PDB-6uhb: Crystal Structure of Human RYR Receptor 3 (848-1055)

ID or keywords:

Entry

Database: PDB / ID: 6uhb

Title

Crystal Structure of Human RYR Receptor 3 (848-1055)

Components

Ryanodine receptor 3

Keywords

METAL 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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.504 Å

Authors

Wu, R. / Joachimiak, A. / Jedrzejczak, R. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To Be Published
Title: Crystal Structure of Human RYR Receptor 3 (848-1055)
Authors: Wu, R. / Jedrzejczak, R. / Joachimiak, A.

History

Deposition	Sep 27, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 5, 2020	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6uhb.cif.gz	185.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6uhb.ent.gz	154.1 KB	Display	PDB format
PDBx/mmJSON format	6uhb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uh/6uhb ftp://data.pdbj.org/pub/pdb/validation_reports/uh/6uhb	HTTPS FTP

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Related structure data

Similar structure data	6ecs-2 6khz-d 5ypb-d 3nqi-4 6ux8-1 5an4-d 6ne1-d 6nui-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#163 - Jul 2013 HIV Capsid similarity (6) #44 - Aug 2003 Calmodulin similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1)

Deposited unit

B: Ryanodine receptor 3

A: Ryanodine receptor 3

hetero molecules

50.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: Ryanodine receptor 3

hetero molecules

defined by author
25.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Ryanodine receptor 3

hetero molecules

defined by author
24.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	84.695, 88.444, 145.206
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

#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.: 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.83 Å³/Da / Density % sol: 56.58 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1 M Na2HPO4:Citric Acid pH 4.2, 1.6 M NaH2PO4/0.4 M K2HPO4

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97927 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97927 Å / Relative weight: 1

Reflection twin

Operator: -k,-h,-l / Fraction: 0.05

Reflection

Resolution: 2.5→50 Å / Num. obs: 18807 / % possible obs: 99.6 % / Redundancy: 6.4 % / R_merge(I) obs: 0.116 / R_pim(I) all: 0.05 / R_rim(I) all: 0.126 / Χ²: 0.908 / Net I/σ(I): 6.4 / Num. measured all: 120407

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.5-2.54	5.6	0.697	892	0.782	0.311	0.765	0.933	95.9
2.54-2.59	5.8	0.61	910	0.84	0.269	0.668	0.971	98.4
2.59-2.64	6	0.548	952	0.872	0.24	0.6	0.958	99.7
2.64-2.69	6.3	0.515	908	0.924	0.22	0.561	0.978	100
2.69-2.75	6.1	0.428	929	0.936	0.187	0.468	0.939	99.8
2.75-2.82	6.2	0.403	926	0.936	0.176	0.441	0.941	100
2.82-2.89	6.8	0.323	943	0.963	0.132	0.35	0.953	100
2.89-2.96	6.8	0.3	914	0.962	0.123	0.325	0.909	100
2.96-3.05	6.8	0.238	947	0.969	0.098	0.258	0.928	100
3.05-3.15	6.7	0.201	921	0.982	0.083	0.218	0.9	99.9
3.15-3.26	6.6	0.171	948	0.986	0.071	0.185	0.896	99.9
3.26-3.39	6.2	0.145	946	0.984	0.063	0.158	0.879	99.9
3.39-3.55	6.6	0.124	946	0.987	0.052	0.135	0.918	100
3.55-3.73	6.9	0.114	917	0.991	0.047	0.124	0.867	100
3.73-3.97	6.8	0.106	946	0.988	0.044	0.115	0.88	99.9
3.97-4.27	6.5	0.099	948	0.991	0.042	0.107	0.831	99.6
4.27-4.7	6.2	0.099	959	0.992	0.043	0.108	0.903	99.8
4.7-5.38	6.8	0.094	956	0.99	0.039	0.102	0.759	100
5.38-6.78	6.2	0.097	980	0.98	0.042	0.106	0.799	99.7
6.78-50	6.2	0.1	1019	0.98	0.045	0.11	1.053	99

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1-2575_1309	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.504→46.78 Å / Cross valid method: THROUGHOUT / σ(F): 4.21 / Phase error: 28.89

	R_factor	Num. reflection	% reflection
R_free	0.2763	922	5.36 %
R_work	0.2339	-	-
obs	0.2401	17195	89.83 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 123.1 Å² / B_iso mean: 43.0782 Å² / B_iso min: 11.97 Å²

Refinement step

Cycle: final / Resolution: 2.504→46.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3379	0	76	91	3546
B_iso mean	-	-	55.89	37.91	-
Num. residues	-	-	-	-	417

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	3535
X-RAY DIFFRACTION	f_angle_d	0.616	4773
X-RAY DIFFRACTION	f_chiral_restr	0.044	513
X-RAY DIFFRACTION	f_plane_restr	0.005	611
X-RAY DIFFRACTION	f_dihedral_angle_d	27.472	1376

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 6

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.5064-2.6634	0.3234	92	0.314	1833	1925	58
2.6634-2.869	0.3385	116	0.2996	2423	2539	78
2.869-3.1576	0.3317	159	0.2807	2961	3120	94
3.1576-3.6142	0.2576	166	0.2392	2987	3153	94
3.6142-4.5522	0.2436	167	0.1981	2992	3159	94
4.5522-37.772	0.2805	174	0.2224	3110	3284	94

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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	1.535	0.0846	0.286	1.5373	-0.0451	1.0733	0.03	-0.1978	0.0638	0.0427	-0.0123	-0.1732	-0.0959	-0.0707	-0.0301	0.1255	0.0155	-0.0111	0.1548	-0.0028	0.1696	14.8357	-27.3994	10.0903
2	1.3241	-0.6595	0.4081	2.4905	-0.1976	1.2893	-0.2148	-0.3918	-0.131	0.5653	0.0682	0.2864	-0.1299	-0.4032	0.1349	0.2386	0.0397	0.0153	0.2954	-0.0036	0.2899	8.2144	-20.5006	19.4413
3	1.0752	-0.4861	-0.0191	1.5582	-0.4071	1.3878	0.0358	-0.1327	0.6667	0.0104	0.0155	-0.3297	-0.3528	0.0723	-0.0832	0.248	-0.0015	-0.0332	0.227	-0.0591	0.5271	19.0209	-11.9041	9.5866
4	5.9874	3.0093	-2.8091	3.7631	-1.7364	3.1222	0.0542	-0.0974	-0.3792	0.1754	-0.1794	0.0136	-0.1673	0.114	0.0644	0.1704	0.0395	-0.0525	0.1087	-0.0332	0.2569	7.0173	-31.9596	1.598
5	1.8788	-1.5297	0.6854	1.7548	0.2377	1.2002	-0.5297	0.1857	0.5364	0.5658	0.2842	0.8501	-0.6738	-0.7032	0.009	0.2279	0.1411	0.1528	0.1239	-0.0594	0.5825	-8.6747	-33.5727	4.0448
6	1.4606	1.6245	1.2075	2.1681	0.404	1.9178	-0.1081	0.4338	0.3093	-0.1283	-0.1328	0.5019	-0.3585	0.1453	0.1588	0.2522	0.0269	0.043	0.1539	-0.0492	0.4151	14.8032	-21.5275	0.6574
7	0.9679	0.035	-0.6792	1.2733	-0.0406	1.9634	0.0162	-0.3258	0.1012	0.4908	0.0868	-0.1128	0.2255	0.6271	0.0564	0.3778	0.1109	-0.0214	0.5313	0.0443	0.2379	20.4344	-53.3315	31.8834
8	1.479	-0.8507	0.809	1.9127	-0.4578	2.9483	-0.1565	-0.0587	0.0011	0.0478	-0.4558	-0.9846	0.2552	1.0401	0.2157	0.4178	0.2936	-0.0091	0.7602	0.0028	0.4418	30.2602	-65.1462	20.0223
9	3.9518	-1.0553	-1.4073	4.0642	1.1137	4.3481	0.4577	0.2337	-0.0626	0.0093	-0.4141	-0.9352	-0.4147	1.5151	-0.1729	0.6138	0.0149	-0.1306	0.6263	-0.0131	0.2815	23.8022	-52.7339	34.6186
10	4.0359	0.7817	-2.4048	0.6319	-1.7971	4.9091	-0.3665	-0.8148	-0.2292	0.8217	0.2072	0.2658	0.7812	0.0431	0.0855	0.425	0.0993	0.183	0.4929	0.1699	0.4135	5.7901	-54.6785	39.8308
11	1.0904	-0.1632	-0.857	1.9805	0.8849	1.8972	-0.3547	0.4644	-0.1586	0.9664	-0.0012	0.0654	0.7965	0.0355	0.0461	0.6309	0.1799	0.1127	0.293	0.0208	0.227	12.4692	-66.0135	22.4328
12	2.3498	0.4929	-1.1407	1.9275	-0.9414	2.0519	0.8825	-0.851	0.0144	0.4738	-0.6614	-0.6451	-0.0182	0.4218	0.0756	0.2695	0.1445	-0.0939	0.1828	0.0776	0.4225	24.5293	-42.6414	23.6795
13	6.6304	-2.9445	-0.7688	3.848	0.3604	2.0006	0.3472	-0.1796	-0.1862	0.1367	-0.3217	-1.0357	-0.1553	0.069	0.1564	0.302	0.0628	0.0027	0.2529	0.0535	0.2704	29.9603	-41.2914	16.3568
14	2.1254	0.9748	-0.1165	3.7661	-1.4029	1.4682	0.0233	-0.3232	0.0512	0.2753	-0.2596	0.2981	-0.0651	0.3371	0.1047	0.2824	-0.005	-0.0088	0.2588	0.0266	0.1953	10.8194	-49.0331	27.8685

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 847 through 884 )	B	847 - 884
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 885 through 932 )	B	885 - 932
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 933 through 976 )	B	933 - 976
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 977 through 1001 )	B	977 - 1001
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1002 through 1026 )	B	0
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1027 through 1055 )	B	0
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 849 through 887 )	A	849 - 887
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 888 through 912 )	A	888 - 912
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 913 through 932 )	A	913 - 932
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 933 through 947 )	A	933 - 947
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 948 through 976 )	A	948 - 976
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 977 through 1010 )	A	977 - 1010
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 1011 through 1026 )	A	0
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 1027 through 1055 )	A	0

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