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- PDB-4nuf: Crystal Structure of SHP/EID1 -

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Basic information

Entry
Database: PDB / ID: 4nuf
TitleCrystal Structure of SHP/EID1
Components
  • EID1 peptide
  • Maltose ABC transporter periplasmic protein, Nuclear receptor subfamily 0 group B member 2 chimeric construct
KeywordsTRANSCRIPTION / protein-peptide complex / peptide mimicking protein helix / sandwich fold / transport protein
Function / homology
Function and homology information


histone acetyltransferase regulator activity / Nuclear Receptor transcription pathway / nuclear retinoic acid receptor binding / bile acid and bile salt transport / peroxisome proliferator activated receptor binding / transcription regulator inhibitor activity / nuclear thyroid hormone receptor binding / histone acetyltransferase binding / detection of maltose stimulus / maltose binding ...histone acetyltransferase regulator activity / Nuclear Receptor transcription pathway / nuclear retinoic acid receptor binding / bile acid and bile salt transport / peroxisome proliferator activated receptor binding / transcription regulator inhibitor activity / nuclear thyroid hormone receptor binding / histone acetyltransferase binding / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / regulation of cell differentiation / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / animal organ regeneration / response to glucose / nuclear retinoid X receptor binding / Notch signaling pathway / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / circadian regulation of gene expression / negative regulation of DNA-binding transcription factor activity / cytoplasmic ribonucleoprotein granule / positive regulation of insulin secretion / response to organic cyclic compound / circadian rhythm / transcription corepressor activity / outer membrane-bounded periplasmic space / response to ethanol / cell differentiation / periplasmic space / cell cycle / protein domain specific binding / negative regulation of gene expression / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / DNA damage response / chromatin / protein-containing complex binding / positive regulation of gene expression / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / nucleoplasm / membrane / nucleus / cytoplasm
Similarity search - Function
EP300-interacting inhibitor of differentiation 1 / EP300-interacting inhibitor of differentiation / Nuclear receptor subfamily 0 group B member 1/2 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Retinoid X Receptor / Retinoid X Receptor ...EP300-interacting inhibitor of differentiation 1 / EP300-interacting inhibitor of differentiation / Nuclear receptor subfamily 0 group B member 1/2 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
alpha-maltose / : / Maltose/maltodextrin-binding periplasmic protein / Nuclear receptor subfamily 0 group B member 2 / EP300-interacting inhibitor of differentiation 1
Similarity search - Component
Biological speciesEscherichia coli O104:H4 (bacteria)
mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsZhi, X. / Zhou, X.E. / He, Y. / Zechner, C. / Suino-Powell, K.M. / Kliewer, S.A. / Melcher, K. / Mangelsdorf, D.J. / Xu, H.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural insights into gene repression by the orphan nuclear receptor SHP.
Authors: Zhi, X. / Zhou, X.E. / He, Y. / Zechner, C. / Suino-Powell, K.M. / Kliewer, S.A. / Melcher, K. / Mangelsdorf, D.J. / Xu, H.E.
History
DepositionDec 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_ref_seq_dif / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose ABC transporter periplasmic protein, Nuclear receptor subfamily 0 group B member 2 chimeric construct
P: EID1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3463
Polymers66,0032
Non-polymers3421
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-12 kcal/mol
Surface area24410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.388, 105.148, 136.277
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Maltose ABC transporter periplasmic protein, Nuclear receptor subfamily 0 group B member 2 chimeric construct


Mass: 64185.230 Da / Num. of mol.: 1 / Fragment: MBP unp residues 27-391, SHP unp residues 55-260 / Mutation: E85D, L126T, E127T, E128R, K228R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O104:H4 (bacteria), (gene. exp.) mus musculus (house mouse)
Strain: 2009EL-2071 / Gene: malE, malE O3O_01660, Nr0b2, Shp / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: K0BGG6, UniProt: Q62227, UniProt: P0AEX9*PLUS
#2: Protein/peptide EID1 peptide / Orphan nuclear receptor SHP / Small heterodimer partner


Mass: 1818.124 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: Q9DCR4*PLUS
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.21 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 298 K / pH: 9.5
Details: PEG 3000, pH 9.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 15, 2012
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 17181 / % possible obs: 83.3 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 0 Å2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2319
RfactorNum. reflection% reflection
Rfree0.245 1158 5.6 %
Rwork0.196 --
obs0.196 17181 83.3 %
Solvent computationBsol: 15.16 Å2
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.924 Å20 Å20 Å2
2---4.433 Å20 Å2
3---16.357 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4421 0 23 49 4493
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.3481.5
X-RAY DIFFRACTIONc_mcangle_it2.3682
X-RAY DIFFRACTIONc_scbond_it1.8472
X-RAY DIFFRACTIONc_scangle_it2.9432.5
LS refinement shellResolution: 2.8→2.9 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3668 67 -
Rwork0.262 1111 -
obs--58.1 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3CNS_TOPPAR:WATER_REP.PARAM
X-RAY DIFFRACTION4CNS_TOPPAR:ION.PARAM
X-RAY DIFFRACTION5CNS_TOPPAR:CARBOHYDRATE.PARAM
X-RAY DIFFRACTION6MAL_PAR.TXT

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