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- PDB-7bu9: Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex -

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Basic information

Entry
Database: PDB / ID: 7bu9
TitleCrystal Structure of Spindlin1-H3(K4me3-K9me2) complex
Components
  • H3(K4me3-K9me2) peptide
  • Spindlin-1
KeywordsGENE REGULATION / Spin/Ssty repeat
Function / homology
Function and homology information


transposable element silencing by piRNA-mediated DNA methylation / gamete generation / histone H3K4me3 reader activity / : / histone reader activity / rRNA transcription / positive regulation of Wnt signaling pathway / Chromatin modifying enzymes / protein localization to chromatin / Interleukin-7 signaling ...transposable element silencing by piRNA-mediated DNA methylation / gamete generation / histone H3K4me3 reader activity / : / histone reader activity / rRNA transcription / positive regulation of Wnt signaling pathway / Chromatin modifying enzymes / protein localization to chromatin / 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 / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / meiotic cell cycle / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / spindle / Wnt signaling pathway / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / nuclear membrane / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytosol
Similarity search - Function
Spindlin/spermiogenesis-specific protein / Spindlin/spermiogenesis-specific domain superfamily / Spin/Ssty Family / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H3.2 / Spindlin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.502 Å
AuthorsZhao, F. / Li, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91753203, 31725014 China
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Molecular basis for histone H3 "K4me3-K9me3/2" methylation pattern readout by Spindlin1.
Authors: Zhao, F. / Liu, Y. / Su, X. / Lee, J.E. / Song, Y. / Wang, D. / Ge, K. / Gao, J. / Zhang, M.Q. / Li, H.
History
DepositionApr 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Spindlin-1
B: H3(K4me3-K9me2) peptide
C: Spindlin-1
D: H3(K4me3-K9me2) peptide
E: Spindlin-1
F: H3(K4me3-K9me2) peptide
G: Spindlin-1
H: H3(K4me3-K9me2) peptide


Theoretical massNumber of molelcules
Total (without water)106,7738
Polymers106,7738
Non-polymers00
Water00
1
A: Spindlin-1
B: H3(K4me3-K9me2) peptide


Theoretical massNumber of molelcules
Total (without water)26,6932
Polymers26,6932
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-7 kcal/mol
Surface area12880 Å2
MethodPISA
2
C: Spindlin-1
D: H3(K4me3-K9me2) peptide


Theoretical massNumber of molelcules
Total (without water)26,6932
Polymers26,6932
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-8 kcal/mol
Surface area13200 Å2
MethodPISA
3
E: Spindlin-1
F: H3(K4me3-K9me2) peptide


Theoretical massNumber of molelcules
Total (without water)26,6932
Polymers26,6932
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-7 kcal/mol
Surface area13170 Å2
MethodPISA
4
G: Spindlin-1
H: H3(K4me3-K9me2) peptide


Theoretical massNumber of molelcules
Total (without water)26,6932
Polymers26,6932
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-9 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.471, 143.783, 129.990
Angle α, β, γ (deg.)90.000, 95.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 25058.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPIN1, OCR, SPIN / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y657
#2: Protein/peptide
H3(K4me3-K9me2) peptide / Histone H3/m / Histone H3/o


Mass: 1634.923 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q71DI3
Has ligand of interestY

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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: 3.79 Å3/Da / Density % sol: 67.54 % / Mosaicity: 1.212 ° / Mosaicity esd: 0.013 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7 / Details: 3.6M sodium formate, 3% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2019 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 18492 / % possible obs: 98.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.096 / Rrim(I) all: 0.181 / Χ2: 1.095 / Net I/σ(I): 4.5 / Num. measured all: 64751
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.5-3.563.60.499300.8120.3040.5780.51599.9
3.56-3.633.60.3919470.8820.2420.4610.53299.9
3.63-3.693.60.2939550.9610.180.3450.57599.8
3.69-3.773.60.3138980.9150.1920.3680.64399.9
3.77-3.853.60.3219040.9080.20.3790.62100
3.85-3.943.60.2789460.9140.1720.3280.6899.6
3.94-4.043.60.2069460.9650.1260.2420.77598.9
4.04-4.153.60.2228960.9390.1370.2620.90499.3
4.15-4.273.60.1829160.9640.1130.2151.12199.6
4.27-4.413.50.1629310.9640.1010.1911.33299.1
4.41-4.573.50.1529280.9610.0950.181.31698.5
4.57-4.753.50.1598820.9590.0990.1881.38998.5
4.75-4.973.50.1449460.9580.090.171.36198.5
4.97-5.233.40.1519090.9530.0970.1811.39498.2
5.23-5.553.20.1559150.9390.1030.1871.1997.8
5.55-5.982.90.1298810.9720.0910.1591.18993.6
5.98-6.583.50.1159210.980.0730.1371.18898.1
6.58-7.533.70.1129280.9870.0670.131.187100
7.53-9.483.60.0919450.990.0560.1071.54799.8
9.48-503.40.0689680.9960.0430.0812.60799.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
DENZOdata reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NS2

2ns2


Resolution: 3.502→48.074 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 28.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2642 875 4.74 %
Rwork0.2457 17582 -
obs0.2466 18457 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 227.84 Å2 / Biso mean: 80.3457 Å2 / Biso min: 26.62 Å2
Refinement stepCycle: final / Resolution: 3.502→48.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6911 0 0 0 6911
Num. residues----854
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.502-3.7210.31231400.3041294799
3.721-4.00820.29471340.26222973100
4.0082-4.41130.21361500.2349289499
4.4113-5.04910.25291480.2134293498
5.0491-6.3590.25571510.2429283197
6.359-48.0740.28291520.24613003100

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