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- PDB-2xpp: Crystal structure of a Spt6-Iws1(Spn1) complex from Encephalitozo... -

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Basic information

Entry
Database: PDB / ID: 2xpp
TitleCrystal structure of a Spt6-Iws1(Spn1) complex from Encephalitozoon cuniculi, Form III
Components
  • CHROMATIN STRUCTURE MODULATOR
  • IWS1
KeywordsTRANSCRIPTION / ELONGATION / HISTONE CHAPERONE / RNA POLYMERASE II / MRNA EXPORT
Function / homology
Function and homology information


nucleosome organization / poly(A)+ mRNA export from nucleus / transcription elongation-coupled chromatin remodeling / nucleosome binding / transcription elongation factor complex / histone binding / nucleus
Similarity search - Function
Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / : / Spt6, Death-like domain / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / TFIIS N-terminal domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain ...Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / : / Spt6, Death-like domain / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / TFIIS N-terminal domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / Transcription Elongation Factor S-II; Chain A / TFIIS/LEDGF domain superfamily / SH2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CHROMATIN STRUCTURE MODULATOR / TFIIS N-terminal domain-containing protein
Similarity search - Component
Biological speciesENCEPHALITOZOON CUNICULI (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsDiebold, M.-L. / Koch, M. / Cura, V. / Cavarelli, J. / Romier, C.
CitationJournal: Embo J. / Year: 2010
Title: The Structure of an Iws1/Spt6 Complex Reveals an Interaction Domain Conserved in Tfiis, Elongin a and Med26
Authors: Diebold, M.-L. / Koch, M. / Loeliger, E. / Cura, V. / Winston, F. / Cavarelli, J. / Romier, C.
History
DepositionAug 27, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IWS1
B: CHROMATIN STRUCTURE MODULATOR


Theoretical massNumber of molelcules
Total (without water)21,2922
Polymers21,2922
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-19.1 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.356, 56.053, 116.444
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 IWS1 / ECU08_0440


Mass: 16424.105 Da / Num. of mol.: 1 / Fragment: EVOLUTIONARY CONSERVED DOMAIN, RESIDUES 55-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENCEPHALITOZOON CUNICULI (fungus) / Plasmid: PNCS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8SUS7
#2: Protein/peptide CHROMATIN STRUCTURE MODULATOR / SPT6


Mass: 4868.177 Da / Num. of mol.: 1 / Fragment: N-TERMINAL FRAGMENT, RESIDUES 34-71
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENCEPHALITOZOON CUNICULI (fungus) / Plasmid: PNEA-TH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8SRG7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsB 30-31 PART OF THROMBIN CLEAVAGE SITE. B 32-33 PART OF NDEI CLONING SITE.

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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: 2.1 Å3/Da / Density % sol: 41.4 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M SUCCINIC ACID/SODIUM DIHYDROGEN PHOSPHATE/GLYCINE SYSTEM PH 7.0 33% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.977
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 18952 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 44.6
Reflection shellResolution: 1.74→1.81 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 9.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XPL

2xpl


Resolution: 1.74→58.22 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.166 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.23381 973 5.1 %RANDOM
Rwork0.19411 ---
obs0.1961 17980 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.464 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.74→58.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 0 0 170 1470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221319
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.9911768
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8245159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.41724.82858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24615272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.22158
X-RAY DIFFRACTIONr_chiral_restr0.1060.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021947
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9581.5798
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75421291
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8893521
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8874.5477
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.741→1.786 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 48 -
Rwork0.268 1236 -
obs--94.76 %
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)
11.30170.0921-0.26931.7415-0.26012.81410.0271-0.0495-0.0284-0.01220.00080.05920.07070.0211-0.02790.0196-0.0070.00690.06350.0120.05513.08015.499715.9035
23.29710.24766.38910.43012.577722.0512-0.36540.07770.2712-0.09920.3255-0.2314-1.58771.31550.03990.1577-0.07580.02520.2221-0.09820.231823.278716.692826.7321
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A57 - 193
2X-RAY DIFFRACTION2B45 - 67

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