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- PDB-5y5w: Crystal structure of human Spindlin1 in complex with a histone H4... -

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Basic information

Entry
Database: PDB / ID: 5y5w
TitleCrystal structure of human Spindlin1 in complex with a histone H4K20(me3) peptide
Components
  • Histone peptide H4K20(me3)
  • Spindlin-1
KeywordsGENE REGULATION / reader / histone
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/Ssty / Spindlin/spermiogenesis-specific protein / Spindlin/spermiogenesis-specific domain superfamily / Spin/Ssty Family / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsWang, C. / Zang, J.
CitationJournal: FEBS Lett. / Year: 2018
Title: Spindlin-1 recognizes methylations of K20 and R23 of histone H4 tail
Authors: Wang, C. / Zhan, L. / Wu, M. / Ma, R. / Yao, J. / Xiong, Y. / Pan, Y. / Guan, S. / Zhang, X. / Zang, J.
History
DepositionAug 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _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 1.2Mar 27, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.3Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spindlin-1
B: Spindlin-1
C: Spindlin-1
D: Spindlin-1
E: Histone peptide H4K20(me3)
F: Histone peptide H4K20(me3)
G: Histone peptide H4K20(me3)


Theoretical massNumber of molelcules
Total (without water)111,1827
Polymers111,1827
Non-polymers00
Water0
1
A: Spindlin-1
E: Histone peptide H4K20(me3)


Theoretical massNumber of molelcules
Total (without water)28,0992
Polymers28,0992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spindlin-1
F: Histone peptide H4K20(me3)


Theoretical massNumber of molelcules
Total (without water)28,0992
Polymers28,0992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Spindlin-1
G: Histone peptide H4K20(me3)


Theoretical massNumber of molelcules
Total (without water)28,0992
Polymers28,0992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Spindlin-1


Theoretical massNumber of molelcules
Total (without water)26,8861
Polymers26,8861
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.769, 148.504, 169.212
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 26886.117 Da / Num. of mol.: 4 / Fragment: UNP residues 51-262
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
#2: Protein/peptide Histone peptide H4K20(me3)


Mass: 1212.469 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: 2.55 Å3/Da / Density % sol: 51.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.5 M (NH4)2SO4, 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.3→84.61 Å / Num. obs: 17175 / % possible obs: 99 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 29.2
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 10.2 / Num. unique obs: 822 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NS2

2ns2


Resolution: 3.3→84.61 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.822 / SU B: 70.425 / SU ML: 0.527 / Cross valid method: THROUGHOUT / ESU R Free: 0.648 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3081 903 5.3 %RANDOM
Rwork0.21922 ---
obs0.22387 16247 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.962 Å2
Baniso -1Baniso -2Baniso -3
1-8.08 Å20 Å2-0 Å2
2---2.27 Å20 Å2
3----5.8 Å2
Refinement stepCycle: 1 / Resolution: 3.3→84.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6351 0 0 0 6351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196520
X-RAY DIFFRACTIONr_bond_other_d0.0070.025868
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.9418888
X-RAY DIFFRACTIONr_angle_other_deg1.053313394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8965812
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.04624.033300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.08615940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3761526
X-RAY DIFFRACTIONr_chiral_restr0.0940.2974
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027478
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021548
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0576.2963278
X-RAY DIFFRACTIONr_mcbond_other4.0576.2953277
X-RAY DIFFRACTIONr_mcangle_it6.9019.4224077
X-RAY DIFFRACTIONr_mcangle_other6.9019.4244078
X-RAY DIFFRACTIONr_scbond_it3.4446.253242
X-RAY DIFFRACTIONr_scbond_other3.4446.2513243
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0079.3034811
X-RAY DIFFRACTIONr_long_range_B_refined10.04848.6056911
X-RAY DIFFRACTIONr_long_range_B_other10.04848.6136912
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.298→3.383 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 58 -
Rwork0.26 1114 -
obs--94.52 %
Refinement TLS params.Method: refined / Origin x: 3.933 Å / Origin y: 2.924 Å / Origin z: -16.335 Å
111213212223313233
T0.0563 Å20.0559 Å2-0.0133 Å2-0.1016 Å20.0002 Å2--0.0254 Å2
L0.0432 °20.0598 °2-0.0363 °2-0.1222 °20.0093 °2--0.3494 °2
S-0.0003 Å °-0.0296 Å °0.0058 Å °-0.0393 Å °-0.0601 Å °0.0339 Å °0.0037 Å °0.1202 Å °0.0604 Å °

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