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- PDB-7cna: Crystal structure of Spindlin1/C11orf84 complex bound to histone ... -

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Basic information

Entry
Database: PDB / ID: 7cna
TitleCrystal structure of Spindlin1/C11orf84 complex bound to histone H3K4me3K9me3 peptide
Components
  • (ALA-ARG-THR-M3L-GLN-THR-ALA-ARG-M3L-SER- ...) x 2
  • Spindlin interactor and repressor of chromatin-binding protein
  • Spindlin-1
KeywordsPROTEIN BINDING / epigenetic reader
Function / homology
Function and homology information


regulation of protein ADP-ribosylation / gamete generation / site of DNA damage / rRNA transcription / positive regulation of Wnt signaling pathway / methylated histone binding / meiotic cell cycle / Wnt signaling pathway / spindle / chromatin organization ...regulation of protein ADP-ribosylation / gamete generation / site of DNA damage / rRNA transcription / positive regulation of Wnt signaling pathway / methylated histone binding / meiotic cell cycle / Wnt signaling pathway / spindle / chromatin organization / nuclear membrane / negative regulation of DNA-templated transcription / DNA damage response / regulation of DNA-templated transcription / nucleolus / positive regulation of DNA-templated transcription / 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
BENZAMIDINE / Spindlin interactor and repressor of chromatin-binding protein / Spindlin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsQian, C.M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)17127917 Hong Kong
CitationJournal: Nat Commun / Year: 2021
Title: Structural mechanism of bivalent histone H3K4me3K9me3 recognition by the Spindlin1/C11orf84 complex in rRNA transcription activation.
Authors: Du, Y. / Yan, Y. / Xie, S. / Huang, H. / Wang, X. / Ng, R.K. / Zhou, M.M. / Qian, C.
History
DepositionJul 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Aug 18, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _entity.formula_weight / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id
Revision 2.1Nov 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: Spindlin interactor and repressor of chromatin-binding protein
D: Spindlin-1
E: Spindlin interactor and repressor of chromatin-binding protein
C: ALA-ARG-THR-M3L-GLN-THR-ALA-ARG-M3L-SER-THR
F: ALA-ARG-THR-M3L-GLN-THR-ALA-ARG-M3L-SER-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,78116
Polymers57,8616
Non-polymers91910
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, no assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10810 Å2
ΔGint-73 kcal/mol
Surface area24550 Å2
Unit cell
Length a, b, c (Å)45.603, 101.184, 56.615
Angle α, β, γ (deg.)90.000, 91.410, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Refine code: 0

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGSERSERAA51 - 2621 - 212
221ARGARGSERSERDC51 - 2621 - 212
132THRTHRTHRTHRBB255 - 2822 - 29
242THRTHRTHRTHRED255 - 2822 - 29
153ALAALATHRTHRCE1 - 111 - 11
263ALAALAGLYGLYFF1 - 111 - 11

NCS ensembles :
ID
1
2
3

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Components

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ALA-ARG-THR-M3L-GLN-THR-ALA-ARG-M3L-SER- ... , 2 types, 2 molecules CF

#3: Protein/peptide ALA-ARG-THR-M3L-GLN-THR-ALA-ARG-M3L-SER-THR


Mass: 1392.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Protein/peptide ALA-ARG-THR-M3L-GLN-THR-ALA-ARG-M3L-SER-GLY


Mass: 1348.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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

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


Mass: 24248.344 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 (E. coli) / References: UniProt: Q9Y657
#2: Protein/peptide Spindlin interactor and repressor of chromatin-binding protein / SPIN1-docking protein / SPIN-DOC


Mass: 3311.634 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

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Non-polymers , 4 types, 293 molecules

#5: Chemical
ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H8N2
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.5, 35% PEG3350, 5% glycerol, 2% Benzamidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→35.11 Å / Num. obs: 66759 / % possible obs: 98.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.026 / Net I/σ(I): 32.7
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.11 / Num. unique obs: 10727

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MZF

4mzf


Resolution: 1.6→35.11 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.381 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 2002 3 %RANDOM
Rwork0.1718 ---
obs0.1727 64741 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.09 Å2 / Biso mean: 20.031 Å2 / Biso min: 9.27 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.6→35.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3891 0 63 283 4237
Biso mean--30.03 25.79 -
Num. residues----491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134060
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173688
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.6455506
X-RAY DIFFRACTIONr_angle_other_deg1.4681.5828526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5125489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05823.077208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41915641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5131519
X-RAY DIFFRACTIONr_chiral_restr0.0920.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024550
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02883
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A61140.1
12D61140.1
21B7380.05
22E7380.05
31C1900.18
32F1900.18
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.195 147 -
Rwork0.183 4687 -
obs--96.66 %

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