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- PDB-4mzg: Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide -

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Basic information

Entry
Database: PDB / ID: 4mzg
TitleCrystal structure of human Spindlin1 bound to histone H3K4me3 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 / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Wnt signaling pathway / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / spindle / 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: 1.698 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: Peptide from Histone H3.2
B: Spindlin-1
C: Peptide from Histone H3.2
D: Spindlin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,08812
Polymers55,4854
Non-polymers6038
Water6,485360
1
A: Peptide from Histone H3.2
B: Spindlin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0396
Polymers27,7422
Non-polymers2964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-28 kcal/mol
Surface area11800 Å2
MethodPISA
2
C: Peptide from Histone H3.2
D: Spindlin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0506
Polymers27,7422
Non-polymers3074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-39 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.168, 122.037, 49.837
Angle α, β, γ (deg.)90.00, 91.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide / Protein , 2 types, 4 molecules ACBD

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


Mass: 2232.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q71DI3
#2: Protein Spindlin-1 / SP1 / Ovarian cancer-related protein


Mass: 25509.748 Da / Num. of mol.: 2 / 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

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Non-polymers , 5 types, 368 molecules

#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.36 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 37.5% MPD_P1K_P3350, 0.1M bicine/Trizma, pH 8.5, 0.06M MgCl2/CaCl2, 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: Jun 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.698→50 Å / Num. all: 56456 / Num. obs: 56230 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 24.8
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.4 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.698-1.730.6452.6428450.64599.6
1.73-1.760.5523.1527730.55299.6
1.76-1.790.434.1328080.4399.8
1.79-1.830.3574.9227910.35799.9
1.83-1.870.2876.1828360.28799.9
1.87-1.910.2347.6428070.23499.9
1.91-1.960.1839.8328150.18399.9
1.96-2.020.15611.2727730.15699.9
2.02-2.070.12414.0628470.124100
2.07-2.140.10316.7227960.10399.9
2.14-2.220.08819.327840.088100

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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: 1.698→32.144 Å / Occupancy max: 1 / Occupancy min: 0.49 / FOM work R set: 0.8643 / SU ML: 0.18 / σ(F): 1.35 / Phase error: 21.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 2845 5.06 %Random
Rwork0.1828 ---
all0.184 ---
obs0.184 56200 99.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.18 Å2 / Biso mean: 29.8743 Å2 / Biso min: 11.58 Å2
Refinement stepCycle: LAST / Resolution: 1.698→32.144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3270 0 36 360 3666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073380
X-RAY DIFFRACTIONf_angle_d1.1684574
X-RAY DIFFRACTIONf_dihedral_angle_d15.0941255
X-RAY DIFFRACTIONf_chiral_restr0.081491
X-RAY DIFFRACTIONf_plane_restr0.005578
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.698-1.72730.25481270.25752406253388
1.7273-1.75870.27991300.246526552785100
1.7587-1.79250.3011300.216226992829100
1.7925-1.82910.20441310.213226592790100
1.8291-1.86880.27271520.214426902842100
1.8688-1.91230.26021690.210626952864100
1.9123-1.96010.23921470.206126722819100
1.9601-2.01310.24171390.202926422781100
2.0131-2.07240.22191470.191227122859100
2.0724-2.13920.20771490.18126672816100
2.1392-2.21570.24351430.174426542797100
2.2157-2.30440.2071360.181327262862100
2.3044-2.40920.20791370.190327192856100
2.4092-2.53620.23351370.194126812818100
2.5362-2.6950.20681550.190827012856100
2.695-2.9030.23421740.20426542828100
2.903-3.19490.20921330.188626782811100
3.1949-3.65660.21261390.174727272866100
3.6566-4.60480.1571360.145527022838100
4.6048-32.14970.16911340.17142616275095

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