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- PDB-6i8b: Crystal structure of Spindlin1 in complex with the inhibitor VinSpinIn -

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Basic information

Entry
Database: PDB / ID: 6i8b
TitleCrystal structure of Spindlin1 in complex with the inhibitor VinSpinIn
ComponentsSpindlin-1
KeywordsCELL CYCLE / Epigenetics / Tudor domain / Methyl-Lysine / methyl-Arginine
Function / homology
Function and homology information


gamete generation / rRNA transcription / positive regulation of Wnt signaling pathway / methylated histone binding / meiotic cell cycle / Wnt signaling pathway / spindle / chromatin organization / nuclear membrane / regulation of DNA-templated transcription ...gamete generation / rRNA transcription / positive regulation of Wnt signaling pathway / methylated histone binding / meiotic cell cycle / Wnt signaling pathway / spindle / chromatin organization / nuclear membrane / regulation of DNA-templated transcription / nucleolus / positive regulation of DNA-templated transcription / nucleoplasm / nucleus / cytosol
Similarity search - Function
Spindlin/spermiogenesis-specific protein / Spindlin/spermiogenesis-specific domain superfamily / Spin/Ssty Family
Similarity search - Domain/homology
GLYCINE / Chem-H7T / PHOSPHATE ION / Spindlin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 Å
AuthorsJohansson, C. / Fagan, V. / Brennan, P.E. / Sorrell, F.J. / Krojer, T. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.C.T.
CitationJournal: J.Med.Chem. / Year: 2019
Title: A Chemical Probe for Tudor Domain Protein Spindlin1 to Investigate Chromatin Function.
Authors: Fagan, V. / Johansson, C. / Gileadi, C. / Monteiro, O. / Dunford, J.E. / Nibhani, R. / Philpott, M. / Malzahn, J. / Wells, G. / Faram, R. / Cribbs, A.P. / Halidi, N. / Li, F. / Chau, I. / ...Authors: Fagan, V. / Johansson, C. / Gileadi, C. / Monteiro, O. / Dunford, J.E. / Nibhani, R. / Philpott, M. / Malzahn, J. / Wells, G. / Faram, R. / Cribbs, A.P. / Halidi, N. / Li, F. / Chau, I. / Greschik, H. / Velupillai, S. / Allali-Hassani, A. / Bennett, J. / Christott, T. / Giroud, C. / Lewis, A.M. / Huber, K.V.M. / Athanasou, N. / Bountra, C. / Jung, M. / Schule, R. / Vedadi, M. / Arrowsmith, C. / Xiong, Y. / Jin, J. / Fedorov, O. / Farnie, G. / Brennan, P.E. / Oppermann, U.
History
DepositionNov 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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
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
B: Spindlin-1
E: Spindlin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,11312
Polymers51,0002
Non-polymers2,11410
Water1,820101
1
B: Spindlin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6267
Polymers25,5001
Non-polymers1,1276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Spindlin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4875
Polymers25,5001
Non-polymers9874
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.875, 118.583, 43.808
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, 2 molecules BE

#1: Protein Spindlin-1 / Ovarian cancer-related protein / Spindlin1


Mass: 25499.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPIN1, OCR, SPIN / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y657

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Non-polymers , 5 types, 111 molecules

#2: Chemical ChemComp-H7T / 2-[4-[2-[[2-[3-[2-azanyl-5-(cyclopropylmethoxy)-3,3-dimethyl-indol-6-yl]oxypropyl]-1,3-dihydroisoindol-5-yl]oxy]ethyl]-1,2,3-triazol-1-yl]-1-[4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]ethanone


Mass: 738.961 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H58N8O4
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 55% MPD and 0.1 M SPG buffer pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.76→41.093 Å / Num. obs: 58414 / % possible obs: 99.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 24.64 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.064 / Rrim(I) all: 0.153 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.76-1.855.21.60883730.4230.7621.78699.5
5.56-41.094.70.05520150.9980.0250.0698.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.87 Å41.09 Å
Translation4.87 Å41.09 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.8.0phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MZG

4mzg


Resolution: 1.76→41.093 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.64
RfactorNum. reflection% reflection
Rfree0.2544 2843 4.88 %
Rwork0.233 --
obs0.2341 58314 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.87 Å2 / Biso mean: 37.8367 Å2 / Biso min: 15.57 Å2
Refinement stepCycle: final / Resolution: 1.76→41.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 295 101 3435
Biso mean--50.09 33.57 -
Num. residues----387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053271
X-RAY DIFFRACTIONf_angle_d0.7214442
X-RAY DIFFRACTIONf_chiral_restr0.052472
X-RAY DIFFRACTIONf_plane_restr0.005606
X-RAY DIFFRACTIONf_dihedral_angle_d16.2721938
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7598-1.79010.40981430.39722664280799
1.7901-1.82270.37931440.37152786293099
1.8227-1.85780.40281260.34752704283099
1.8578-1.89570.33361330.3332762289599
1.8957-1.93690.32381290.324527382867100
1.9369-1.9820.34171650.29912727289299
1.982-2.03150.29221200.274327642884100
2.0315-2.08640.29791330.257527802913100
2.0864-2.14780.29661560.244827262882100
2.1478-2.21720.29591140.240127942908100
2.2172-2.29640.2341320.234227862918100
2.2964-2.38830.26171600.234527312891100
2.3883-2.4970.21081450.235127632908100
2.497-2.62860.27071230.23422807293099
2.6286-2.79330.29161660.23912758292499
2.7933-3.00890.25791380.22652790292899
3.0089-3.31160.24231370.22432807294499
3.3116-3.79050.2411580.20222789294799
3.7905-4.77450.15731610.17632831299299
4.7745-41.10470.27811600.2282964312498
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)
15.60934.8423-1.70285.8326-1.31314.8250.086-0.30090.16280.4204-0.29490.0941-0.0417-0.11770.09640.30180.0255-0.01420.1715-0.00850.297325.302110.521351.7529
22.45620.06360.92863.53570.60783.247-0.0054-0.0607-0.02670.1653-0.0390.0596-0.1221-0.17070.04640.24590.05060.00380.1452-0.00370.194324.142118.298849.7549
38.6743-0.84592.41826.27750.15884.2767-0.3336-0.43310.23670.79660.24820.0989-0.1821-0.37220.00470.3234-0.01040.04280.23720.03680.209221.504211.055858.1868
42.9812-1.590.4263.6226-0.62732.1089-0.01090.55450.3294-0.0151-0.3073-0.5075-0.54270.25330.23330.4015-0.08840.03440.28220.03070.289833.587423.734740.2788
56.0445-1.02680.87513.1029-1.09524.5706-0.03060.4481-0.0563-0.3459-0.0757-0.052-0.3898-0.17130.07040.3760.11770.01320.2374-0.01830.201219.393427.157934.9213
62.8034-0.0818-1.09481.72610.09295.1131-0.06460.30070.1181-0.27090.1418-0.219-0.00540.3381-0.04120.27690.0726-0.0080.25070.03830.274723.26530.339734.7451
72.359-1.1571-0.40552.1580.00112.7755-0.0443-0.04250.0460.16580.04870.1009-0.2273-0.2671-0.03870.34480.1015-0.0090.25580.00810.239612.624231.97752.2524
84.3352-4.20540.11838.3707-0.57273.5963-0.2786-0.44370.02090.12370.26070.172-0.15220.02860.01140.2579-0.04050.00080.1653-0.00320.158839.32463.397961.4775
92.7989-0.0848-0.35820.4511-0.70682.4345-0.1290.0859-0.20930.151-0.0196-0.16930.16540.01680.13740.2367-0.0748-0.0190.2069-0.00330.250947.51792.790759.9357
106.554-2.28271.3855.5493-2.91475.98010.36990.5157-0.0754-0.3863-0.08330.1264-0.3230.325-0.16230.4522-0.1791-0.01490.331-0.02770.212453.662712.514241.1838
110.19420.9538-0.01693.08131.13934.7947-0.10740.077-0.1598-0.23480.1852-0.04520.13850.34550.02590.2676-0.06060.020.2791-0.0170.271456.29646.34548.2476
124.50331.75470.8644.09242.04685.1694-0.1134-0.02620.25390.29520.14050.01370.4386-0.175-0.05170.2416-0.0787-0.01450.2510.03330.205758.92314.986964.4738
133.61923.22391.72442.55261.58532.8594-0.09430.06820.25560.01390.12530.104-0.48320.2210.09630.3385-0.0846-0.01180.20360.00410.240158.437118.847262.1988
141.999922.00022.00041.99931.9999-7.3758-6.22128.00645.78040.112-2.5829-7.8029-1.57047.22770.97620.6011-0.5994-0.0520.5090.890413.815735.089440.8389
152.00041.99981.99992.00050.46721.9999-4.869410.0263-2.9374-12.64520.77793.3095-5.46874.90994.06391.06630.0310.05790.5959-0.29990.597161.729816.075750.7033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 50 through 69 )B50 - 69
2X-RAY DIFFRACTION2chain 'B' and (resid 70 through 101 )B70 - 101
3X-RAY DIFFRACTION3chain 'B' and (resid 102 through 111 )B102 - 111
4X-RAY DIFFRACTION4chain 'B' and (resid 112 through 135 )B112 - 135
5X-RAY DIFFRACTION5chain 'B' and (resid 136 through 176 )B136 - 176
6X-RAY DIFFRACTION6chain 'B' and (resid 177 through 216 )B177 - 216
7X-RAY DIFFRACTION7chain 'B' and (resid 217 through 269 )B217 - 269
8X-RAY DIFFRACTION8chain 'E' and (resid 52 through 79 )E52 - 79
9X-RAY DIFFRACTION9chain 'E' and (resid 80 through 135 )E80 - 135
10X-RAY DIFFRACTION10chain 'E' and (resid 136 through 158 )E136 - 158
11X-RAY DIFFRACTION11chain 'E' and (resid 159 through 216 )E159 - 216
12X-RAY DIFFRACTION12chain 'E' and (resid 217 through 247 )E217 - 247
13X-RAY DIFFRACTION13chain 'E' and (resid 248 through 269 )E248 - 269
14X-RAY DIFFRACTION14chain 'B' and (resid 306 through 306 )B306
15X-RAY DIFFRACTION15chain 'E' and (resid 304 through 304 )E304

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