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- PDB-5y9v: Crystal structure of diamondback moth ryanodine receptor N-termin... -

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Basic information

Entry
Database: PDB / ID: 5y9v
TitleCrystal structure of diamondback moth ryanodine receptor N-terminal domain
ComponentsRyanodine receptor 1
KeywordsTRANSPORT PROTEIN / diamondback moth / ryanodine receptor / ion channel
Function / homology
Function and homology information


ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / smooth endoplasmic reticulum / striated muscle contraction / sarcoplasmic reticulum membrane / calcium channel complex / sarcolemma / Z disc / intracellular calcium ion homeostasis
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/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 / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Ryanodine receptor 1
Similarity search - Component
Biological speciesPlutella xylostella (diamondback moth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.841 Å
AuthorsLin, L. / Yuchi, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Key Research and Development Program of China2017YFD0201403 China
CitationJournal: Insect Biochem. Mol. Biol. / Year: 2017
Title: Crystal structure of ryanodine receptor N-terminal domain from Plutella xylostella reveals two potential species-specific insecticide-targeting sites.
Authors: Lin, L. / Liu, C. / Qin, J. / Wang, J. / Dong, S. / Chen, W. / He, W. / Gao, Q. / You, M. / Yuchi, Z.
History
DepositionAug 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ryanodine receptor 1
B: Ryanodine receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3524
Polymers45,2242
Non-polymers1282
Water181
1
A: Ryanodine receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7042
Polymers22,6121
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ryanodine receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6482
Polymers22,6121
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.130, 170.130, 51.763
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 14 through 40 or (resid 41...
21(chain B and ((resid 14 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLYGLY(chain A and (resid 14 through 40 or (resid 41...AA14 - 4017 - 43
12PHEPHEPHEPHE(chain A and (resid 14 through 40 or (resid 41...AA4144
13VALVALGLYGLY(chain A and (resid 14 through 40 or (resid 41...AA14 - 20217 - 205
14VALVALGLYGLY(chain A and (resid 14 through 40 or (resid 41...AA14 - 20217 - 205
15VALVALGLYGLY(chain A and (resid 14 through 40 or (resid 41...AA14 - 20217 - 205
16VALVALGLYGLY(chain A and (resid 14 through 40 or (resid 41...AA14 - 20217 - 205
21VALVALVALVAL(chain B and ((resid 14 and (name N or name...BB1417
22VALVALTYRTYR(chain B and ((resid 14 and (name N or name...BB14 - 20117 - 204
23VALVALTYRTYR(chain B and ((resid 14 and (name N or name...BB14 - 20117 - 204
24VALVALTYRTYR(chain B and ((resid 14 and (name N or name...BB14 - 20117 - 204
25VALVALTYRTYR(chain B and ((resid 14 and (name N or name...BB14 - 20117 - 204

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Components

#1: Protein Ryanodine receptor 1


Mass: 22612.170 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plutella xylostella (diamondback moth) / Production host: Escherichia coli (E. coli) / References: UniProt: G8EME3
#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 4.78 Å3/Da / Density % sol: 74.28 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.841→44.24 Å / Num. obs: 20497 / % possible obs: 99.66 % / Redundancy: 6.6 % / Biso Wilson estimate: 87.14 Å2 / Net I/σ(I): 18.9
Reflection shellResolution: 2.84→2.94 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ILA

3ila


Resolution: 2.841→40.864 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.85
RfactorNum. reflection% reflection
Rfree0.2452 1985 9.69 %
Rwork0.2132 --
obs0.2163 20492 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 163.84 Å2 / Biso mean: 81.8934 Å2 / Biso min: 40.24 Å2
Refinement stepCycle: final / Resolution: 2.841→40.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 15 1 2554
Biso mean--109.56 78.99 -
Num. residues----347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042618
X-RAY DIFFRACTIONf_angle_d0.7023577
X-RAY DIFFRACTIONf_chiral_restr0.044428
X-RAY DIFFRACTIONf_plane_restr0.003457
X-RAY DIFFRACTIONf_dihedral_angle_d15.6851526
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1331X-RAY DIFFRACTION12.884TORSIONAL
12B1331X-RAY DIFFRACTION12.884TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8413-2.91230.40321350.39041260139596
2.9123-2.9910.42031440.333912931437100
2.991-3.0790.34261440.284213301474100
3.079-3.17840.29251390.250112991438100
3.1784-3.29190.27581440.25113261470100
3.2919-3.42370.29641390.24813171456100
3.4237-3.57940.31491390.256513001439100
3.5794-3.7680.25811420.227313301472100
3.768-4.00390.25871430.186313231466100
4.0039-4.31270.22241380.178613321470100
4.3127-4.74610.16521440.151713221466100
4.7461-5.43150.2111430.178113161459100
5.4315-6.8380.23781490.235413581507100
6.838-40.86810.23821420.216714011543100

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