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

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Basic information

Entry
Database: PDB / ID: 4mzh
TitleCrystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) 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 / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation ...gamete generation / rRNA transcription / positive regulation of Wnt signaling pathway / Chromatin modifying enzymes / methylated histone binding / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / meiotic cell cycle / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Wnt signaling pathway / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / spindle / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / nuclear membrane / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / protein heterodimerization activity / Amyloid fiber formation / regulation of DNA-templated transcription / nucleolus / 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: 2.204 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,7663
Polymers26,7422
Non-polymers241
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-6 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.985, 41.315, 50.461
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
11A-301-

MG

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Components

#1: 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
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
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: 2.2→50 Å / Num. all: 13567 / Num. obs: 13269 / % possible obs: 97.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.2-2.244.30.6122.986550.61297.5
2.24-2.284.30.6043.246290.60496.8
2.28-2.324.50.4524.086240.45294.3
2.32-2.374.30.4164.426420.41697.6
2.37-2.424.30.3855.056460.38595
2.42-2.484.30.3415.696360.34196.8
2.48-2.544.30.2677.26410.26798.2
2.54-2.614.30.2228.76440.22295.4
2.61-2.694.40.29.716500.298
2.69-2.774.30.17910.926500.17997
2.77-2.874.40.14414.116490.14498.5

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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: 2.204→39.008 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7975 / SU ML: 0.29 / σ(F): 1.36 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 1318 9.96 %RANDOM
Rwork0.1962 ---
all0.2014 ---
obs0.2014 13238 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.94 Å2 / Biso mean: 36.5421 Å2 / Biso min: 6.24 Å2
Refinement stepCycle: LAST / Resolution: 2.204→39.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1681 0 1 75 1757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041721
X-RAY DIFFRACTIONf_angle_d0.992326
X-RAY DIFFRACTIONf_dihedral_angle_d14.728628
X-RAY DIFFRACTIONf_chiral_restr0.074247
X-RAY DIFFRACTIONf_plane_restr0.003295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2039-2.29220.33231250.25771241136692
2.2922-2.39650.28341310.2341277140896
2.3965-2.52280.31261530.2391285143896
2.5228-2.68080.3261380.21281284142297
2.6808-2.88780.27241510.20881316146798
2.8878-3.17820.24281510.19311338148998
3.1782-3.63790.25741370.190213721509100
3.6379-4.58220.21691760.164313641540100
4.5822-39.01440.2291560.20271443159998

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