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- PDB-4h75: Crystal structure of human Spindlin1 in complex with a histone H3... -

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Basic information

Entry
Database: PDB / ID: 4h75
TitleCrystal structure of human Spindlin1 in complex with a histone H3K4(me3) peptide
Components
  • Histone H3
  • Spindlin-1
KeywordsGENE REGULATION / Tudor domain / H3K4me3 binding / methylation
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 / structural constituent of chromatin / nucleosome / chromatin organization ...gamete generation / rRNA transcription / positive regulation of Wnt signaling pathway / methylated histone binding / meiotic cell cycle / Wnt signaling pathway / spindle / structural constituent of chromatin / nucleosome / chromatin organization / nuclear membrane / protein heterodimerization activity / regulation of DNA-templated transcription / nucleolus / positive regulation of DNA-templated transcription / DNA binding / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A ...Spindlin/Ssty / Spindlin/spermiogenesis-specific protein / Spindlin/spermiogenesis-specific domain superfamily / Spin/Ssty Family / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Mainly Beta
Similarity search - Domain/homology
Histone H3-7 / Spindlin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å
AuthorsYang, N. / Wang, W. / Wang, Y. / Wang, M. / Zhao, Q. / Rao, Z. / Zhu, B. / Xu, R.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Distinct mode of methylated lysine-4 of histone H3 recognition by tandem tudor-like domains of Spindlin1.
Authors: Yang, N. / Wang, W. / Wang, Y. / Wang, M. / Zhao, Q. / Rao, Z. / Zhu, B. / Xu, R.M.
History
DepositionSep 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 14, 2012Group: Database references
Revision 1.3Sep 20, 2023Group: 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spindlin-1
B: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6927
Polymers28,1052
Non-polymers5885
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-35 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.429, 42.685, 50.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 27128.732 Da / Num. of mol.: 1 / Fragment: UNP residues 27-262
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPIN1, OCR, SPIN / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y657
#2: Protein/peptide Histone H3


Mass: 976.155 Da / Num. of mol.: 1 / Fragment: H3K4(me3) peptide (UNP residues 2-9) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5TEC6

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Non-polymers , 4 types, 115 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.1 M CHES, pH 9.5, 2.1 M ammonium sulfate, 0.2 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2011 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.098→50 Å / Num. all: 16132 / Num. obs: 16119 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 24.3
Reflection shellResolution: 2.098→2.18 Å / Redundancy: 8 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 6.6 / Num. unique all: 1567 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NS2

2ns2


Resolution: 2.098→38.866 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 808 5.03 %RANDOM
Rwork0.181 ---
all0.1828 16132 --
obs0.1828 16078 99.84 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.898 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2204 Å2-0 Å20 Å2
2---4.0807 Å2-0 Å2
3---2.8603 Å2
Refinement stepCycle: LAST / Resolution: 2.098→38.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 34 110 1819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071767
X-RAY DIFFRACTIONf_angle_d1.0642396
X-RAY DIFFRACTIONf_dihedral_angle_d14.195666
X-RAY DIFFRACTIONf_chiral_restr0.073254
X-RAY DIFFRACTIONf_plane_restr0.004301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.098-2.22940.25251330.18372475X-RAY DIFFRACTION100
2.2294-2.40150.23131400.18422509X-RAY DIFFRACTION100
2.4015-2.64310.24081380.18532505X-RAY DIFFRACTION100
2.6431-3.02540.26371330.2032522X-RAY DIFFRACTION100
3.0254-3.81120.19871270.17352563X-RAY DIFFRACTION100
3.8112-38.87280.20371370.17712696X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 20.6656 Å / Origin y: 9.2954 Å / Origin z: 10.3739 Å
111213212223313233
T0.1608 Å20.0439 Å2-0.0035 Å2-0.1224 Å20.0302 Å2--0.1135 Å2
L2.6415 °20.1618 °2-0.1579 °2-2.4075 °2-0.1706 °2--2.4369 °2
S-0.0491 Å °-0.1913 Å °-0.0505 Å °0.2128 Å °0.1823 Å °0.246 Å °0.1104 Å °-0.2058 Å °-0.0512 Å °
Refinement TLS groupSelection details: all

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