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- PDB-3psk: Crystal Structure of the Spt6 Tandem SH2 Domain from Saccharomyce... -

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Basic information

Entry
Database: PDB / ID: 3psk
TitleCrystal Structure of the Spt6 Tandem SH2 Domain from Saccharomyces cerevisiae, Form Native Spt6 (1247-1451)
ComponentsTranscription elongation factor SPT6
KeywordsTRANSCRIPTION / Tandem SH2 Domain / Transcription Elongation / 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 / 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 antitermination factor activity, DNA binding / regulation of transcriptional start site selection at RNA polymerase II promoter / 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 / 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 / histone binding / chromatin remodeling / 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
: / 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 ...: / 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 / SH2 domain / SHC Adaptor Protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcription elongation factor SPT6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsClose, D. / Hill, C.P.
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 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Transcription elongation factor SPT6
B: Transcription elongation factor SPT6
C: Transcription elongation factor SPT6
D: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,41416
Polymers100,2624
Non-polymers1,15312
Water5,044280
1
A: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5466
Polymers25,0651
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5466
Polymers25,0651
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1612
Polymers25,0651
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1612
Polymers25,0651
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Transcription elongation factor SPT6
hetero molecules

C: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7078
Polymers50,1312
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area1970 Å2
ΔGint-83 kcal/mol
Surface area21010 Å2
MethodPISA
6
A: Transcription elongation factor SPT6
hetero molecules

D: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7078
Polymers50,1312
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546x+1/2,-y-1/2,-z+11
Buried area1730 Å2
ΔGint-65 kcal/mol
Surface area20740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.778, 105.176, 119.481
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 25065.430 Da / Num. of mol.: 4 / Fragment: unp residues 1247-1451
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: SPT6, CRE2, SSN20, YGR116W, G6169 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P23615
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Tris pH5.5 25% PEG 3350 0.2M (NH4)2SO4 , VAPOR DIFFUSION, SITTING DROP, temperature 294K

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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: Mar 1, 2008
RadiationMonochromator: Varimax confocal optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 58489 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.066 / Χ2: 0.978 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.184.30.47857521.033199.2
2.18-2.264.30.35857311.06199
2.26-2.374.40.27557431.058199.2
2.37-2.494.40.22157811.052199.4
2.49-2.654.50.17158131.044199.6
2.65-2.854.50.12858241.008199.7
2.85-3.144.50.08958570.9611100
3.14-3.594.50.06158900.857199.9
3.59-4.524.50.04759350.826199.9
4.52-304.20.04261630.899199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.45 Å
Translation2.5 Å29.45 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PSJ

3psj


Resolution: 2.1→28.229 Å / Occupancy max: 1 / Occupancy min: 0.03 / SU ML: 0.27 / σ(F): 0 / Phase error: 21.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 1931 3.43 %Random
Rwork0.1841 ---
obs0.1851 56332 95.93 %-
all-58263 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.727 Å2 / ksol: 0.423 e/Å3
Displacement parametersBiso max: 179.27 Å2 / Biso mean: 50.7154 Å2 / Biso min: 19.65 Å2
Baniso -1Baniso -2Baniso -3
1--1.3119 Å2-0 Å20 Å2
2---2.9742 Å2-0 Å2
3---4.2861 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6444 0 60 280 6784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036652
X-RAY DIFFRACTIONf_angle_d0.6878998
X-RAY DIFFRACTIONf_chiral_restr0.049946
X-RAY DIFFRACTIONf_plane_restr0.0021140
X-RAY DIFFRACTIONf_dihedral_angle_d11.7062464
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 (%)
2.1-2.17350.26411790.22414996517589
2.1735-2.26050.2441900.20715119530992
2.2605-2.36340.26991810.20045219540093
2.3634-2.48790.26071860.20255358554495
2.4879-2.64370.23951920.19045407559996
2.6437-2.84760.22611950.1945467566297
2.8476-3.13380.24291950.1885560575598
3.1338-3.58650.2162000.18025651585199
3.5865-4.51560.17362030.157257135916100
4.5156-28.23120.19752100.18985911612199
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)
15.281.95110.08214.5086-0.87931.3633-1.00590.70550.4026-0.92540.4792-0.6677-0.1573-0.16310.45740.3406-0.0195-0.00930.3074-0.02540.398741.3392-8.642959.5431
20.30910.0448-0.20213.0456-0.08021.94560.0558-0.2519-0.04480.1336-0.1846-0.57380.25950.36830.12310.29320.00340.02770.3239-0.02310.33240.5599-8.804444.2
32.60060.1310.32580.67281.23241.8255-0.2170.03620.0932-0.23010.1171-0.1318-0.35030.12910.05170.2834-0.0432-0.02150.2567-0.0160.265333.5286-0.37444.9505
40.1674-0.2130.64990.9285-0.36331.54330.0411-0.05240.0184-0.10840.0120.15660.0109-0.1242-0.01590.2145-0.0286-0.00550.24690.00130.303628.5547-16.153146.1648
51.0191-0.85040.47761.42680.31550.50370.06990.08710.2196-0.2687-0.3141-0.1167-0.2118-0.36590.23410.27370.0666-0.03520.2782-0.04690.260118.26125.856335.2856
65.4842-1.60131.76915.1432-1.57053.62620.1406-0.08450.09870.79950.01960.3096-0.38920.2234-0.11270.4480.1702-0.02980.4622-0.0690.493810.564723.372139.4746
72.45080.5875-0.08451.7607-1.51910.74450.1131-0.33130.55680.40520.06870.238-0.1552-0.4234-0.08540.39750.12950.00070.3416-0.07830.411613.113511.831342.0905
80.0938-0.4115-0.23483.8498-0.11880.9204-0.1253-0.04830.21631.10790.19180.7316-0.5736-0.2662-0.09570.58290.27650.16270.50410.00510.5585.328715.572645.4601
90.0798-0.0153-0.12691.93040.32051.4796-0.2211-0.296-0.31750.06930.2130.7994-0.3132-0.81580.04210.26820.07480.00060.42660.01250.47599.6677-1.028540.2667
100.08430.2155-0.4280.6405-0.58153.5341-0.08770.72451.211-0.05030.01050.48490.2747-0.9725-0.13640.37890.1594-0.04390.6998-0.15710.9323-1.53256.453141.8108
110.48730.60220.55410.30760.41791.1167-0.0155-0.2588-0.0448-0.03390.0140.3622-0.210.23090.06640.3011-0.0063-0.01710.3551-0.01310.4309-1.5134-9.46497.9941
120.83450.4297-0.18390.7423-0.63020.6668-0.2160.1090.060.0570.11210.1754-0.1902-0.16490.07790.21680.0445-0.0420.2334-0.01980.30954.7239-0.963714.867
131.02060.9080.64952.28340.31560.8934-0.27950.10050.1575-0.19710.3464-0.1714-0.29560.47380.01720.32640.006-0.05680.2885-0.00520.242511.361.777713.9763
141.8298-0.49930.52950.0567-0.18491.491-0.06660.1865-0.21050.08440.14190.06580.33060.0023-0.06140.29210.0098-0.01670.2288-0.01460.34669.4392-17.88810.1741
151.21381.71731.46473.25911.80571.70890.3303-0.10670.00560.6173-0.25370.19980.4511-0.0231-0.11060.3317-0.0019-0.03980.2713-0.00290.29216.3359-7.339522.5751
162.5030.02950.2112.5070.56180.20710.0282-0.62610.28570.56020.09580.1679-0.15-0.26370.03130.3203-0.0847-0.01590.43290.03580.266725.714511.916623.2107
171.32070.7769-0.34282.61820.4560.6432-0.11010.27350.1082-0.48140.1535-0.2716-0.2164-0.0756-0.08280.3495-0.0444-0.02470.3232-0.00830.365734.436521.501320.1149
180.91430.5558-0.83962.63590.02560.45340.1007-0.0137-0.001-0.410.0026-0.4566-0.26350.0977-0.08340.3533-0.0405-0.00280.31650.05890.35631.516211.523715.0984
190.8334-0.115-0.99422.24190.0142.05570.0183-0.07950.0209-0.1468-0.1152-0.5214-0.12550.54230.12120.22690.0298-0.02420.32040.04340.3430.7235-2.229918.3227
200.26290.6716-0.4531.9655-0.21134.3376-0.9155-0.74111.37550.45190.0539-1.22890.730.90710.91420.27030.05630.05050.5510.13630.753342.57423.380116.9799
211.40740.0652-0.41040.99950.70492.5259-0.24080.4458-0.1402-0.287-0.06990.2956-0.1585-0.64190.23640.34230.0528-0.00630.4269-0.05410.383128.871-35.1291-0.1357
220.18740.269-0.04011.19761.26510.907-0.0023-0.1129-0.02870.2413-0.0823-0.00190.09360.12030.02520.33170.0799-0.01110.2611-0.01730.337939.1448-34.91197.7846
230.66661.06681.39383.2921.7264.19310.43150.3469-0.13330.0985-0.38460.63370.6759-0.80970.06090.42250.05990.03870.4426-0.06020.486422.1806-34.66937.9048
243.85450.4610.61660.76230.04740.19980.3422-0.6217-0.37630.227-0.14140.15120.3152-0.0996-0.12310.35930.081-0.02280.30170.01230.287137.2181-30.884113.3063
252.07390.54821.22450.48021.14544.08710.08660.0494-0.8960.118-0.25550.73990.7394-0.34490.13660.3630.0482-0.00810.3278-0.09830.51516.3171-28.03632.8345
262.7097-0.17680.5230.63030.23291.1390.06590.35840.39530.0297-0.11180.0486-0.11060.15090.0170.28850.05530.01740.27510.03380.312931.0627-19.50058.5246
271.3682-1.14490.30282.136-2.24394.51550.12920.02820.1107-0.1269-0.4638-0.32620.370.80860.23050.2718-0.00060.00380.3875-0.00780.395250.3896-24.007828.2859
282.10860.2285-2.57487.62722.59964.4741-0.0831-0.00060.59630.24030.8711-1.8074-0.57990.2498-0.76430.3458-0.0909-0.03560.5222-0.18380.496353.6016-16.3737.8294
291.2721-0.06911.19371.02010.37651.98290.1269-0.3018-0.1268-0.04540.0364-0.18510.2143-0.1141-0.13190.26560.0445-0.04170.3222-0.0040.276340.9493-22.597430.9265
301.1477-1.24210.28911.8375-0.78310.7084-0.058-0.14130.01490.41930.0635-0.0872-0.18190.1237-0.02010.35580.0447-0.0240.32630.00830.377735.9624-12.083123.8789
310.4045-0.0035-0.87481.9057-0.69621.79760.0405-0.0115-0.3242-0.267-0.0270.16330.04440.45070.07990.2714-0.10690.0230.2979-0.02890.39563.9591-35.023755.4777
320.9318-0.5022-1.25212.48220.00473.11890.0253-0.1585-0.3691-0.4573-0.01970.18310.12110.597-0.06910.3374-0.0579-0.00430.2986-0.0310.511711.9341-32.494551.9126
330.5162-1.03880.1011.90090.27451.4964-0.13840.2447-0.0824-0.01280.14290.3070.03740.33350.01570.3168-0.0892-0.11140.27930.0160.54320.1196-30.056546.4258
340.4690.4176-1.15374.1876-3.52514.3323-0.1995-0.3467-0.8844-0.0113-0.7725-1.00230.40280.3410.73310.3518-0.08540.060.36640.07740.68721.8428-28.747356.3053
351.54540.1347-0.14230.371-0.17390.5393-0.00120.22050.4126-0.2238-0.0963-0.1091-0.10320.1996-0.07360.2559-0.10160.03240.3026-0.08270.435212.9322-19.847453.7425
361.7886-1.0840.61070.9932-0.90173.2797-0.096-0.02470.4514-0.1052-0.07970.0382-0.043-0.67340.22290.3712-0.08590.08390.3499-0.0420.504-6.6863-17.38845.4021
372.383-0.23640.0860.6969-0.56122.0620.07640.22281.04230.13860.20490.1508-0.1414-0.9714-0.38970.3453-0.08950.00010.62030.16730.5205-16.0094-25.477929.0244
380.1057-0.02210.71181.21960.1352.64790.01950.4542-0.0861-0.23760.52160.21240.0080.1925-0.50920.3228-0.1183-0.080.37230.06040.5872-6.7772-20.169429.4046
392.03060.72231.44351.6815-0.36181.4775-0.40750.47580.72730.40290.16320.0478-0.86960.21820.23960.3174-0.1476-0.05320.42470.04220.606-0.1474-11.253338.5731
405.53772.9853.38785.8127-0.33513.41050.55881.05970.13281.51110.89580.07230.0838-0.1544-0.82020.60180.01410.08440.4690.08220.3974-6.2742-7.799528.3191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1242:1251)A1242 - 1251
2X-RAY DIFFRACTION2(chain A and resid 1252:1264)A1252 - 1264
3X-RAY DIFFRACTION3(chain A and resid 1265:1306)A1265 - 1306
4X-RAY DIFFRACTION4(chain A and resid 1307:1340)A1307 - 1340
5X-RAY DIFFRACTION5(chain A and resid 1341:1361)A1341 - 1361
6X-RAY DIFFRACTION6(chain A and resid 1362:1375)A1362 - 1375
7X-RAY DIFFRACTION7(chain A and resid 1376:1394)A1376 - 1394
8X-RAY DIFFRACTION8(chain A and resid 1395:1410)A1395 - 1410
9X-RAY DIFFRACTION9(chain A and resid 1411:1433)A1411 - 1433
10X-RAY DIFFRACTION10(chain A and resid 1434:1440)A1434 - 1440
11X-RAY DIFFRACTION11(chain B and resid 1242:1258)B1242 - 1258
12X-RAY DIFFRACTION12(chain B and resid 1259:1298)B1259 - 1298
13X-RAY DIFFRACTION13(chain B and resid 1299:1307)B1299 - 1307
14X-RAY DIFFRACTION14(chain B and resid 1308:1329)B1308 - 1329
15X-RAY DIFFRACTION15(chain B and resid 1330:1350)B1330 - 1350
16X-RAY DIFFRACTION16(chain B and resid 1351:1361)B1351 - 1361
17X-RAY DIFFRACTION17(chain B and resid 1362:1378)B1362 - 1378
18X-RAY DIFFRACTION18(chain B and resid 1379:1408)B1379 - 1408
19X-RAY DIFFRACTION19(chain B and resid 1409:1433)B1409 - 1433
20X-RAY DIFFRACTION20(chain B and resid 1434:1440)B1434 - 1440
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23X-RAY DIFFRACTION23(chain C and resid 1281:1292)C1281 - 1292
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25X-RAY DIFFRACTION25(chain C and resid 1306:1322)C1306 - 1322
26X-RAY DIFFRACTION26(chain C and resid 1323:1350)C1323 - 1350
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35X-RAY DIFFRACTION35(chain D and resid 1320:1340)D1320 - 1340
36X-RAY DIFFRACTION36(chain D and resid 1341:1356)D1341 - 1356
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38X-RAY DIFFRACTION38(chain D and resid 1379:1410)D1379 - 1410
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40X-RAY DIFFRACTION40(chain D and resid 1434:1438)D1434 - 1438

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