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- PDB-3oak: Crystal structure of a Spn1 (Iws1)-Spt6 complex -

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Basic information

Entry
Database: PDB / ID: 3oak
TitleCrystal structure of a Spn1 (Iws1)-Spt6 complex
Components
  • Transcription elongation factor SPT6
  • Transcription factor IWS1
KeywordsTRANSCRIPTION / Transcription factor complex / Nucleus
Function / homology
Function and homology information


transcription antitermination factor activity, DNA binding / regulation of transcriptional start site selection at RNA polymerase II promoter / regulation of mRNA 3'-end processing / regulation of transcription elongation by RNA polymerase II / nucleosome organization / poly(A)+ mRNA export from nucleus / transcription elongation-coupled chromatin remodeling / cellular response to stress / RNA polymerase II complex binding / RNA polymerase II, core complex ...transcription antitermination factor activity, DNA binding / regulation of transcriptional start site selection at RNA polymerase II promoter / regulation of mRNA 3'-end processing / regulation of transcription elongation by RNA polymerase II / nucleosome organization / poly(A)+ mRNA export from nucleus / transcription elongation-coupled chromatin remodeling / cellular response to stress / RNA polymerase II complex binding / RNA polymerase II, core complex / nucleosome binding / transcription elongation factor complex / transcription antitermination / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / euchromatin / G1/S transition of mitotic cell cycle / nucleosome assembly / chromatin organization / RNA polymerase II-specific DNA-binding transcription factor binding / histone binding / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleus
Similarity search - Function
Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / : / Spt6, S1/OB domain / : / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif ...Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / : / Spt6, S1/OB domain / : / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 / Helix-hairpin-helix motif / Holliday-junction resolvase-like of SPT6 / Helix-turn-helix DNA-binding domain of SPT6 / Tex-like protein, HTH domain superfamily / Tex-like domain superfamily / Spt6, Death-like domain / : / Tex central region-like / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / YqgF/RNase H-like domain superfamily / TFIIS N-terminal domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / Transcription Elongation Factor S-II; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / RuvA domain 2-like / TFIIS/LEDGF domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Ribonuclease H-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription elongation factor SPT6 / Transcription factor SPN1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsMcDonald, S.M. / Close, D. / Hill, C.P.
CitationJournal: Mol.Cell / Year: 2010
Title: Structure and biological importance of the spn1-spt6 interaction, and its regulatory role in nucleosome binding.
Authors: McDonald, S.M. / Close, D. / Xin, H. / Formosa, T. / Hill, C.P.
History
DepositionAug 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor IWS1
B: Transcription factor IWS1
C: Transcription elongation factor SPT6
D: Transcription elongation factor SPT6


Theoretical massNumber of molelcules
Total (without water)41,5374
Polymers41,5374
Non-polymers00
Water4,828268
1
A: Transcription factor IWS1
D: Transcription elongation factor SPT6


Theoretical massNumber of molelcules
Total (without water)20,7692
Polymers20,7692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-10 kcal/mol
Surface area10220 Å2
MethodPISA
2
B: Transcription factor IWS1
C: Transcription elongation factor SPT6


Theoretical massNumber of molelcules
Total (without water)20,7692
Polymers20,7692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-10 kcal/mol
Surface area10390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.858, 68.697, 73.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-6-

HOH

21B-59-

HOH

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Components

#1: Protein Transcription factor IWS1 / Interacts with SPT6 protein 1 / Suppresses postrecruitment functions protein 1


Mass: 17045.719 Da / Num. of mol.: 2 / Fragment: Spn1 core domain, UNP reisudes 148-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: IWS1, SPN1, YPR133C / Production host: Escherichia coli (E. coli) / References: UniProt: Q06505
#2: Protein/peptide Transcription elongation factor SPT6 / Chromatin elongation factor SPT6


Mass: 3722.953 Da / Num. of mol.: 2 / Fragment: Spt6 N-terminal segment, UNP residues 239-263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPT6, CRE2, SSN20, YGR116W, G6169 / Production host: Escherichia coli (E. coli) / References: UniProt: P23615
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 0.2 M magnesium acetate, 0.1 M MES pH 6.5, 20% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 2009
RadiationMonochromator: varimax optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 30152 / % possible obs: 100 %
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.544 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.15 Å29.87 Å
Translation2.15 Å29.87 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→27.73 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / Phase error: 22.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 1526 5.07 %
Rwork0.186 --
obs0.189 30095 99.8 %
all-30152 -
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.73 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 62.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.6397 Å20 Å20 Å2
2--1.5107 Å2-0 Å2
3---5.1289 Å2
Refinement stepCycle: LAST / Resolution: 2.15→27.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2903 0 0 268 3171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122952
X-RAY DIFFRACTIONf_angle_d1.2793995
X-RAY DIFFRACTIONf_dihedral_angle_d16.3841111
X-RAY DIFFRACTIONf_chiral_restr0.065464
X-RAY DIFFRACTIONf_plane_restr0.005510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.22270.26641600.23222745X-RAY DIFFRACTION99
2.2227-2.31170.27221750.2082800X-RAY DIFFRACTION100
2.3117-2.41680.24171380.19692811X-RAY DIFFRACTION100
2.4168-2.54420.2811460.18532847X-RAY DIFFRACTION100
2.5442-2.70350.23451400.17712840X-RAY DIFFRACTION100
2.7035-2.9120.24031400.18012843X-RAY DIFFRACTION100
2.912-3.20460.25991640.18752874X-RAY DIFFRACTION100
3.2046-3.66750.22661650.17352857X-RAY DIFFRACTION100
3.6675-4.61720.21891470.1472922X-RAY DIFFRACTION100
4.6172-27.73750.231510.19453030X-RAY DIFFRACTION99
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)
10.03220.0485-0.04130.0572-0.03110.00310.0803-0.19670.27581.535-0.7233-0.3805-0.9177-1.30310.00270.3902-0.04250.29671.1972-0.54831.6518-38.176433.4262-13.5807
20.5243-0.04750.14520.23980.05270.4308-0.5731-0.84720.397-0.40710.82831.49240.6193-1.4929-0.00030.45410.0723-0.04260.48440.01220.5672-33.976240.8771-13.4106
31.05050.83451.00172.03671.27243.10860.29630.4525-0.3263-0.591-0.04390.2065-0.1109-0.2385-0.00030.3022-0.02910.01460.306-0.06190.2171-15.905129.4518-14.5999
40.2728-0.2441-0.26770.18160.17840.2398-0.10290.00360.34430.63150.3435-1.5483-0.07730.5486-0.00130.33420.1570.09430.478-0.12271.09443.248222.9337-16.9753
50.69190.1468-0.1151-0.04790.17280.48010.03650.33040.1048-0.4448-0.16250.1618-0.26870.2115-0.00050.3505-0.0152-0.0130.33990.02630.3379-13.106437.6176-8.9274
60.62880.790.31161.5043-1.28834.15420.0849-0.2861-0.3188-0.1096-0.0826-0.0547-0.0251-0.0134-0.00020.3376-0.03010.0030.3030.01780.3396-14.357729.7813-3.819
71.83990.2690.35021.3364-1.74931.87640.186-0.9153-0.28610.25910.06360.15810.302-0.44190.00020.3821-0.0983-0.01980.43020.09640.3752-18.35425.26813.2694
80.35470.1447-0.57170.4798-0.3740.75560.5156-0.9091-1.111-0.9171-0.5742-1.6978-0.05830.36740.00470.4613-0.19740.00390.57750.17220.6178-1.941927.04865.978
90.8752-0.0774-0.09450.632-0.12430.87721.4160.21650.753-0.4315-0.7296-0.9472-0.62651.3068-0.00440.5325-0.2038-0.13620.4346-0.05340.3962-12.25928.583411.1321
100.098-0.0176-0.09010.6923-0.34870.2165-0.5403-0.09161.09411.49050.15380.3389-1.0201-0.73270.00110.4258-0.26570.00070.9567-0.07160.6581-21.907726.35412.7663
110.1543-0.0972-0.1310.04250.07240.1093-1.2566-0.474-0.3171-1.9922-0.4101-1.3605-1.60910.995-0.00220.620.03290.14621.27150.17560.6911-15.511739.8177-20.7896
120.55991.11840.68381.7714-0.69641.73620.5205-0.5094-0.50040.927-0.5039-1.21-0.04080.41960.00170.34110.0023-0.01740.34820.03140.3438-31.987236.0769-23.0003
130.0491-0.0140.01950.11710.03850.03711.0431-0.24350.19911.60660.12881.11291.9937-0.2854-0.00011.2971-0.3515-0.10471.43230.23250.5482-50.775418.5862-21.6998
140.37880.22050.86780.14920.2214.89930.667-1.0257-0.50710.3014-0.26331.1798-0.2178-1.5437-0.06640.6247-0.56760.12471.16410.34841.1587-55.07420.1385-19.5573
150.4451-0.33350.07340.764-0.28410.11250.0257-0.32890.50560.62250.10320.9134-0.5358-1.44650.0120.38510.03860.020.58290.01830.4542-45.219135.7008-24.9759
161.36480.20760.60382.30971.52193.9656-0.1744-0.0587-0.1328-0.1442-0.0694-0.1110.05350.2316-00.35260.02930.01060.30970.00420.3216-35.54433.6175-32.3801
170.6268-0.26850.72591.085-0.2870.77230.01680.13970.4492-0.3688-0.050.0722-0.1722-0.2941-0.00010.40260.01050.00310.3821-0.01780.3765-40.848536.3578-38.8731
180.8269-0.2305-0.84641.40951.25691.74060.2540.3791-1.0317-0.07830.0605-0.50090.38460.2809-0.00050.41180.03590.01080.5054-0.09390.34-34.138526.0672-40.96
190.7084-0.6988-0.04350.75580.26350.49470.30030.5254-0.3950.1656-0.25950.8079-1.3566-1.41250.00080.48950.1182-0.05890.557-0.03680.3882-46.250730.1514-45.9459
200.16670.0755-0.05810.11830.16760.1862-0.77582.1427-0.2901-0.75390.0360.29750.03-0.4761-0.00150.4407-0.01250.01240.5695-0.05760.3448-31.747431.2646-49.6263
211.3791-0.5994-0.73520.3135-0.11961.11780.2416-0.58941.3948-0.3606-0.01540.0296-0.64881.28330.02620.53720.1216-0.04180.38790.03120.3929-19.189717.8472-56.0241
220.28450.0370.03980.0813-0.0490.1111-0.6541-0.7044-0.5670.0507-0.2131-1.39810.36870.08210.00550.58480.06040.00460.40460.04920.5469-24.711719.6034-46.4018
230.2366-0.25680.0190.25170.01620.30320.42250.7138-1.7347-1.4401-0.76960.0892-0.0999-0.76360.00060.57790.1144-0.01510.4689-0.2470.4849-32.387118.9465-44.0934
240.1435-0.09880.01340.18460.15520.19350.37181.0058-0.2370.42540.10760.25580.1743-0.338400.5077-0.0088-0.120.5537-0.08610.618-41.254316.2065-38.0014
251.1339-0.2148-0.55590.04950.12230.2721.43372.4989-0.5440.0883-1.3086-1.0251.57090.8437-0.00191.0284-0.0056-0.08870.4354-0.0010.7227-49.316814.1753-39.2156
260.1015-0.0489-0.01340.1023-0.10690.2712-0.33690.8756-0.05090.8447-0.0069-1.07180.9148-1.6375-0.00230.36350.2352-0.18030.9073-0.12641.2463-33.359618.035619.6436
270.2177-0.22750.04310.17050.02720.3110.5611-0.2411-0.02980.6133-0.78440.93880.84480.01940.00020.6615-0.23830.07430.3378-0.01130.3582-26.215315.538711.1407
282.0132-9.0335-3.91945.58072.46671.3097-0.45160.2982-2.93850.9889-0.48781.56080.7493-1.174-0.14180.4747-0.08-0.00280.41280.11270.4323-18.456514.34375.3155
290.09470.05480.03750.23180.00020.01860.3390.1414-0.5176-0.4911-0.64420.78050.1380.26580.00150.4850.0183-0.02910.42860.08980.7582-7.757414.1189-0.4591
300.1387-0.05460.10130.4884-0.24340.15761.9256-0.7637-0.25380.9094-0.24490.36520.72830.07270.00590.97610.0444-0.30660.37050.20541.40750.512413.69571.0877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 142:147)A142 - 147
2X-RAY DIFFRACTION2(chain A and resid 148:153)A148 - 153
3X-RAY DIFFRACTION3(chain A and resid 154:177)A154 - 177
4X-RAY DIFFRACTION4(chain A and resid 178:190)A178 - 190
5X-RAY DIFFRACTION5(chain A and resid 191:205)A191 - 205
6X-RAY DIFFRACTION6(chain A and resid 206:245)A206 - 245
7X-RAY DIFFRACTION7(chain A and resid 246:271)A246 - 271
8X-RAY DIFFRACTION8(chain A and resid 272:279)A272 - 279
9X-RAY DIFFRACTION9(chain A and resid 280:287)A280 - 287
10X-RAY DIFFRACTION10(chain A and resid 288:292)A288 - 292
11X-RAY DIFFRACTION11(chain B and resid 142:147)B142 - 147
12X-RAY DIFFRACTION12(chain B and resid 148:175)B148 - 175
13X-RAY DIFFRACTION13(chain B and resid 176:180)B176 - 180
14X-RAY DIFFRACTION14(chain B and resid 181:188)B181 - 188
15X-RAY DIFFRACTION15(chain B and resid 189:198)B189 - 198
16X-RAY DIFFRACTION16(chain B and resid 199:234)B199 - 234
17X-RAY DIFFRACTION17(chain B and resid 235:251)B235 - 251
18X-RAY DIFFRACTION18(chain B and resid 252:272)B252 - 272
19X-RAY DIFFRACTION19(chain B and resid 273:284)B273 - 284
20X-RAY DIFFRACTION20(chain B and resid 285:292)B285 - 292
21X-RAY DIFFRACTION21(chain C and resid 233:242)C233 - 242
22X-RAY DIFFRACTION22(chain C and resid 243:247)C243 - 247
23X-RAY DIFFRACTION23(chain C and resid 248:253)C248 - 253
24X-RAY DIFFRACTION24(chain C and resid 254:259)C254 - 259
25X-RAY DIFFRACTION25(chain C and resid 260:265)C260 - 265
26X-RAY DIFFRACTION26(chain D and resid 235:239)D235 - 239
27X-RAY DIFFRACTION27(chain D and resid 240:246)D240 - 246
28X-RAY DIFFRACTION28(chain D and resid 247:253)D247 - 253
29X-RAY DIFFRACTION29(chain D and resid 254:259)D254 - 259
30X-RAY DIFFRACTION30(chain D and resid 260:265)D260 - 265

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