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

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Basic information

Entry
Database: PDB / ID: 2xpo
TitleCrystal structure of a Spt6-Iws1(Spn1) complex from Encephalitozoon cuniculi, Form II
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: 2.1 Å
AuthorsDiebold, M.-L. / Koch, M. / Cura, V. / Moras, D. / 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
C: IWS1
D: CHROMATIN STRUCTURE MODULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3456
Polymers38,2744
Non-polymers712
Water2,720151
1
A: IWS1
B: CHROMATIN STRUCTURE MODULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1723
Polymers19,1372
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-28.5 kcal/mol
Surface area8750 Å2
MethodPISA
2
C: IWS1
D: CHROMATIN STRUCTURE MODULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1723
Polymers19,1372
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-26.9 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.578, 112.578, 51.481
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein IWS1 / ECU08_0440


Mass: 16424.105 Da / Num. of mol.: 2 / 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: 2712.939 Da / Num. of mol.: 2 / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsB, D 49-50 PART OF THROMBIN CLEAVAGE SITE. B, D 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: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 5 / Details: 0.1 M SODIUM ACETATE 18% PEG1500 0.05 M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 21935 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 33.6
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 10.47 / % possible all: 100

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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: 2.1→97.5 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.188 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.181 / 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
Rfree0.23862 1124 5.1 %RANDOM
Rwork0.18777 ---
obs0.19031 20780 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0.47 Å20 Å2
2---0.95 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.1→97.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2474 0 2 151 2627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222512
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.9913369
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8355303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16425108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13315518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2351514
X-RAY DIFFRACTIONr_chiral_restr0.110.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211800
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_it0.771.51525
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37922472
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7543987
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5294.5897
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: 2.099→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 80 -
Rwork0.178 1485 -
obs--98.06 %
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)
12.70980.1060.69992.86490.1021.942-0.0507-0.03520.03280.02920.03580.1599-0.0348-0.16510.0150.0704-0.00320.02770.06-0.01560.028-29.0492-25.29570.8511
228.5688-3.31242.08079.44142.00243.3933-0.08440.4057-2.14260.00790.37420.23630.44570.0163-0.28980.2618-0.04720.06210.1375-0.010.2272-32.3544-40.3745-5.2229
32.6941-0.2671-0.08163.1223-0.91061.86730.0223-0.0657-0.1686-0.11830.05910.11070.1469-0.0948-0.08150.0618-0.00020.00210.0926-0.02120.0319-35.5234-15.228426.0902
45.19629.1064-2.98627.52150.02944.08230.488-0.48940.7440.2835-0.50782.176-0.33470.04870.01980.1177-0.0440.02960.5220.00030.3323-50.278-11.86932.973
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A54 - 192
2X-RAY DIFFRACTION2B53 - 67
3X-RAY DIFFRACTION3C54 - 192
4X-RAY DIFFRACTION4D53 - 66

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