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

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Basic information

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


transcription elongation-coupled chromatin remodeling / 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 helical bundle-like domain / Transcription factor IIS, N-terminal / TFIIS N-terminal domain profile. / Transcription Elongation Factor S-II; Chain A ...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 helical bundle-like domain / Transcription factor IIS, N-terminal / TFIIS N-terminal domain profile. / Transcription Elongation Factor S-II; Chain A / TFIIS/LEDGF domain superfamily / SH2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / CHROMATIN STRUCTURE MODULATOR / TFIIS N-terminal domain-containing protein
Similarity search - Component
Biological speciesENCEPHALITOZOON CUNICULI (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IWS1
B: CHROMATIN STRUCTURE MODULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2173
Polymers19,1372
Non-polymers801
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-17 kcal/mol
Surface area8620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.311, 52.311, 151.125
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein IWS1 /


Mass: 16424.105 Da / Num. of mol.: 1 / Fragment: 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: 2712.939 Da / Num. of mol.: 1 / Fragment: N-TERMINAL FRAGMENT, RESIDUES 53-71
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: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsB 49-50 PART OF THROMBIN CLEAVAGE SITE. B 51-52 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: 2.71 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growDetails: 22% PEG3350, 0.2 M NABR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 16077 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 12.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 78.8
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 17 / % possible all: 99.6

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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: 1.95→49.45 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.239 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.142 / 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
Rfree0.23486 803 5 %RANDOM
Rwork0.20985 ---
obs0.21112 15204 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.327 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1269 0 1 132 1402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221288
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9911727
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6045156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79425.09155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47515267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.227157
X-RAY DIFFRACTIONr_chiral_restr0.0990.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021921
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_it0.8091.5785
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4721272
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.573503
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0454.5455
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: 1.949→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 67 -
Rwork0.214 1079 -
obs--99.48 %
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)
12.15080.5344-1.34311.6427-0.39123.99310.1968-0.09680.0439-0.0207-0.1077-0.0799-0.18590.138-0.08920.0364-0.0014-0.01610.072-0.00650.078-7.366618.2967-11.8654
26.7512-4.371-0.824318.64445.471-0.90690.131-0.12-0.16990.7616-0.4271.64630.0437-0.24710.2960.1992-0.06740.09880.2496-0.08350.1484-21.139522.8723-2.3163
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A54 - 191
2X-RAY DIFFRACTION2B50 - 69

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