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- PDB-6uhh: Crystal Structure of Human RYR Receptor 3 ( 848-1055) in Complex ... -

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Basic information

Entry
Database: PDB / ID: 6uhh
TitleCrystal Structure of Human RYR Receptor 3 ( 848-1055) in Complex with ATP
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 ATP / cellular response to caffeine / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / striated muscle contraction / Ion homeostasis ...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 / Ion homeostasis / release of sequestered calcium ion into cytosol / calcium channel complex / sarcoplasmic reticulum membrane / 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, 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
ADENOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Ryanodine receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.138 Å
AuthorsWu, R. / Kim, Y. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Crystal Structure of Human RYR Receptor 3 ( 848-1055) in Complex with ATP
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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)100,30621
Polymers97,8664
Non-polymers2,44017
Water1,63991
1
A: Ryanodine receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2805
Polymers24,4661
Non-polymers8144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ryanodine receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1724
Polymers24,4661
Non-polymers7053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ryanodine receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9276
Polymers24,4661
Non-polymers4605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ryanodine receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9276
Polymers24,4661
Non-polymers4605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.043, 61.855, 279.128
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#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: 24466.447 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

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Non-polymers , 5 types, 108 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris:HCl pH 8.5, 20% (w/v) PEG 1000, protein in co-crystallization with 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: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.16
ReflectionResolution: 3.138→50 Å / Num. obs: 18902 / % possible obs: 96 % / Redundancy: 3 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.065 / Rrim(I) all: 0.118 / Χ2: 0.781 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.14-3.193.10.5479190.5930.3630.660.82997.7
3.19-3.2530.4569820.730.3040.5510.82797.4
3.25-3.312.90.3778690.7640.2580.460.77395.3
3.31-3.3830.2919490.8350.1940.3520.75997.2
3.38-3.463.20.2799620.8580.1810.3340.9598.6
3.46-3.543.20.2259400.8880.1450.2690.77799.3
3.54-3.623.10.1919740.8930.1240.2290.77399.2
3.62-3.723.20.1849360.8870.120.2210.88598.8
3.72-3.833.10.1459660.9340.0930.1740.70198.6
3.83-3.963.10.1399270.9390.0890.1660.896.8
3.96-4.12.90.1089300.9540.0690.1290.695.1
4.1-4.263.10.1019310.9480.0650.1210.58696.2
4.26-4.453.10.0939790.9630.0580.1110.60497.5
4.45-4.693.10.0879250.9640.0550.1030.56896.4
4.69-4.9830.0839280.9640.0540.10.52694.9
4.98-5.372.90.089370.9540.0510.0960.48994.2
5.37-5.913.10.0769630.9580.0470.090.79796
5.91-6.763.10.0759830.9620.0470.0890.995.9
6.76-8.512.80.0659370.9620.0420.0780.98691.3
8.51-502.70.0869650.940.0610.1061.57786.1

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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: 6UHB

6uhb


Resolution: 3.138→46.521 Å / Cross valid method: THROUGHOUT / σ(F): 3.66 / Phase error: 29.7
RfactorNum. reflection% reflection
Rfree0.2874 916 5.44 %
Rwork0.233 --
obs0.2372 16849 85.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.94 Å2 / Biso mean: 53.1847 Å2 / Biso min: 0.45 Å2
Refinement stepCycle: final / Resolution: 3.138→46.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6662 0 152 91 6905
Biso mean--72.16 32.23 -
Num. residues----821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046980
X-RAY DIFFRACTIONf_angle_d0.8389443
X-RAY DIFFRACTIONf_chiral_restr0.071018
X-RAY DIFFRACTIONf_plane_restr0.0051202
X-RAY DIFFRACTIONf_dihedral_angle_d16.0334293
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.138-3.33920.3903770.2753156049
3.3392-3.59680.29221070.2612265683
3.5968-3.95820.30611440.2328294592
3.9582-4.52990.29641870.208289890
4.5299-5.7030.2771720.2272293089
5.703-34.46380.26141730.2328296386
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)
12.72140.2134-0.73714.31210.23190.4791-0.0708-0.0213-0.33090.0529-0.19950.31510.0859-0.0847-0.46580.3031-0.1544-0.03590.0886-0.00070.12953.8115-15.17246.905
20.93520.3926-1.42350.3421-0.00124.0135-0.01720.8429-0.0452-0.2551-0.09420.1964-0.057-0.58080.14080.30870.0494-0.02380.48730.03040.22378.3239-4.9395-16.0659
31.04770.31860.11660.9444-0.55071.5414-0.29330.291-0.1333-0.61050.19910.23980.588-0.1104-0.20690.6136-0.20950.2040.09630.01850.38413.3039-9.5788-3.881
40.88230.24430.14671.25170.14091.25350.21180.09720.2717-0.1424-0.355-0.0056-0.311-0.35750.06980.13650.15460.06030.2824-0.00190.45911.89676.3742-7.8077
52.6705-1.7619-1.816.07511.35255.606-0.028-0.1362-0.4049-0.45890.10490.6259-0.1177-0.6723-0.12330.13090.0294-0.06210.52350.13910.185114.5156-14.27610.608
64.552.56962.49074.85062.0978.29920.12550.5882-0.242-0.8492-0.16410.65750.3292-0.78690.12020.34720.1429-0.12160.5-0.10660.468819.0494-24.4325-11.0537
71.0596-0.10040.37852.0776-0.48151.80980.0101-0.45610.16360.31590.2223-0.0118-0.36450.13310.03690.1481-0.0863-0.00540.2602-0.10380.045315.8476-2.03690.6202
81.00750.3711-0.00061.09110.4771.6638-0.011-0.4075-0.07650.4643-0.12670.12580.464-0.44320.10690.3814-0.03810.03440.32050.04550.15058.0668-5.0166-57.9223
91.53440.0036-0.41482.936-3.04536.83010.0821-0.77420.05580.36940.14340.5607-0.0626-0.7751-0.37230.1188-0.07120.13220.4526-0.03510.42275.8282-8.9242-66.6011
101.8746-0.597-0.11431.3993-0.76141.83770.09790.0271-0.0932-0.0816-0.1371-0.05570.16950.19560.00490.2353-0.0217-0.00120.225-0.09070.150514.69490.3548-64.5775
112.59370.6108-0.47346.2017-1.21515.72070.0391-0.7103-0.25581.3079-0.5330.09060.3715-0.01830.30980.5663-0.103-0.05650.46450.13520.2982-8.76425.6816-58.6746
124.2091-1.4618-1.01984.39081.02443.1869-0.32630.12540.3659-0.28550.0143-0.3766-0.3535-0.28660.04560.1621-0.0192-0.01110.3510.08370.263713.1753.3914-70.1094
131.7287-0.30633.15973.53080.21588.64260.0004-0.0059-0.4766-0.1874-0.3496-0.21410.951-0.00640.26430.24250.01620.05650.3943-0.00050.515442.5105-9.0003-26.9099
140.0071-0.01670.09230.0376-0.20861.1784-0.22350.19290.4181-0.20490.0092-0.6142-0.50740.34880.07040.4144-0.25330.1110.6962-0.01060.873347.88114.3715-31.3341
151.21110.00331.36290.455-0.4291.9401-0.0434-0.51030.29050.1979-0.1138-0.0133-0.4568-0.11520.0920.48990.06630.22541.3589-0.09250.835156.326114.5776-30.5742
163.76340.4966-1.565.64930.31496.16310.2177-0.15490.4403-0.38820.2755-0.8473-0.56220.8538-1.25530.42790.13770.00130.4164-0.32080.547146.1999-3.2274-25.3944
171.9297-0.791-0.07191.5851-0.77940.51820.22120.88260.102-0.8602-0.1462-0.1931-0.16990.2598-0.0230.7544-0.27060.14270.7356-0.00880.258536.54646.2032-38.0906
181.8807-0.38810.5295.88041.49212.94210.21780.19270.31270.39770.198-1.1532-0.1620.199-0.12170.11490.02380.13690.26790.05390.242741.48734.45-13.3677
195.60780.3412-0.55944.7813-1.49822.2796-0.33040.1560.05410.42550.2384-0.8889-0.34260.6354-0.01750.3103-0.0524-0.0770.4705-0.14330.234846.111712.311-8.54
203.65572.12981.28343.63780.11642.4776-0.4537-0.24460.04060.20840.02680.2348-0.1365-0.3320.35590.30610.08470.10560.3539-0.08230.21433.28864.0485-26.132
213.30340.0626-1.30652.9014-0.04066.2931-0.01320.49090.5111-0.4030.18590.1963-0.186-0.5818-0.07260.3965-0.12080.01490.5104-0.0950.35416.867530.0892-51.347
224.07133.003-1.63983.8709-0.13464.37610.08720.04970.33160.21920.3467-0.2815-0.34670.283-0.25990.6096-0.14310.16230.3878-0.19330.361421.42731.5584-37.6481
233.5295-0.6542-0.82482.69170.69852.5155-0.42570.20070.2418-0.33740.1553-0.148-0.06730.02150.04420.8955-0.35670.13620.6038-0.33590.694333.663640.0276-40.8482
243.38164.04494.33175.51965.02255.5829-0.57760.5874-0.2882-0.60690.5667-0.2377-0.46620.18590.13510.37970.17130.13790.5589-0.00270.471114.126933.7975-45.4546
252.3311.1111.28483.86890.83830.72620.19090.2027-0.47231.02040.3686-0.23850.2408-0.2114-0.49530.7325-0.18940.19760.7388-0.05630.385423.702627.0211-30.7074
262.83672.3417-2.3319.9346-3.04552.10.0649-0.30260.050.7152-0.0308-0.84440.61550.4093-0.02720.53610.1142-0.05850.6133-0.10670.331321.814816.8775-34.9087
274.22522.2145-1.23716.0608-2.89494.532-0.03750.47710.3551-0.2745-0.25660.2340.3781-0.35380.21120.35690.09930.06430.3913-0.03330.193517.114126.4506-54.4952
283.76262.7572-0.05039.1999-3.99252.22020.09930.40440.50220.27630.2352-0.691-0.3930.56-0.210.4860.09640.12280.5177-0.16310.426128.416733.719-62.5501
292.0060.41630.74617.0681-5.09844.2322-0.03480.6048-0.4115-0.8082-0.9042-0.80150.22520.50230.61550.29570.0997-0.06460.3448-0.06040.482126.153922.1322-50.3826
300.1991-0.15290.77122.15330.83313.99670.24140.1863-0.16190.4343-0.11410.34930.3622-0.79370.67970.434-0.14160.1460.4573-0.24070.39912.339518.9477-39.21
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 851 through 862 )A851 - 862
2X-RAY DIFFRACTION2chain 'A' and (resid 863 through 912 )A863 - 912
3X-RAY DIFFRACTION3chain 'A' and (resid 913 through 932 )A913 - 932
4X-RAY DIFFRACTION4chain 'A' and (resid 933 through 976 )A933 - 976
5X-RAY DIFFRACTION5chain 'A' and (resid 977 through 1001 )A977 - 1001
6X-RAY DIFFRACTION6chain 'A' and (resid 1002 through 1026 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1027 through 1054 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 849 through 912 )B849 - 912
9X-RAY DIFFRACTION9chain 'B' and (resid 913 through 933 )B913 - 933
10X-RAY DIFFRACTION10chain 'B' and (resid 934 through 1000 )B934 - 1000
11X-RAY DIFFRACTION11chain 'B' and (resid 1001 through 1026 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 1027 through 1054 )B0
13X-RAY DIFFRACTION13chain 'C' and (resid 852 through 873 )C852 - 873
14X-RAY DIFFRACTION14chain 'C' and (resid 874 through 893 )C874 - 893
15X-RAY DIFFRACTION15chain 'C' and (resid 894 through 912 )C894 - 912
16X-RAY DIFFRACTION16chain 'C' and (resid 913 through 933 )C913 - 933
17X-RAY DIFFRACTION17chain 'C' and (resid 934 through 976 )C934 - 976
18X-RAY DIFFRACTION18chain 'C' and (resid 977 through 1009 )C977 - 1009
19X-RAY DIFFRACTION19chain 'C' and (resid 1010 through 1026 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 1027 through 1053 )C0
21X-RAY DIFFRACTION21chain 'D' and (resid 849 through 865 )D849 - 865
22X-RAY DIFFRACTION22chain 'D' and (resid 866 through 884 )D866 - 884
23X-RAY DIFFRACTION23chain 'D' and (resid 885 through 912 )D885 - 912
24X-RAY DIFFRACTION24chain 'D' and (resid 913 through 933 )D913 - 933
25X-RAY DIFFRACTION25chain 'D' and (resid 934 through 966 )D934 - 966
26X-RAY DIFFRACTION26chain 'D' and (resid 967 through 976 )D967 - 976
27X-RAY DIFFRACTION27chain 'D' and (resid 977 through 1002 )D977 - 1002
28X-RAY DIFFRACTION28chain 'D' and (resid 1003 through 1026 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 1027 through 1038 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 1039 through 1055 )D0

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