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- PDB-4zqa: Crystal Structure of the Sds3 Dimerization Domain -

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Basic information

Entry
Database: PDB / ID: 4zqa
TitleCrystal Structure of the Sds3 Dimerization Domain
ComponentsSin3 histone deacetylase corepressor complex component SDS3
KeywordsTRANSCRIPTION REPRESSOR / transcription repression / histone deacetylase complex / coiled-coil / corepressor complex
Function / homology
Function and homology information


HDACs deacetylate histones / blastocyst hatching / negative regulation of stem cell population maintenance / Ub-specific processing proteases / Sin3-type complex / positive regulation of stem cell population maintenance / negative regulation of cell migration / negative regulation of transforming growth factor beta receptor signaling pathway / histone deacetylase binding / nuclear body ...HDACs deacetylate histones / blastocyst hatching / negative regulation of stem cell population maintenance / Ub-specific processing proteases / Sin3-type complex / positive regulation of stem cell population maintenance / negative regulation of cell migration / negative regulation of transforming growth factor beta receptor signaling pathway / histone deacetylase binding / nuclear body / chromatin remodeling / negative regulation of DNA-templated transcription / apoptotic process / negative regulation of transcription by RNA polymerase II / enzyme binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Sds3-like / Sds3-like / Sds3-like
Similarity search - Domain/homology
Sin3 histone deacetylase corepressor complex component SDS3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.65 Å
AuthorsChan, C.W. / Mondragon, A. / Clark, M. / Radhakrishnan, I.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM64715 United States
American Heart Association14GRNT20170003 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex.
Authors: Clark, M.D. / Marcum, R. / Graveline, R. / Chan, C.W. / Xie, T. / Chen, Z. / Ding, Y. / Zhang, Y. / Mondragon, A. / David, G. / Radhakrishnan, I.
History
DepositionMay 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sin3 histone deacetylase corepressor complex component SDS3


Theoretical massNumber of molelcules
Total (without water)10,3971
Polymers10,3971
Non-polymers00
Water2,162120
1
A: Sin3 histone deacetylase corepressor complex component SDS3

A: Sin3 histone deacetylase corepressor complex component SDS3


Theoretical massNumber of molelcules
Total (without water)20,7942
Polymers20,7942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3590 Å2
ΔGint-30 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.460, 49.390, 106.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Sin3 histone deacetylase corepressor complex component SDS3 / Suppressor of defective silencing 3 protein homolog


Mass: 10396.940 Da / Num. of mol.: 1 / Fragment: UNP residues 90-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Suds3, Sds3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BR65
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 15% ethanol (v/v), 200 mM MgCl2, and 100 mM imidazole
PH range: 7.2-7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856, 0.97872
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978561
20.978721
ReflectionResolution: 1.65→35.5 Å / Num. obs: 13534 / % possible obs: 94.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 11.3
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 2.8 / Num. unique all: 667 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimlessdata scaling
MOSFLMdata reduction
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.65→33 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.328 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20896 685 5.1 %RANDOM
Rwork0.15998 ---
obs0.16257 12803 93.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.075 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å2-0 Å2
2--2.57 Å20 Å2
3----3.79 Å2
Refinement stepCycle: LAST / Resolution: 1.65→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms726 0 0 120 846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.019753
X-RAY DIFFRACTIONr_bond_other_d0.0010.02775
X-RAY DIFFRACTIONr_angle_refined_deg1.3072.0011001
X-RAY DIFFRACTIONr_angle_other_deg0.78131799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.509591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66125.95242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95415183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.809156
X-RAY DIFFRACTIONr_chiral_restr0.0630.2108
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02830
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02156
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4221.705349
X-RAY DIFFRACTIONr_mcbond_other2.281.692348
X-RAY DIFFRACTIONr_mcangle_it3.1992.551436
X-RAY DIFFRACTIONr_mcangle_other3.2112.554437
X-RAY DIFFRACTIONr_scbond_it4.8012.351404
X-RAY DIFFRACTIONr_scbond_other4.7972.353405
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7133.261563
X-RAY DIFFRACTIONr_long_range_B_refined5.98116.641977
X-RAY DIFFRACTIONr_long_range_B_other5.41814.639910
X-RAY DIFFRACTIONr_rigid_bond_restr2.95631528
X-RAY DIFFRACTIONr_sphericity_free39.751533
X-RAY DIFFRACTIONr_sphericity_bonded15.06451608
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 46 -
Rwork0.238 950 -
obs--95.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
118.27762.68126.987210.99892.575837.63220.10620.7876-0.1521-0.49990.058-0.1572-0.16990.8248-0.16420.12590.01050.03680.17810.0030.1598-5.1788-9.3765-72.6208
22.6264-0.52424.40390.5822-0.931111.26830.07490.1939-0.05-0.0639-0.03060.03980.18220.2387-0.04430.0614-0.0094-0.00070.1246-0.00530.1347-0.4023-12.7338-48.6122
31.32870.39773.5320.45131.823814.4930.00760.0992-0.0234-0.08440.0893-0.0477-0.24030.2292-0.09690.0809-0.00260.0050.1120.0060.13819.6032-9.2313-6.8288
41.6005-3.816-6.00539.804615.307823.9263-0.16310.0261-0.09740.25020.04570.07630.43830.050.11740.20350.0046-0.00280.1474-0.00190.179211.25692.507729.6652
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 9
2X-RAY DIFFRACTION2A10 - 36
3X-RAY DIFFRACTION3A37 - 67
4X-RAY DIFFRACTION4A68 - 87

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