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- PDB-4mzf: Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8... -

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Basic information

Entry
Database: PDB / ID: 4mzf
TitleCrystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide
Components
  • Peptide from Histone H3.2
  • Spindlin-1
KeywordsGENE REGULATION / Wnt signal / histone H3 / nuclear
Function / homology
Function and homology information


gamete generation / rRNA transcription / positive regulation of Wnt signaling pathway / Chromatin modifying enzymes / methylated histone binding / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes ...gamete generation / rRNA transcription / positive regulation of Wnt signaling pathway / Chromatin modifying enzymes / methylated histone binding / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / meiotic cell cycle / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Wnt signaling pathway / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / nuclear membrane / Estrogen-dependent gene expression / Amyloid fiber formation / protein heterodimerization activity / nucleolus / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / extracellular exosome / extracellular region / 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 H3.2 / Spindlin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å
AuthorsSu, X. / Ding, X. / Li, H.
CitationJournal: Genes Dev. / Year: 2014
Title: Molecular basis underlying histone H3 lysine-arginine methylation pattern readout by Spin/Ssty repeats of Spindlin1
Authors: Su, X. / Zhu, G. / Ding, X. / Lee, S.Y. / Dou, Y. / Zhu, B. / Wu, W. / Li, H.
History
DepositionSep 30, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide from Histone H3.2
B: Spindlin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8375
Polymers26,7422
Non-polymers953
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-3 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.679, 43.309, 50.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-303-

MG

21B-461-

HOH

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Components

#1: Protein/peptide Peptide from Histone H3.2 / / Histone H3/m / Histone H3/o


Mass: 1132.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q71DI3
#2: Protein Spindlin-1 / Sp1 / Ovarian cancer-related protein


Mass: 25609.760 Da / Num. of mol.: 1 / Fragment: UNP residues 50-262
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPIN1, OCR, SPIN / Plasmid: pRSFDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y657
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 8000, 20% PEG 400, 0.1M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.098→50 Å / Num. all: 15988 / Num. obs: 15029 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 30.57 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 28.47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.098-2.144.70.5923.747230.59290.5
2.14-2.184.70.5184.517130.51889.1
2.18-2.224.70.4934.766910.49391.5
2.22-2.264.60.4685.257060.46890.7
2.26-2.314.70.3836.366930.38390.2
2.31-2.374.60.3446.427200.34490
2.37-2.424.60.3027.777160.30292.4
2.42-2.494.50.2768.227120.27690.9
2.49-2.564.50.22710.437260.22791.9
2.56-2.654.50.19213.087200.19290.7
2.65-2.744.40.17912.567470.17994.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.098→32.778 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.8119 / SU ML: 0.2 / σ(F): 1.35 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2552 1152 7.69 %RANDOM
Rwork0.2009 ---
all0.205 ---
obs0.205 14987 93.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.96 Å2 / Biso mean: 30.544 Å2 / Biso min: 9.7 Å2
Refinement stepCycle: LAST / Resolution: 2.098→32.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1724 0 3 113 1840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081765
X-RAY DIFFRACTIONf_angle_d1.1822385
X-RAY DIFFRACTIONf_dihedral_angle_d15.448647
X-RAY DIFFRACTIONf_chiral_restr0.08251
X-RAY DIFFRACTIONf_plane_restr0.004305
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0984-2.19380.29331110.2047156986
2.1938-2.30950.28951320.2014163390
2.3095-2.45410.2621580.2013165291
2.4541-2.64350.23411440.2015166091
2.6435-2.90940.26791430.2052173494
2.9094-3.33010.25281490.1928179497
3.3301-4.19410.20641640.1957184099
4.1941-32.7820.28271510.2063195398

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