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- PDB-2e50: Crystal structure of SET/TAF-1beta/INHAT -

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Basic information

Entry
Database: PDB / ID: 2.0E+50
TitleCrystal structure of SET/TAF-1beta/INHAT
ComponentsProtein SET
KeywordsPROTEIN BINDING / Histone chaperone / INHAT / SET / PP2AI
Function / homology
Function and homology information


HuR (ELAVL1) binds and stabilizes mRNA / protein phosphatase regulator activity / nucleosome disassembly / protein phosphatase inhibitor activity / lipid droplet / Condensation of Prophase Chromosomes / nucleosome assembly / histone binding / DNA replication / negative regulation of neuron apoptotic process ...HuR (ELAVL1) binds and stabilizes mRNA / protein phosphatase regulator activity / nucleosome disassembly / protein phosphatase inhibitor activity / lipid droplet / Condensation of Prophase Chromosomes / nucleosome assembly / histone binding / DNA replication / negative regulation of neuron apoptotic process / negative regulation of DNA-templated transcription / chromatin binding / chromatin / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1500 / Nucleosome assembly protein / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Arylsulfatase, C-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
trehalose / Protein SET
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsMuto, S. / Senda, M. / Senda, T. / Horikoshi, M.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Relationship between the structure of SET/TAF-Ibeta/INHAT and its histone chaperone activity
Authors: Muto, S. / Senda, M. / Akai, Y. / Sato, L. / Suzuki, T. / Nagai, R. / Senda, T. / Horikoshi, M.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Purification, crystallization and preliminary X-ray diffraction analysis of human oncoprotein SET/TAF-1beta
Authors: Muto, S. / Senda, M. / Adachi, N. / Suzuki, T. / Nagai, R. / Senda, T. / Horikoshi, M.
History
DepositionDec 18, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: 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 / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein SET
B: Protein SET
P: Protein SET
Q: Protein SET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8498
Polymers105,4804
Non-polymers1,3694
Water2,360131
1
A: Protein SET
B: Protein SET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4254
Polymers52,7402
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-35 kcal/mol
Surface area21020 Å2
MethodPISA
2
P: Protein SET
Q: Protein SET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4254
Polymers52,7402
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-36 kcal/mol
Surface area20960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.913, 64.435, 124.421
Angle α, β, γ (deg.)90.00, 90.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein SET / SET/TAF-1beta / Phosphatase 2A inhibitor I2PP2A / I-2PP2A / Template-activating factor I / TAF-I / ...SET/TAF-1beta / Phosphatase 2A inhibitor I2PP2A / I-2PP2A / Template-activating factor I / TAF-I / HLA-DR associated protein II / PHAPII / Inhibitor of granzyme A-activated DNase / IGAAD


Mass: 26369.982 Da / Num. of mol.: 4 / Fragment: SET/TAF-1beta(residues 1-225) / Mutation: L104M, L145M, L166M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SET / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: Q01105
#2: Polysaccharide
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 2.75M Ammonium sulfate, 0.1M sodium citrate buffer, 0.2M potassium/sodium tartrate, 30mM MgCl2, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A11
SYNCHROTRONPhoton Factory BL-5A20.9791, 0.9794, 0.9850, 0.9740
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDNov 28, 2004
ADSC QUANTUM 3152CCDMay 27, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97911
30.97941
40.9851
50.9741
ReflectionResolution: 2.1→36.25 Å / Num. obs: 54757 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.42 / Num. unique all: 5265 / % possible all: 93.4

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 12.266 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.25 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2104 5 %RANDOM
Rwork0.218 ---
obs0.22 39770 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.11 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å20 Å2-1.17 Å2
2---1.27 Å20 Å2
3---3.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5841 0 92 131 6064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226072
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9588195
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0535676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18525.673342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.483151085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9091520
X-RAY DIFFRACTIONr_chiral_restr0.1040.2880
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024592
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.22576
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24049
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.2160
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9791.53578
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57925616
X-RAY DIFFRACTIONr_scbond_it2.40532871
X-RAY DIFFRACTIONr_scangle_it3.774.52579
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 158 -
Rwork0.218 2931 -
obs--99.13 %
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)
12.6999-1.24560.38171.3492-0.06340.25950.2330.42680.212-0.2042-0.1881-0.1714-0.04540.0326-0.0449-0.1544-0.01890.0552-0.0970.02820.07994.411-1.6980.778
24.13971.67990.05958.0923-1.20543.74050.5192-0.87790.0531.4857-0.5820.1386-0.56590.16520.06280.1071-0.18740.07180.0411-0.0627-0.1487-15.90414.46616.277
34.2349-1.82020.20781.83120.1790.14780.15930.0764-0.3447-0.084-0.11580.28920.0853-0.0122-0.0434-0.1747-0.03380.0161-0.06630.05720.0654-4.96-7.6413.728
44.52890.07072.51455.3681-1.72415.7682-0.1234-0.96710.0610.70310.1722-0.2367-0.2636-0.6539-0.0488-0.1250.055-0.00040.08950.0187-0.126915.853-12.50322.281
53.2921.46880.36651.4634-0.10220.24420.2387-0.41010.33340.2162-0.17660.24-0.0677-0.0238-0.0621-0.15670.01880.0505-0.1014-0.02440.0942-5.2921.38761.621
64.101-0.6996-0.06828.47530.16833.29130.44110.71720.1236-1.5936-0.55760.111-0.3276-0.18440.11650.15750.2028-0.018-0.01670.0705-0.152314.83717.42245.803
75.52162.12990.47852.0047-0.120.11990.09760.085-0.48120.0201-0.0768-0.28770.07130.0108-0.0208-0.15710.02580.0071-0.0609-0.04910.06284.061-4.54758.641
84.50191.58180.95646.36810.72394.9792-0.14931.09220.3015-0.85770.43940.1274-0.02910.3544-0.2901-0.0852-0.0157-0.0610.10670.0158-0.1167-17.015-8.82340.88
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA25 - 7825 - 78
2X-RAY DIFFRACTION2AA79 - 22079 - 220
3X-RAY DIFFRACTION3BB25 - 7825 - 78
4X-RAY DIFFRACTION4BB79 - 22079 - 220
5X-RAY DIFFRACTION5PC25 - 7825 - 78
6X-RAY DIFFRACTION6PC79 - 22079 - 220
7X-RAY DIFFRACTION7QD25 - 7825 - 78
8X-RAY DIFFRACTION8QD79 - 22079 - 220

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