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- PDB-8gtx: Crystal Structure of human Spindlin1-HBx complex -

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Basic information

Entry
Database: PDB / ID: 8gtx
TitleCrystal Structure of human Spindlin1-HBx complex
Components
  • HBx
  • Spindlin-1
KeywordsSTRUCTURAL PROTEIN / Tudor domain
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 / protein localization to chromatin / meiotic cell cycle / spindle ...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 / protein localization to chromatin / meiotic cell cycle / spindle / Wnt signaling pathway / nuclear membrane / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / nucleolus / nucleoplasm / nucleus / cytosol
Similarity search - Function
Spindlin/spermiogenesis-specific protein / Spindlin/spermiogenesis-specific domain superfamily / Spin/Ssty Family
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi, H. / Liu, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92153302 China
CitationJournal: To be published
Title: Crystal Structure of human Spindlin1-HBx complex
Authors: Liu, W. / Li, H.T.
History
DepositionSep 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spindlin-1
B: HBx
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2504
Polymers27,0662
Non-polymers1842
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-14 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.788, 67.096, 93.695
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 24816.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPIN1, OCR, SPIN / Plasmid: pGex-6p / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y657
#2: Protein/peptide HBx


Mass: 2248.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
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: 2.77 Å3/Da / Density % sol: 55.67 % / Mosaicity: 0.39 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 16%(w/v) PEG 8000, 0.04M Potassium phosphate dibasic, 20% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2021 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 28755 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.043 / Rrim(I) all: 0.11 / Χ2: 0.836 / Net I/σ(I): 4.9 / Num. measured all: 185436
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.836.50.57714310.9050.2430.6270.531100
1.83-1.866.40.48513940.8980.2050.5280.60199.8
1.86-1.96.20.43113850.9170.1870.470.62299.7
1.9-1.946.10.35914170.9460.1580.3930.64799.9
1.94-1.986.80.32814430.9560.1350.3550.63399.9
1.98-2.036.80.28614090.9640.1190.310.73699.9
2.03-2.086.70.24414100.9660.1020.2650.809100
2.08-2.136.60.21414180.9750.090.2330.8599.9
2.13-2.26.50.19614170.9760.0830.2130.92199.9
2.2-2.276.30.1814280.9820.0780.1960.89599.9
2.27-2.355.90.15914280.9840.0710.1750.903100
2.35-2.446.80.15314250.9840.0630.1660.885100
2.44-2.556.80.13314340.9870.0550.1440.922100
2.55-2.696.60.11914480.9920.050.1290.92599.9
2.69-2.866.50.10314280.9920.0440.1120.89999.9
2.86-3.086.10.08714350.9920.0370.0951.02699.7
3.08-3.396.80.07614690.9950.0310.0821.05499.9
3.39-3.886.60.06414560.9960.0270.0691.06799.9
3.88-4.886.10.05314910.9970.0230.0580.99799.7
4.88-5060.04815890.9970.0210.0520.76299.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17.1_3660refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4mzg

4mzg


Resolution: 1.8→46.85 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1967 1396 4.87 %
Rwork0.1631 27292 -
obs0.1647 28688 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.53 Å2 / Biso mean: 23.835 Å2 / Biso min: 9.23 Å2
Refinement stepCycle: final / Resolution: 1.8→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 12 302 2079
Biso mean--34.64 33.62 -
Num. residues----220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.860.26061400.20672599273996
1.86-1.930.25651350.185426742809100
1.93-2.020.22741260.172227132839100
2.02-2.130.17561350.158527112846100
2.13-2.260.17471360.154427122848100
2.26-2.440.21891450.171827172862100
2.44-2.680.21921520.170227402892100
2.68-3.070.20441250.170227482873100
3.07-3.870.17931480.151527742922100
3.87-46.850.17441540.15392904305899

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