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- PDB-3psi: Crystal Structure of the Spt6 core domain from Saccharomyces cere... -

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Basic information

Entry
Database: PDB / ID: 3psi
TitleCrystal Structure of the Spt6 core domain from Saccharomyces cerevisiae, Form Spt6(239-1451)
ComponentsTranscription elongation factor SPT6
KeywordsTRANSCRIPTION / Transcription Elongation / Nucleus
Function / homology
Function and homology information


transcription antitermination factor activity, DNA binding / regulation of mRNA 3'-end processing / nucleosome organization / poly(A)+ mRNA export from nucleus / transcription elongation-coupled chromatin remodeling / cellular response to stress / nucleosome binding / transcription elongation factor complex / transcription antitermination / transcription elongation by RNA polymerase II ...transcription antitermination factor activity, DNA binding / regulation of mRNA 3'-end processing / nucleosome organization / poly(A)+ mRNA export from nucleus / transcription elongation-coupled chromatin remodeling / cellular response to stress / nucleosome binding / transcription elongation factor complex / transcription antitermination / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle / euchromatin / nucleosome assembly / histone binding / transcription by RNA polymerase II / chromatin remodeling / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleus
Similarity search - Function
Spt6, Death-like domain / Spt6, helix-hairpin-helix domain / RuvA domain 2-like / Tex N-terminal region-like / Tex N-terminal region-like / YqgF/RNase H-like domain / : / Spt6, S1/OB domain / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. ...Spt6, Death-like domain / Spt6, helix-hairpin-helix domain / RuvA domain 2-like / Tex N-terminal region-like / Tex N-terminal region-like / YqgF/RNase H-like domain / : / 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 / RuvA domain 2-like / Nucleic acid-binding proteins / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Ribonuclease H-like superfamily / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transcription elongation factor SPT6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsClose, D. / Hill, C.P. / Johnson, S.J.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal structures of the S. cerevisiae Spt6 core and C-terminal tandem SH2 domain.
Authors: Close, D. / Johnson, S.J. / Sdano, M.A. / McDonald, S.M. / Robinson, H. / Formosa, T. / Hill, C.P.
History
DepositionDec 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 elongation factor SPT6


Theoretical massNumber of molelcules
Total (without water)141,7191
Polymers141,7191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.747, 118.747, 214.408
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Transcription elongation factor SPT6 / Chromatin elongation factor SPT6


Mass: 141719.000 Da / Num. of mol.: 1 / Fragment: Core Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: CRE2, G6169, SPT6, SSN20, YGR116W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P23615
Has protein modificationY

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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: 3.08 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Na-MES 13% PEG 4000 0.2 M MgCl2 12% Glycerol , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 8, 2005
RadiationMonochromator: Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 27025 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.058 / Χ2: 1.599 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.3-3.426.60.56926711.003199.9
3.42-3.556.70.40826721.0881100
3.55-3.726.80.26826721.1541100
3.72-3.916.80.17626521.272199.8
3.91-4.166.80.11827031.44199.9
4.16-4.486.80.0826841.749199.7
4.48-4.936.80.06526992.025199.8
4.93-5.646.70.05827151.98199.6
5.64-7.16.80.04527491.922199.5
7.1-506.70.03228082.288196.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→45.67 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.49 / σ(F): 1.44 / Phase error: 30.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3084 2836 7.44 %
Rwork0.2654 --
obs0.2687 27003 99.4 %
all-29013 -
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 125.003 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 523.2 Å2 / Biso mean: 170.0162 Å2 / Biso min: 15.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.3792 Å2-0 Å20 Å2
2---1.3792 Å2-0 Å2
3---2.7584 Å2
Refinement stepCycle: LAST / Resolution: 3.3→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6877 0 0 0 6877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137016
X-RAY DIFFRACTIONf_angle_d1.5779487
X-RAY DIFFRACTIONf_chiral_restr0.0791049
X-RAY DIFFRACTIONf_plane_restr0.0111234
X-RAY DIFFRACTIONf_dihedral_angle_d10.1882651
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.293-3.41060.36821960.32972427262398
3.4106-3.54710.34771960.316124772673100
3.5471-3.70850.32882010.306124842685100
3.7085-3.90390.35741970.282724562653100
3.9039-4.14840.29992010.272224952696100
4.1484-4.46840.26592000.22724822682100
4.4684-4.91760.25841990.213425162715100
4.9176-5.62810.29932040.274225132717100
5.6281-7.08650.35722030.297925462749100
7.0865-45.67420.30022130.25362597281097
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)
13.5497-1.1348-0.6937-0.0529-0.00885.274-0.38880.1813-0.20320.3059-0.3380.4492-0.0397-0.0262-0.45420.95420.2332-0.10550.1918-0.01760.623-69.170432.818844.0608
20.9735-1.946-0.89864.3165-1.19485.31630.8346-0.15870.3135-0.6951.1113-0.2640.4533-1.24191.09161.25520.0430.23660.9226-0.32950.8001-58.339962.466359.0512
36.69094.0511-5.00969.77541.92926.9030.41791.9041-0.80250.35332.55142.65181.813-2.61951.37942.2268-0.323-0.04640.60280.04912.4575-57.958782.941847.0921
41.2854-1.36010.13851.54440.07640.4790.24351.48461.19250.2505-0.3950.58590.18370.26790.07043.9015-1.15461.38540.4382-0.74196.1532-42.145289.304453.6816
56.3281-5.7749-8.30895.29957.59772.00051.3017-2.77591.82223.1519-3.19183.4441.18425.21990.21353.6581-0.36781.68131.05860.35073.8683-37.124682.405557.8838
64.3569-4.6265-2.89414.29311.15665.37071.611-1.34930.8101-0.48750.8521-1.5981-2.3586-1.2070.19182.1477-0.28370.37850.8041-0.19731.1301-48.830762.156942.6642
71.99150.16021.9982.87130.63881.99932.43260.8927-2.3149-1.41513.05320.33512.9801-4.27210.54561.5838-0.43371.59471.41940.26853.8822-26.253243.972227.7532
85.1169-1.3575-2.02260.21940.57420.7604-0.1391-1.28642.6376-0.70650.8559-0.0931-0.477-0.44950.01431.9201-0.38560.32251.37350.05380.8342-43.091644.883324.9731
91.9911-5.30962.89332.0021-4.91442.4095-3.8690.3081-2.7453-0.54111.84291.6836-2.93043.16820.42982.0414-0.06470.75231.4203-0.2619-0.1637-35.755142.634434.7652
105.13391.04722.75356.47674.21853.64080.1756-0.3892-0.54250.761.6387-0.6750.66270.34469.1071.7595-0.75681.41761.0278-0.20990.6971-46.353262.694233.0551
114.06213.34191.99452.75212.17027.88411.47660.35290.6481.62271.09321.4018-0.1867-3.0366.67590.0833-0.26962.02430.68542.03270.2686-54.189477.18738.4331
121.99482.0114-1.45341.99640.94020.9293-0.8665-2.19733.35663.16850.7522-5.1281-3.06083.23630.44663.45141.20750.34082.07620.63191.1238-51.16891.213141.1331
134.9643-0.14170.85310.5504-0.45930.4801-0.00311.2932-0.8595-1.2053-1.82630.7499-0.13591.09620.01974.5655-0.2327-1.520.48731.18013.2384-46.562987.665246.3924
142.0187-1.2963-0.52926.60272.57011.10140.3247-0.0313-0.45480.1306-0.1515-0.3813-0.22280.64550.00081.09110.3185-0.06940.80930.10720.6291-42.441311.950731.448
153.8965-0.8812-2.47711.3946-0.11680.962-0.65390.3418-1.16970.40870.48250.35250.32240.86050.1181.24380.39510.08950.2880.26730.8227-69.15439.859744.4213
160.21930.6573-1.8844-1.2511-0.5738-2.2076-0.7360.11320.62070.09720.3646-0.11450.3530.6832-0.22171.34770.3930.04660.9394-0.32141.1713-66.859215.312628.712
170.3762-1.8822-1.23572.04513.99655.04840.96390.6188-0.7985-2.0666-0.2396-1.5548-0.57783.18852.42441.03361.0811-0.3651.74520.26031.4272-25.070718.47946.3794
181.58770.9213-2.33470.153-1.20543.2959-1.32660.3397-1.45710.91930.7256-1.27240.9294-0.5511-0.05941.26130.2506-0.50341.31930.23191.3833-25.488820.11413.5191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 312:429)A312 - 429
2X-RAY DIFFRACTION2(chain A and resid 430:530)A430 - 530
3X-RAY DIFFRACTION3(chain A and resid 531:543)A531 - 543
4X-RAY DIFFRACTION4(chain A and resid 544:547)A544 - 547
5X-RAY DIFFRACTION5(chain A and resid 548:572)A548 - 572
6X-RAY DIFFRACTION6(chain A and resid 573:608)A573 - 608
7X-RAY DIFFRACTION7(chain A and resid 609:613)A609 - 613
8X-RAY DIFFRACTION8(chain A and resid 615:644)A615 - 644
9X-RAY DIFFRACTION9(chain A and resid 645:653)A645 - 653
10X-RAY DIFFRACTION10(chain A and resid 654:667)A654 - 667
11X-RAY DIFFRACTION11(chain A and resid 668:676)A668 - 676
12X-RAY DIFFRACTION12(chain A and resid 677:681)A677 - 681
13X-RAY DIFFRACTION13(chain A and resid 682:686)A682 - 686
14X-RAY DIFFRACTION14(chain A and resid 687:901)A687 - 901
15X-RAY DIFFRACTION15(chain A and resid 902:1070)A902 - 1070
16X-RAY DIFFRACTION16(chain A and resid 1071:1131)A1071 - 1131
17X-RAY DIFFRACTION17(chain A and resid 1133:1148)A1133 - 1148
18X-RAY DIFFRACTION18(chain A and resid 1149:1210)A1149 - 1210

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