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- PDB-8dvc: Receptor ShHTL5 from Striga hermonthica in complex with strigolac... -

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Basic information

Entry
Database: PDB / ID: 8dvc
TitleReceptor ShHTL5 from Striga hermonthica in complex with strigolactone agonist GR24
ComponentsHyposensitive to light 5
KeywordsSIGNALING PROTEIN / Striga hermonthica / strigolactone / signalling / receptor / ShHTL5 / alpha/beta hydrolase / Signalling protein / receptor-agonist complex
Function / homologyAlpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / metal ion binding / Chem-TZU / Hyposensitive to light 5
Function and homology information
Biological speciesStriga hermonthica (purple witchweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.638 Å
AuthorsArellano-Saab, A. / Skarina, T. / Yim, V. / Savchenko, A. / Stogios, P.J. / McCourt, P.
Funding support Canada, Mexico, 5items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)06752 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)507992 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)00356 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)04298 Canada
Consejo Nacional de Ciencia y Tecnologia (CONACYT) Mexico
CitationJournal: Nat.Plants / Year: 2023
Title: Structural analysis of a hormone-bound Striga strigolactone receptor.
Authors: Arellano-Saab, A. / Skarina, T. / Xu, Z. / McErlean, C.S.P. / Savchenko, A. / Lumba, S. / Stogios, P.J. / McCourt, P.
History
DepositionJul 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hyposensitive to light 5
B: Hyposensitive to light 5
C: Hyposensitive to light 5
D: Hyposensitive to light 5
E: Hyposensitive to light 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,39738
Polymers149,8755
Non-polymers3,52233
Water3,819212
1
A: Hyposensitive to light 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,85510
Polymers29,9751
Non-polymers8809
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hyposensitive to light 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6617
Polymers29,9751
Non-polymers6866
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hyposensitive to light 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6207
Polymers29,9751
Non-polymers6456
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hyposensitive to light 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6347
Polymers29,9751
Non-polymers6596
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Hyposensitive to light 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6277
Polymers29,9751
Non-polymers6526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.269, 352.967, 124.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Hyposensitive to light 5 / ShHTL5


Mass: 29975.021 Da / Num. of mol.: 5 / Mutation: S95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Striga hermonthica (purple witchweed) / Gene: ShHTL5 / Plasmid: p15Tv lic / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0M5I297

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Non-polymers , 5 types, 245 molecules

#2: Chemical
ChemComp-TZU / (3R,3aR,8bS)-3-({[(2R)-4-methyl-5-oxo-2,5-dihydrofuran-2-yl]oxy}methyl)-3,3a,4,8b-tetrahydro-2H-indeno[1,2-b]furan-2-one / GR24


Mass: 300.306 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C17H16O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.65 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, 8 mM GR24, 1% DMSO, 1% isopropanol, cryoprotectant: ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97903 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 18, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.63→25 Å / Num. obs: 61856 / % possible obs: 96.1 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.04 / Net I/σ(I): 13.36
Reflection shellResolution: 2.63→2.68 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.889 / Mean I/σ(I) obs: 0.89 / Num. unique obs: 3168 / CC1/2: 0.536 / Rpim(I) all: 0.457 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(dev_3092: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5CBK

5cbk


Resolution: 2.638→24.801 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.02
RfactorNum. reflection% reflectionSelection details
Rfree0.2419 1998 3.23 %RANDOM
Rwork0.1852 ---
obs0.187 61813 95.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.638→24.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10453 0 217 212 10882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610897
X-RAY DIFFRACTIONf_angle_d1.1614823
X-RAY DIFFRACTIONf_dihedral_angle_d20.6463919
X-RAY DIFFRACTIONf_chiral_restr0.0721662
X-RAY DIFFRACTIONf_plane_restr0.0081902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6381-2.7040.36561290.29793848X-RAY DIFFRACTION87
2.704-2.7770.34831480.27884413X-RAY DIFFRACTION100
2.777-2.85860.30661480.26434443X-RAY DIFFRACTION100
2.8586-2.95080.29851480.26664421X-RAY DIFFRACTION100
2.9508-3.0560.34461480.24684445X-RAY DIFFRACTION100
3.056-3.17820.28151480.22764437X-RAY DIFFRACTION100
3.1782-3.32250.27531500.2154471X-RAY DIFFRACTION100
3.3225-3.49720.29821490.2054445X-RAY DIFFRACTION100
3.4972-3.71560.28711010.21773025X-RAY DIFFRACTION68
3.7156-4.00140.23181280.1713850X-RAY DIFFRACTION86
4.0014-4.40210.21421510.14594484X-RAY DIFFRACTION100
4.4021-5.03450.20771500.14324510X-RAY DIFFRACTION100
5.0345-6.32540.19941530.17074554X-RAY DIFFRACTION100
6.3254-100.19931470.15994469X-RAY DIFFRACTION95
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)
15.2390.0574-0.85543.8719-0.63077.10770.0572-0.38580.43280.2213-0.26290.3055-0.1319-0.10180.20030.4531-0.01870.05070.5486-0.31530.844-7.1164-8.1057-3.7224
21.18331.48810.12262.80950.36768.03910.029-0.17030.30570.01030.0872-0.1657-0.2430.3513-0.15310.418-0.00850.11160.4941-0.2030.8331.6701-8.4713-9.681
33.1763-1.68850.35624.2621.09572.4370.128-0.90170.1437-0.1297-0.0231-0.1835-0.2461-0.2258-0.09540.3865-0.02140.0510.5745-0.24770.60690.8253-18.5807-6.8882
45.33073.94062.61116.38352.79424.58360.1564-0.1265-0.10310.07410.1404-0.51660.52890.5419-0.38730.39240.06460.05270.4135-0.0570.7181-1.8449-26.4683-11.3105
53.0061.6539-2.28435.6116-4.76514.3446-0.330.1468-0.1032-0.13460.74011.49710.1073-0.3583-0.40590.4904-0.11640.07470.6641-0.12070.911-7.6613-23.413-31.3324
67.78718.5895-6.64579.7438-8.09518.0726-1.21341.4977-0.6908-0.4866-0.3223-0.23260.5422-0.26451.35870.4403-0.04370.18630.7883-0.16911.0807-16.5335-16.1068-25.8669
74.91864.7745-6.76984.6673-6.61129.372-0.07950.9498-0.13230.43590.52380.0501-0.9565-1.4303-0.38250.60610.11440.11780.6223-0.15910.9938-18.9774-10.7968-18.0271
82.79192.6353-0.02443.9487-1.60472.7297-0.0133-0.14160.2523-0.1326-0.0209-0.42850.2135-0.00640.07690.30880.03260.07360.5074-0.14340.6259-0.602-22.5956-14.6032
93.8765-1.5811-0.58558.01211.84945.577-0.0131-0.39860.2240.4732-0.22370.23090.2462-0.20420.19240.3432-0.13970.13380.5025-0.13080.6027-10.8202-26.3589-3.9234
108.7424.42021.73367.0649-1.68526.0155-0.4696-0.46551.55810.0830.0313-0.67971.38551.8025-0.07120.50520.1251-0.07160.91830.06670.855646.8411-29.307-17.2589
112.6802-1.2599-0.05932.03520.25912.7909-0.0822-0.49460.41930.28210.103-0.2352-0.07920.5561-0.0380.35680.0019-0.01010.6945-0.07710.737537.1903-31.5718-15.669
125.5896-2.10663.51263.9296-1.21797.5740.1627-0.34570.07980.0230.06850.4301-0.0785-0.3353-0.2550.3596-0.06270.18260.64710.00190.721622.0028-36.614-17.0024
136.14530.1872-3.4075.9486-0.15337.82140.26530.34830.3153-0.2405-0.42060.2152-0.16530.12180.14190.39370.0574-0.04060.5141-0.03150.773822.8917-27.7628-36.5168
145.6008-6.9641-6.71539.06537.68658.8810.4886-0.13251.16760.13760.1638-0.9543-0.42240.1046-0.69240.5207-0.14090.0190.6505-0.04431.009730.341-16.8493-28.4482
153.5323-0.9426-0.63212.0182-0.57061.8525-0.048-0.5340.24110.18850.00260.0393-0.07380.0720.05570.34670.04620.01160.6257-0.08480.681721.5707-32.4694-17.3978
163.68115.4212-1.98568.3344-1.5954.72180.9124-1.5620.83481.1579-0.51491.1664-0.02510.8305-0.19270.6333-0.0480.00611.0791-0.29280.858424.6083-23.9345-3.5192
173.46491.1522-1.2055.06362.2524.21330.0723-0.9126-0.6430.6524-0.2998-0.99670.5850.58690.15610.62840.1368-0.04570.92820.33950.74237.7797-75.2527-13.3541
180.99021.301-0.71023.099-1.03855.7131-0.0262-0.1794-0.26610.0401-0.264-0.139-0.102-0.16210.30810.48990.1303-0.0360.52780.11120.498426.8739-70.0993-23.3654
197.65611.01071.71655.1503-0.29972.4345-0.295-0.260.48950.5298-0.2532-0.2648-0.5510.23890.53240.6427-0.0325-0.10420.52070.08820.39727.6332-58.6983-13.0719
207.2396-0.11523.56084.0645-1.01225.9527-0.2617-0.7174-0.58380.57620.07350.04520.4235-0.03860.18220.86080.12130.24340.59470.19120.5557-9.4976-88.3391-3.1167
215.98080.53772.70353.3804-3.25219.3259-0.615-0.6696-0.08960.71030.47730.4295-0.4596-0.88840.090.70840.12590.19210.64030.03370.5255-19.5726-79.4483-6.685
221.17280.60171.03711.1502-1.14184.2318-0.6488-1.5272-0.62271.2170.56940.29360.08450.59010.10290.83040.08560.05470.64850.13550.3686-8.8497-75.141-4.8343
239.13031.2024-2.30984.8160.43725.6704-0.3243-0.04610.88190.13720.47150.072-0.71880.3647-0.17260.6311-0.0231-0.04220.34460.00950.513-4.0528-69.8579-10.9279
242.4839-0.69361.1512.30692.67545.0976-0.20570.51240.0087-0.5357-0.0375-0.0330.2923-0.55830.22650.7481-0.0510.13610.67370.14470.6707-7.0814-79.7618-29.9336
253.73383.05312.45682.51471.93853.9266-0.12030.4308-2.35850.0440.2727-0.46470.37820.3227-0.09240.85120.02580.16860.5290.16970.7867-3.0034-91.9645-21.2798
264.84412.20592.1563.34712.88153.98-0.3677-0.1850.44740.038-0.31960.3316-0.209-0.42680.74170.58860.04590.0150.50940.06360.4851-8.3869-72.0105-13.0292
274.6508-5.0287-2.94846.86291.83493.3392-0.1110.24911.3209-0.77850.0308-0.8492-1.36390.3579-0.06540.9055-0.1868-0.09640.73110.05320.80094.0737-69.4337-13.8002
284.7837-0.5926-0.24579.2977-3.50491.3513-0.7817-0.6074-0.33711.1480.2916-0.38270.2310.91690.44990.65110.19410.02950.81360.22150.54565.7017-78.8925-4.6056
299.4213-0.14054.65680.79590.53714.2876-0.9830.1324-0.16832.44730.7811.5041-1.8314-1.62020.00031.13010.04290.33050.78340.02110.5901-40.0332-39.96282.5881
305.22-0.95682.1416.7632-2.173.1002-0.2117-0.95240.1561.30880.09830.17210.049-0.84340.10650.8397-0.14660.26730.8008-0.11920.6347-34.6518-48.90892.4016
313.7391-1.57582.02353.9225-0.53769.0786-0.298-0.43720.47690.8736-0.1450.1834-0.132-0.76950.41960.5736-0.07760.12540.4719-0.170.6296-28.7965-38.0397-3.3276
325.7384-1.26-2.15097.13244.73059.04420.08040.45180.61210.7592-0.3385-0.79160.38370.06060.18040.5412-0.0372-0.0210.49270.12060.6563-17.8622-47.2948-7.84
332.1725-0.8729-0.10562.1118-1.07352.13970.02650.3201-1.072-0.0212-0.808-0.9960.10650.49270.80060.52420.00530.03390.78450.19680.7625-26.2722-47.8077-27.3441
343.1526-3.2862.06444.2192-0.71025.41750.016-0.26860.17550.03930.14610.24940.6015-0.9599-0.2090.5248-0.22140.1240.7004-0.04960.7406-37.7365-56.3934-16.9277
358.54170.43546.0052.8150.94626.0147-0.28070.06941.51380.2877-0.2467-0.3813-0.24080.43440.62530.469-0.0978-0.05780.4311-0.03440.7232-22.6384-41.7302-12.6686
362.4169-0.2946-0.04294.8273.99568.8124-0.2094-0.09240.31211.0075-0.2243-0.11860.82140.22940.36340.79450.1205-0.05470.47990.040.5733-15.6335-54.6959-4.9937
375.9151-1.89921.53928.59921.84258.1726-0.2914-0.4239-0.27041.188-0.0520.19461.2830.35450.29670.9085-0.05830.20370.67890.03530.5149-24.6295-59.3161.7624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 40 )
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 88 )
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 107 )
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 135 )
5X-RAY DIFFRACTION5chain 'A' and (resid 136 through 148 )
6X-RAY DIFFRACTION6chain 'A' and (resid 149 through 162 )
7X-RAY DIFFRACTION7chain 'A' and (resid 163 through 182 )
8X-RAY DIFFRACTION8chain 'A' and (resid 183 through 214 )
9X-RAY DIFFRACTION9chain 'A' and (resid 215 through 270 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 14 )
11X-RAY DIFFRACTION11chain 'B' and (resid 15 through 107 )
12X-RAY DIFFRACTION12chain 'B' and (resid 108 through 135 )
13X-RAY DIFFRACTION13chain 'B' and (resid 136 through 162 )
14X-RAY DIFFRACTION14chain 'B' and (resid 163 through 182 )
15X-RAY DIFFRACTION15chain 'B' and (resid 183 through 252 )
16X-RAY DIFFRACTION16chain 'B' and (resid 253 through 270 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 58 )
18X-RAY DIFFRACTION18chain 'C' and (resid 59 through 195 )
19X-RAY DIFFRACTION19chain 'C' and (resid 196 through 270 )
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 58 )
21X-RAY DIFFRACTION21chain 'D' and (resid 59 through 88 )
22X-RAY DIFFRACTION22chain 'D' and (resid 89 through 107 )
23X-RAY DIFFRACTION23chain 'D' and (resid 108 through 135 )
24X-RAY DIFFRACTION24chain 'D' and (resid 136 through 162 )
25X-RAY DIFFRACTION25chain 'D' and (resid 163 through 182 )
26X-RAY DIFFRACTION26chain 'D' and (resid 183 through 214 )
27X-RAY DIFFRACTION27chain 'D' and (resid 215 through 231 )
28X-RAY DIFFRACTION28chain 'D' and (resid 232 through 270 )
29X-RAY DIFFRACTION29chain 'E' and (resid 2 through 14 )
30X-RAY DIFFRACTION30chain 'E' and (resid 15 through 58 )
31X-RAY DIFFRACTION31chain 'E' and (resid 59 through 107 )
32X-RAY DIFFRACTION32chain 'E' and (resid 108 through 135 )
33X-RAY DIFFRACTION33chain 'E' and (resid 136 through 148 )
34X-RAY DIFFRACTION34chain 'E' and (resid 149 through 182 )
35X-RAY DIFFRACTION35chain 'E' and (resid 183 through 207 )
36X-RAY DIFFRACTION36chain 'E' and (resid 208 through 241 )
37X-RAY DIFFRACTION37chain 'E' and (resid 242 through 270 )

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

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Yorodumi

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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