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- PDB-7e9m: Crystal Structure of Spindlin1 bound to SPINDOC Docpep3 -

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Basic information

Entry
Database: PDB / ID: 7e9m
TitleCrystal Structure of Spindlin1 bound to SPINDOC Docpep3
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: 2.5 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 4, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)65,1964
Polymers65,1964
Non-polymers00
Water1,67593
1
A: Spindlin-1
B: Peptide from Spindlin interactor and repressor of chromatin-binding protein


Theoretical massNumber of molelcules
Total (without water)32,5982
Polymers32,5982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-22 kcal/mol
Surface area12240 Å2
MethodPISA
2
C: Spindlin-1
D: Peptide from Spindlin interactor and repressor of chromatin-binding protein


Theoretical massNumber of molelcules
Total (without water)32,5982
Polymers32,5982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-22 kcal/mol
Surface area11950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.612, 45.541, 85.984
Angle α, β, γ (deg.)90.000, 93.090, 90.000
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 52 through 194 or resid 206 through 262))
21chain C
12chain B
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNPROPRO(chain A and (resid 52 through 194 or resid 206 through 262))AA52 - 19452 - 194
121PROPROSERSER(chain A and (resid 52 through 194 or resid 206 through 262))AA206 - 262206 - 262
211ASNASNSERSERchain CCC52 - 26252 - 262
112PHEPHEHISHISchain BBB256 - 2811 - 26
212PHEPHEHISHISchain DDD256 - 2811 - 26

NCS ensembles :
ID
1
2

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Components

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


Mass: 29644.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPIN1, OCR, SPIN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y657
#2: Protein/peptide Peptide from Spindlin interactor and repressor of chromatin-binding protein / SPIN1-docking protein / SPIN-DOC


Mass: 2953.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPINDOC, C11orf84 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BUA3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 0.567 ° / Mosaicity esd: 0.017 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 0.2M magnesium acetate, 0.1M Sodium cacodylate pH 6.5, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2020 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 20960 / % possible obs: 99.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.079 / Rrim(I) all: 0.137 / Χ2: 0.934 / Net I/σ(I): 5.9 / Num. measured all: 61133
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.542.90.67610010.910.4980.8441.3597.7
2.54-2.5930.66310290.6580.4530.8060.47799.9
2.59-2.6430.63410590.670.4370.7730.43999.7
2.64-2.692.80.59210270.7780.4240.7311.07899.5
2.69-2.752.70.44410330.7970.3240.5520.491100
2.75-2.822.90.43410460.7810.3120.5370.97399.4
2.82-2.893.10.37210490.8890.2510.4510.48799.8
2.89-2.963.10.28510310.8760.1930.3450.51998.9
2.96-3.053.10.21110600.9370.1430.2560.534100
3.05-3.1530.15810340.960.1090.1920.594100
3.15-3.262.90.20410370.9690.1550.2581.4298.8
3.26-3.392.90.11810430.9790.0840.1460.699100
3.39-3.552.80.12410550.9680.090.1541.19799.1
3.55-3.7330.11410670.9730.0790.1391.39799.6
3.73-3.9730.09110180.980.0630.1111.41799.3
3.97-4.273.10.05110740.9940.0350.0621.04699.6
4.27-4.72.80.04510540.9950.0330.0561.24399.4
4.7-5.382.90.04210670.9960.0290.0511.14699.6
5.38-6.782.90.04510740.9960.0310.0551.05599.9
6.78-502.60.03711020.9970.0260.0451.29197.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DENZOdata reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NS2

2ns2


Resolution: 2.5→38.75 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 1017 4.87 %
Rwork0.2036 19864 -
obs0.2061 20881 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.16 Å2 / Biso mean: 43.0809 Å2 / Biso min: 16.09 Å2
Refinement stepCycle: final / Resolution: 2.5→38.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3593 0 0 93 3686
Biso mean---40.33 -
Num. residues----448
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1858X-RAY DIFFRACTION11.633TORSIONAL
12C1858X-RAY DIFFRACTION11.633TORSIONAL
21B232X-RAY DIFFRACTION11.633TORSIONAL
22D232X-RAY DIFFRACTION11.633TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.630.32421370.32682726286397
2.63-2.80.32651440.26962833297799
2.8-3.010.26821700.23942790296099
3.01-3.320.2961210.20692862298399
3.32-3.80.26091310.19472864299599
3.8-4.780.21491620.16052857301999
4.78-38.750.22761520.18682932308499

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