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- PDB-6i8y: Crystal structure of Spindlin1 in complex with the Methyltransfer... -

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Basic information

Entry
Database: PDB / ID: 6i8y
TitleCrystal structure of Spindlin1 in complex with the Methyltransferase inhibitor A366
ComponentsSpindlin-1
KeywordsGENE REGULATION / 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 / spindle / Wnt signaling pathway / chromatin organization / nuclear membrane / nucleolus ...gamete generation / rRNA transcription / positive regulation of Wnt signaling pathway / methylated histone binding / meiotic cell cycle / spindle / Wnt signaling pathway / chromatin organization / nuclear membrane / nucleolus / regulation of DNA-templated transcription / 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
Chem-2OD / Spindlin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsSrikannathasan, V. / Johansson, C. / Gileadi, C. / Shrestha, L. / Sorrell, F.J. / Krojer, T. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. ...Srikannathasan, V. / Johansson, C. / Gileadi, C. / Shrestha, L. / Sorrell, F.J. / Krojer, T. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.C.T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
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 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spindlin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5949
Polymers25,5001
Non-polymers1,0948
Water1,928107
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-8 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.170, 116.170, 43.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 25499.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPIN1, OCR, SPIN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y657

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Non-polymers , 7 types, 115 molecules

#2: Chemical ChemComp-2OD / 5'-methoxy-6'-[3-(pyrrolidin-1-yl)propoxy]spiro[cyclobutane-1,3'-indol]-2'-amine


Mass: 329.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H27N3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M Bis-Tris pH=6.5,0.2M CaCl2, 45% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.52→82.145 Å / Num. obs: 46462 / % possible obs: 99.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 19.09 Å2 / Rpim(I) all: 0.033 / Rrim(I) all: 0.111 / Rsym value: 0.106 / Net I/av σ(I): 4 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.6-1.699.70.791157360.2660.8360.791100
1.69-1.7910.50.5191.454210.1670.5460.519100
1.79-1.9111.30.3222.351000.10.3370.322100
1.91-2.0712.30.2083.547780.0620.2170.208100
2.07-2.2612.10.1554.644020.0470.1620.155100
2.26-2.5312.10.1275.540110.0380.1320.127100
2.53-2.9211.90.1056.335680.0320.110.105100
2.92-3.5810.90.088730310.0270.0920.088100
3.58-5.0610.70.0758.124100.0230.0780.075100
5.06-19.33210.50.0688.513950.0210.0710.06898.2

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.22data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H75

4h75


Resolution: 1.52→82.145 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.88
RfactorNum. reflection% reflection
Rfree0.2054 2335 5.03 %
Rwork0.1903 --
obs0.1911 46462 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 160.62 Å2 / Biso mean: 33.782 Å2 / Biso min: 11.71 Å2
Refinement stepCycle: final / Resolution: 1.52→82.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 115 107 1748
Biso mean--57.94 34.56 -
Num. residues----190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141658
X-RAY DIFFRACTIONf_angle_d1.3912247
X-RAY DIFFRACTIONf_chiral_restr0.077232
X-RAY DIFFRACTIONf_plane_restr0.009275
X-RAY DIFFRACTIONf_dihedral_angle_d17.939968
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.52-1.55110.3421380.334825602698
1.5511-1.58480.3121160.296425442660
1.5848-1.62170.28191290.263925652694
1.6217-1.66220.26291410.24225562697
1.6622-1.70720.24671260.219525712697
1.7072-1.75740.22631310.208425642695
1.7574-1.81410.18341050.198826012706
1.8141-1.8790.22471350.198825612696
1.879-1.95420.20851650.187225442709
1.9542-2.04320.21761330.179825942727
2.0432-2.15090.17921450.175125702715
2.1509-2.28570.1741360.176825882724
2.2857-2.46210.19671340.180126042738
2.4621-2.70990.20061430.17726182761
2.7099-3.10210.1781520.176926302782
3.1021-3.90830.18951470.171526532800
3.9083-82.26480.21711590.195128042963
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)
13.1094-1.4126-0.59047.30962.30584.14380.0202-0.14120.38710.0179-0.23250.5504-0.5181-0.16930.00360.16130.00780.00490.1365-0.05160.253744.05842.8491.7932
25.2702-1.0466-1.88490.57940.17892.446-0.12560.0024-0.12970.1111-0.00170.01530.1788-0.06610.07140.1297-0.03960.0050.0672-0.01720.138142.7639-5.28062.7499
32.15680.49981.68230.97260.73193.316-0.04640.10390.0762-0.16150.05030.0211-0.081-0.0777-0.06080.1222-0.02220.01940.14060.02090.141338.4418-4.6633-7.0724
40.91810.374-0.93371.8152-0.7825.06240.02420.13410.0988-0.11340.01180.0903-0.0828-0.2750.01170.1571-0.0593-0.0040.2057-0.00440.178629.2757-7.1675-12.8261
52.44641.2012-1.2320.9676-0.68531.6236-0.0054-0.0263-0.21660.0428-0.03110.02180.2867-0.29780.02050.2208-0.1051-0.0050.204-0.01680.167526.7338-16.16363.1282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 51 through 62 )A51 - 62
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 91 )A63 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 147 )A92 - 147
4X-RAY DIFFRACTION4chain 'A' and (resid 148 through 216 )A148 - 216
5X-RAY DIFFRACTION5chain 'A' and (resid 217 through 269 )A217 - 269

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