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- PDB-7ea1: Crystal Structure of Spindlin1 bound to SPINDOC Docpep2 -

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Basic information

Entry
Database: PDB / ID: 7ea1
TitleCrystal Structure of Spindlin1 bound to SPINDOC Docpep2
Components
  • Peptide from Spindlin interactor and repressor of chromatin-binding protein
  • Spindlin-1
KeywordsTRANSCRIPTION / Spin/Ssty repeat
Function / homology
Function and homology information


regulation of protein ADP-ribosylation / transposable element silencing by piRNA-mediated DNA methylation / gamete generation / histone H3K4me3 reader activity / : / histone reader activity / rRNA transcription / site of DNA damage / positive regulation of Wnt signaling pathway / protein localization to chromatin ...regulation of protein ADP-ribosylation / transposable element silencing by piRNA-mediated DNA methylation / gamete generation / histone H3K4me3 reader activity / : / histone reader activity / rRNA transcription / site of DNA damage / positive regulation of Wnt signaling pathway / protein localization to chromatin / meiotic cell cycle / spindle / Wnt signaling pathway / nuclear membrane / negative regulation of DNA-templated transcription / DNA damage response / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / nucleolus / nucleoplasm / nucleus / cytosol
Similarity search - Function
SPIN-DOC-like, zinc-finger / : / Spin-doc zinc-finger / Spindlin/spermiogenesis-specific protein / Spindlin/spermiogenesis-specific domain superfamily / Spin/Ssty Family
Similarity search - Domain/homology
Spindlin interactor and repressor of chromatin-binding protein / Spindlin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhao, F. / Li, H.
CitationJournal: to be published
Title: Molecular basis for SPINDOC-Spindlin1 engagement and its role in transcriptional inhibition
Authors: Zhao, F. / Li, H.
History
DepositionMar 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spindlin-1
B: Peptide from Spindlin interactor and repressor of chromatin-binding protein
C: Spindlin-1
D: Peptide from Spindlin interactor and repressor of chromatin-binding protein


Theoretical massNumber of molelcules
Total (without water)52,0534
Polymers52,0534
Non-polymers00
Water23413
1
A: Spindlin-1
B: Peptide from Spindlin interactor and repressor of chromatin-binding protein


Theoretical massNumber of molelcules
Total (without water)26,0272
Polymers26,0272
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Spindlin-1
D: Peptide from Spindlin interactor and repressor of chromatin-binding protein


Theoretical massNumber of molelcules
Total (without water)26,0272
Polymers26,0272
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.795, 136.904, 42.240
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: 24549.670 Da / Num. of mol.: 2
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 Peptide from Spindlin interactor and repressor of chromatin-binding protein / SPINDOC Docpep2


Mass: 1476.836 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BUA3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.33 Å3/Da / Density % sol: 47.15 % / Mosaicity: 1.069 ° / Mosaicity esd: 0.011 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M Sodium chloride, 0.1M BIS-TRIS pH 6.5, 1.5M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 3, 2018 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.689→50 Å / Num. obs: 14134 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.045 / Rrim(I) all: 0.113 / Χ2: 1.085 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.755.60.4226710.9140.1920.4650.59799.9
2.75-2.86.60.3847080.9620.1610.4170.559100
2.8-2.856.80.347010.9730.140.3680.628100
2.85-2.916.80.316800.9710.1280.3360.66299.9
2.91-2.976.80.256870.9720.1040.2720.69599.9
2.97-3.046.70.2347070.9750.0970.2530.74699.9
3.04-3.126.70.1886850.9870.0790.2050.81499.9
3.12-3.26.70.196950.9830.0790.2060.86599.9
3.2-3.36.60.1776930.9880.0750.1931.049100
3.3-3.46.60.1416970.9880.060.1531.021100
3.4-3.526.50.1287140.9880.0560.141.178100
3.52-3.666.30.126810.9910.0520.1311.17799.9
3.66-3.8360.1097230.9920.0490.121.24899.9
3.83-4.035.30.1076880.9910.050.1181.44999.6
4.03-4.296.60.0967140.9920.040.1041.5199.9
4.29-4.626.70.0937120.990.0390.1011.45299.9
4.62-5.086.50.0917090.9930.0390.0991.45199.9
5.08-5.816.40.0867220.9910.0370.0941.51499.3
5.81-7.325.80.0897480.9920.0390.0971.4399.7
7.32-505.60.0847990.9930.0380.0931.75299

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
DENZOdata reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NS2

2ns2


Resolution: 2.7→40.363 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 34.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2859 666 4.74 %
Rwork0.2537 13396 -
obs0.2553 14062 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 234.11 Å2 / Biso mean: 100.4159 Å2 / Biso min: 35.4 Å2
Refinement stepCycle: final / Resolution: 2.7→40.363 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3168 0 20 13 3201
Biso mean--145.13 60.83 -
Num. residues----389
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.89680.37911420.3069257898
2.8968-3.18820.33751010.29112672100
3.1882-3.64930.33571410.26642637100
3.6493-4.59670.28291400.22832696100
4.5967-40.3630.24481420.2493281399
Refinement TLS params.Method: refined / Origin x: -0.525 Å / Origin y: 9.626 Å / Origin z: -6.152 Å
111213212223313233
T0.4864 Å20.0116 Å2-0.0385 Å2-0.5391 Å20.0449 Å2--0.4996 Å2
L1.4971 °2-0.3793 °20.4297 °2-3.0495 °2-0.2184 °2--1.5537 °2
S-0.11 Å °-0.1311 Å °0.223 Å °-0.1067 Å °0.1735 Å °0.4227 Å °-0.2181 Å °-0.2558 Å °-0.0786 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 48:261 OR RESID 301:310 ) ) OR ( CHAIN B AND RESID 228:232 ) OR ( CHAIN C AND ( RESID 48:262 OR RESID 301:303 ) ) OR ( CHAIN D AND RESID 229:230 )A48 - 261
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 48:261 OR RESID 301:310 ) ) OR ( CHAIN B AND RESID 228:232 ) OR ( CHAIN C AND ( RESID 48:262 OR RESID 301:303 ) ) OR ( CHAIN D AND RESID 229:230 )A301 - 310
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 48:261 OR RESID 301:310 ) ) OR ( CHAIN B AND RESID 228:232 ) OR ( CHAIN C AND ( RESID 48:262 OR RESID 301:303 ) ) OR ( CHAIN D AND RESID 229:230 )B228 - 232
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 48:261 OR RESID 301:310 ) ) OR ( CHAIN B AND RESID 228:232 ) OR ( CHAIN C AND ( RESID 48:262 OR RESID 301:303 ) ) OR ( CHAIN D AND RESID 229:230 )C48 - 262
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 48:261 OR RESID 301:310 ) ) OR ( CHAIN B AND RESID 228:232 ) OR ( CHAIN C AND ( RESID 48:262 OR RESID 301:303 ) ) OR ( CHAIN D AND RESID 229:230 )C301 - 303
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 48:261 OR RESID 301:310 ) ) OR ( CHAIN B AND RESID 228:232 ) OR ( CHAIN C AND ( RESID 48:262 OR RESID 301:303 ) ) OR ( CHAIN D AND RESID 229:230 )D229 - 230

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