.7
4.68-5.043.70.04111180.9880.0230.0470.55495.1
5.04-5.554.30.04311480.9910.0230.0490.55998.4
5.55-6.354.20.04111570.9910.0220.0470.47298.2
6.35-840.03811560.9910.0210.0430.48197.3
8-5040.04511380.9860.0250.0520.97993.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1-2575_1309refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.892→32.34 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 37.4
RfactorNum. reflection% reflection
Rfree0.3016 1235 5.06 %
Rwork0.2538 --
obs0.2561 24385 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 224.2 Å2 / Biso mean: 118.6869 Å2 / Biso min: 50.4 Å2
Refinement stepCycle: final / Resolution: 2.892→32.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6689 0 0 21 6710
Biso mean---92.14 -
Num. residues----825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046844
X-RAY DIFFRACTIONf_angle_d0.9389270
X-RAY DIFFRACTIONf_chiral_restr0.0451013
X-RAY DIFFRACTIONf_plane_restr0.0051198
X-RAY DIFFRACTIONf_dihedral_angle_d21.522663
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8921-3.00780.39231370.358255398
3.0078-3.14460.30891660.3509252899
3.1446-3.31020.37721680.32082574100
3.3102-3.51740.4721420.3048258499
3.5174-3.78860.30451130.2866262399
3.7886-4.16910.31441330.2519258199
4.1691-4.77070.2711080.2242259399
4.7707-6.00430.31231370.2563256898
6.0043-32.3360.23781310.2115254697
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)
19.73091.78185.16550.41920.92722.7241-0.4183-0.74650.7314-0.57540.48480.3424-0.72110.1618-0.36711.147-0.7207-0.09931.4518-0.14591.148919.272320.166614.0726
22.992-0.81920.84784.22332.73686.2509-0.382-0.4817-0.36580.1850.4721-0.0844-0.29530.6944-0.19640.5799-0.2434-0.05741.35110.2270.860122.572223.871938.095
30.35210.1465-0.89412.5837-2.62334.26310.06690.95890.10680.48651.04770.1636-0.13050.4685-1.04510.7409-0.6264-0.11761.5990.01731.041725.137320.991223.6811
41.8081-1.49063.18422.7504-2.07155.8683-0.34252.41611.16120.351-0.357-0.6917-0.21881.7330.29990.86-0.58820.05662.67230.18681.331540.589829.017420.2976
56.6647-6.2699-1.36726.29622.46434.1577-0.4579-0.49071.11590.10051.5773-1.1923-0.08951.0051-0.82261.105-0.4038-0.22251.3675-0.1810.884930.229832.629943.7311
62.6552-1.6186-0.66530.80610.82561.6529-0.28550.01830.6001-0.24970.06560.2494-0.2540.84810.23661.3881-0.6676-0.13311.34690.11020.952922.093831.856221.7217
79.1666-5.33592.92592.0203-0.61145.4712-0.6858-1.3399-1.02641.3036-0.51451.3260.1414-0.42340.50741.9458-1.14710.02651.68220.21780.93342.119124.360429.1468
82.9023-1.62120.08511.07650.89263.3531-0.2564-0.0312-0.02650.7259-0.27670.15520.32320.05340.29821.1063-0.69750.151.6210.09570.884.765228.283625.8539
90.1202-0.18810.1424-0.0077-0.3082.2158-0.14550.60460.834-0.1271-0.1033-0.2404-0.86760.67270.02141.363-0.8445-0.04281.5960.02161.091926.598134.600123.3136
103.40180.5003-0.21885.49640.2855.29420.8398-1.29970.96890.2207-0.71050.4239-1.73650.60240.04511.2521-0.67550.06851.1911-0.25390.885414.710524.14120.2789
110.64580.37171.37793.85191.30153.2862-0.37420.13070.8048-0.8532-0.37061.2087-1.5543-0.65970.39681.23020.1384-0.17430.7872-0.11220.9903-3.028916.9912-12.9589
122.8254-1.8771.61323.01341.60284.73210.0182-0.87131.46810.5139-0.93991.1987-0.6845-1.32530.48212.09840.3812-0.21481.5188-0.46921.4521-9.864219.6942-12.1635
139.44230.46650.08292.2921-0.1275.6320.2421-2.07580.6284-0.4794-0.1007-0.4408-2.11840.1225-0.0041.4194-0.3987-0.07590.6888-0.05250.80128.03523.5811-6.0137
144.29880.7592-0.41883.91360.1054.0323-0.8630.26851.0541-1.64540.19410.3655-1.42490.3480.26591.4783-0.04110.00810.7414-0.20980.89575.604114.2961-21.5369
157.3-0.95531.92375.309-0.67375.18570.08720.1757-0.2132-1.1570.190.6431-0.0130.88080.15340.9092-0.35070.02120.7881-0.02560.784913.40616.0665-17.5171
164.62880.4719-0.41883.6760.74625.2748-0.4608-0.7096-0.13810.0861-0.46531.76891.289-1.19730.61131.0898-0.39870.08881.0431-0.15781.10465.561113.86263.6483
175.2455-1.3285-1.40968.73960.32426.1480.1536-0.0169-0.3287-0.1516-1.58762.08071.0062-1.62091.20921.1809-0.46830.08811.7333-0.40021.3352-1.631910.48938.1831
184.8763-2.62831.27464.59034.06627.6098-0.66720.2499-1.25460.36620.41130.41631.094-1.23160.19291.1323-0.31850.0650.7726-0.11610.9538.7927.9034-7.3329
190.9713-0.98072.89692.0709-2.58638.5003-0.9280.0329-0.8668-0.72030.0962-0.71830.30430.20230.62271.183-0.45140.13821.2418-0.16321.38121.243615.4845-14.1924
201.4518-1.25451.97321.2615-0.94693.18950.5445-0.85340.0675-0.2115-0.626-0.45371.0855-0.83650.00130.9166-0.6253-0.03991.4337-0.07420.9831.6952-9.671912.9621
211.61541.49413.39996.58171.14787.99590.5067-0.30841.0021-0.7978-0.1292-0.68490.90180.98990.31311.0437-0.21670.21081.3731-0.05960.997136.53330.1698-6.8438
223.24510.23061.02950.6499-1.92715.55880.1735-0.5733-0.0530.1248-0.5974-0.8263-0.45380.52620.23811.001-0.29680.10271.129-0.15190.790435.5568-8.67335.1991
231.87562.53831.71843.50672.58872.0303-0.294-0.1064-2.0751-0.0498-0.94641.20470.4813-0.9060.53640.9424-1.4470.49482.3391-0.16181.700318.4497-19.612117.0157
245.8507-0.4197-2.84558.87920.44685.95810.4906-1.0875-0.4056-1.0362-0.8721.577-0.1104-0.89260.04370.9287-0.1581-0.18611.2801-0.23760.834522.3912-8.5489-6.4831
25-0.1010.22730.53593.96750.17741.7933-0.0017-0.93451.1093-0.1919-0.31590.4690.41010.0650.30210.6948-0.30080.05241.8581-0.05151.061929.6555-0.220315.4013
261.3469-0.51170.29177.1971-0.4636.49930.42110.62831.071-0.3343-0.6623-0.1302-0.024-0.09830.20350.8171-0.42720.04251.54920.00230.760938.005610.022811.8609
272.32822.68890.58546.13130.61331.5335-0.3348-0.12920.2249-0.5020.57311.1852-0.4242-1.3292-0.14070.7064-0.311-0.00122.2918-0.09180.998222.0094-2.793113.013
284.9509-1.81143.17230.6331-1.10672.0019-0.4681-0.43911.0907-0.2921-0.71521.1081-0.5426-2.67270.8146-0.7057-3.79451.06832.73091.16560.952819.0681-15.139522.5346
293.6191-0.88263.19350.95690.56525.1993-0.0396-0.1037-0.5671-0.4978-0.49050.5201-0.2443-0.54840.23691.9117-0.3184-0.24580.61740.01781.0074-13.1467-23.344-44.3174
304.3113-0.42721.88533.35132.8023.88370.1459-1.0240.39960.3496-0.63911.7471-0.3046-2.22870.41260.8683-0.0860.03581.1398-0.20720.8502-16.1671-8.6601-26.568
317.4376-0.3889-0.58894.40273.98917.7388-0.7473-0.3567-0.1405-0.7848-0.52291.5121-1.3306-0.70430.9430.9840.2575-0.27151.8375-0.51591.2866-21.9689-1.344-27.5204
324.7105-0.55562.20162.22511.83257.3735-0.0111-0.28880.5624-0.538-0.19950.34050.0323-0.42470.31120.9933-0.2256-0.08610.5574-0.00910.8821-8.7904-12.1667-32.9702
334.12390.3222-4.7240.0068-0.34675.56980.0880.6092-1.24260.6726-0.6805-0.7628-0.32270.83010.6531.3344-0.222-0.47121.23360.16581.2596-1.4284-26.78-27.9445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 848 through 862 )A848 - 862
2X-RAY DIFFRACTION2chain 'A' and (resid 863 through 914 )A863 - 914
3X-RAY DIFFRACTION3chain 'A' and (resid 915 through 933 )A915 - 933
4X-RAY DIFFRACTION4chain 'A' and (resid 934 through 945 )A934 - 945
5X-RAY DIFFRACTION5chain 'A' and (resid 946 through 967 )A946 - 967
6X-RAY DIFFRACTION6chain 'A' and (resid 968 through 1000 )A968 - 1000
7X-RAY DIFFRACTION7chain 'A' and (resid 1001 through 1010 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 1011 through 1026 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 1027 through 1054 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 848 through 866 )B848 - 866
11X-RAY DIFFRACTION11chain 'B' and (resid 867 through 896 )B867 - 896
12X-RAY DIFFRACTION12chain 'B' and (resid 897 through 912 )B897 - 912
13X-RAY DIFFRACTION13chain 'B' and (resid 913 through 933 )B913 - 933
14X-RAY DIFFRACTION14chain 'B' and (resid 934 through 967 )B934 - 967
15X-RAY DIFFRACTION15chain 'B' and (resid 968 through 976 )B968 - 976
16X-RAY DIFFRACTION16chain 'B' and (resid 977 through 1009 )B977 - 1009
17X-RAY DIFFRACTION17chain 'B' and (resid 1010 through 1026 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 1027 through 1046 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 1047 through 1053 )B0
20X-RAY DIFFRACTION20chain 'C' and (resid 847 through 886 )C847 - 886
21X-RAY DIFFRACTION21chain 'C' and (resid 887 through 896 )C887 - 896
22X-RAY DIFFRACTION22chain 'C' and (resid 897 through 932 )C897 - 932
23X-RAY DIFFRACTION23chain 'C' and (resid 933 through 947 )C933 - 947
24X-RAY DIFFRACTION24chain 'C' and (resid 948 through 967 )C948 - 967
25X-RAY DIFFRACTION25chain 'C' and (resid 968 through 1009 )C968 - 1009
26X-RAY DIFFRACTION26chain 'C' and (resid 1010 through 1026 )C0
27X-RAY DIFFRACTION27chain 'C' and (resid 1027 through 1047 )C0
28X-RAY DIFFRACTION28chain 'C' and (resid 1048 through 1054 )C0
29X-RAY DIFFRACTION29chain 'D' and (resid 848 through 862 )D848 - 862
30X-RAY DIFFRACTION30chain 'D' and (resid 863 through 896 )D863 - 896
31X-RAY DIFFRACTION31chain 'D' and (resid 897 through 912 )D897 - 912
32X-RAY DIFFRACTION32chain 'D' and (resid 913 through 1046 )D913 - 1046
33X-RAY DIFFRACTION33chain 'D' and (resid 1047 through 1055 )D0

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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