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- PDB-6g5p: Crystal structure of human SP100 in complex with bromodomain-focu... -

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Basic information

Entry
Database: PDB / ID: 6g5p
TitleCrystal structure of human SP100 in complex with bromodomain-focused fragment FM009493b 2,3-Dimethoxy-2,3-dimethyl-2,3-dihydro-1,4-benzodioxin-6-amine
ComponentsNuclear autoantigen Sp-100
KeywordsTRANSCRIPTION / FRAGMENT SCREENING / EPIGENETICS / BROMODOMAIN / STRUCTURAL GENOMICS CONSORTIUM / SGC / XCHEM / DIAMOND I04-1 / PANDDA / XCHEMEXPLORER
Function / homology
Function and homology information


regulation of Fas signaling pathway / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell migration / type I interferon-mediated signaling pathway / response to type II interferon ...regulation of Fas signaling pathway / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell migration / type I interferon-mediated signaling pathway / response to type II interferon / negative regulation of DNA binding / DNA damage response, signal transduction by p53 class mediator / retinoic acid receptor signaling pathway / regulation of angiogenesis / SUMOylation of DNA damage response and repair proteins / type II interferon-mediated signaling pathway / response to retinoic acid / telomere maintenance / nuclear periphery / response to cytokine / negative regulation of DNA-binding transcription factor activity / PML body / kinase binding / positive regulation of DNA-binding transcription factor activity / Interferon gamma signaling / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / nuclear body / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / protein domain specific binding / negative regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily / HMG-box domain ...HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Bromodomain-like / Histone Acetyltransferase; Chain A / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-EN8 / Nuclear autoantigen Sp-100
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsTalon, R.P.H. / Krojer, T. / Tallant, C. / Nunez-Alonso, G. / Fairhead, M. / Szykowska, A. / Collins, P. / Pearce, N.M. / Ng, J. / MacLean, E. ...Talon, R.P.H. / Krojer, T. / Tallant, C. / Nunez-Alonso, G. / Fairhead, M. / Szykowska, A. / Collins, P. / Pearce, N.M. / Ng, J. / MacLean, E. / Wright, N. / Douangamath, A. / Brandao-Neto, J. / Burgess-Brown, N. / Huber, K. / Knapp, S. / Brennan, P.E. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: Biorxiv / Year: 2018
Title: Identifying small molecule binding sites for epigenetic proteins at domain-domain interfaces
Authors: Talon, R.P.H. / Bowkett, D. / Tallant, C. / Schofield, C. / von Delft, F. / Knapp, S. / Bruton, G. / Brennan, P.E.
History
DepositionMar 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _citation.journal_id_ISSN ..._chem_comp.name / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear autoantigen Sp-100
B: Nuclear autoantigen Sp-100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,97713
Polymers42,9972
Non-polymers98011
Water9,530529
1
A: Nuclear autoantigen Sp-100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2508
Polymers21,4991
Non-polymers7527
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear autoantigen Sp-100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7275
Polymers21,4991
Non-polymers2284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.855, 45.429, 83.715
Angle α, β, γ (deg.)90.00, 101.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nuclear autoantigen Sp-100 / Nuclear dot-associated Sp100 protein / Speckled 100 kDa


Mass: 21498.564 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SP100 / Variant: SP100C / Plasmid: Plasmid / Details (production host): PSUMO-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: P23497

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Non-polymers , 6 types, 540 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-EN8 / (2~{R},3~{R})-2,3-dimethoxy-2,3-dimethyl-1,4-benzodioxin-6-amine


Mass: 239.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17NO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.77 Å3/Da / Density % sol: 55.56 % / Description: Prism
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 17-23% PEG20K, 0.1M MES 6.1, 2-4% Ethylene glycol, 4 days
Temp details: Rigaku Minstrel imagers

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryo stream
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.35→28.59 Å / Num. obs: 101393 / % possible obs: 97.8 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.028 / Rrim(I) all: 0.041 / Net I/σ(I): 16
Reflection shellResolution: 1.35→1.38 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7160 / CC1/2: 0.615 / Rpim(I) all: 0.495 / Rrim(I) all: 0.74 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1682refinement
XDSdata reduction
Aimless0.3.6data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Internal

Resolution: 1.35→28.589 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.55
RfactorNum. reflection% reflection
Rfree0.1738 5097 5.03 %
Rwork0.1375 --
obs0.1392 101332 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→28.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2881 0 50 529 3460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143145
X-RAY DIFFRACTIONf_angle_d1.4024258
X-RAY DIFFRACTIONf_dihedral_angle_d14.4551279
X-RAY DIFFRACTIONf_chiral_restr0.228433
X-RAY DIFFRACTIONf_plane_restr0.008557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3487-1.3640.3211480.2782832X-RAY DIFFRACTION86
1.364-1.38010.28571690.23873267X-RAY DIFFRACTION99
1.3801-1.39690.23121680.22723205X-RAY DIFFRACTION99
1.3969-1.41460.23521870.21153272X-RAY DIFFRACTION100
1.4146-1.43320.22391670.20273221X-RAY DIFFRACTION99
1.4332-1.45280.24241760.17933248X-RAY DIFFRACTION100
1.4528-1.47360.21321630.17293285X-RAY DIFFRACTION99
1.4736-1.49560.19961650.15683227X-RAY DIFFRACTION99
1.4956-1.5190.20991730.14163260X-RAY DIFFRACTION100
1.519-1.54390.18781850.13333241X-RAY DIFFRACTION99
1.5439-1.57050.15121880.12233223X-RAY DIFFRACTION99
1.5705-1.5990.14681720.10793202X-RAY DIFFRACTION99
1.599-1.62980.14041670.10863176X-RAY DIFFRACTION97
1.6298-1.66310.15361670.10482948X-RAY DIFFRACTION90
1.6631-1.69920.14891930.10473205X-RAY DIFFRACTION98
1.6992-1.73870.13461730.10173268X-RAY DIFFRACTION99
1.7387-1.78220.13451760.10053227X-RAY DIFFRACTION100
1.7822-1.83040.1461760.10223294X-RAY DIFFRACTION100
1.8304-1.88420.16731680.10813252X-RAY DIFFRACTION100
1.8842-1.9450.18111740.14063199X-RAY DIFFRACTION97
1.945-2.01450.14111560.11613230X-RAY DIFFRACTION99
2.0145-2.09520.15951630.11693273X-RAY DIFFRACTION98
2.0952-2.19050.14171750.11933227X-RAY DIFFRACTION98
2.1905-2.30590.15911510.13633064X-RAY DIFFRACTION93
2.3059-2.45030.1721850.12813117X-RAY DIFFRACTION95
2.4503-2.63940.17981710.13513287X-RAY DIFFRACTION99
2.6394-2.90480.16281770.14053271X-RAY DIFFRACTION99
2.9048-3.32460.18581730.15283212X-RAY DIFFRACTION97
3.3246-4.18650.18851450.13513242X-RAY DIFFRACTION95
4.1865-28.59550.18131460.15353260X-RAY DIFFRACTION94

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