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- PDB-3pjp: A Tandem SH2 Domain in Transcription Elongation Factor Spt6 Binds... -

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Basic information

Entry
Database: PDB / ID: 3pjp
TitleA Tandem SH2 Domain in Transcription Elongation Factor Spt6 Binds the Phosphorylated RNA Polymerase II C-terminal Repeat Domain(CTD)
ComponentsTranscription elongation factor SPT6
KeywordsTRANSCRIPTION / SH2 / transcription elongation / CTD binding / nucleus
Function / homology
Function and homology information


carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / regulation of transcriptional start site selection at RNA polymerase II promoter / transcription antitermination factor activity, DNA binding / regulation of mRNA 3'-end processing / transcription elongation-coupled chromatin remodeling / poly(A)+ mRNA export from nucleus / nucleosome binding / transcription elongation factor complex / positive regulation of transcription elongation by RNA polymerase II / euchromatin ...carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / regulation of transcriptional start site selection at RNA polymerase II promoter / transcription antitermination factor activity, DNA binding / regulation of mRNA 3'-end processing / transcription elongation-coupled chromatin remodeling / poly(A)+ mRNA export from nucleus / nucleosome binding / transcription elongation factor complex / positive regulation of transcription elongation by RNA polymerase II / euchromatin / nucleosome assembly / histone binding / negative regulation of transcription by RNA polymerase II / DNA binding
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 / 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 / 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
ACETATE ION / Transcription elongation factor SPT6
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSun, M. / Lariviere, L. / Dengl, S. / Mayer, A. / Cramer, P.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: A tandem SH2 domain in transcription elongation factor Spt6 binds the phosphorylated RNA polymerase II C-terminal repeat domain (CTD).
Authors: Sun, M. / Lariviere, L. / Dengl, S. / Mayer, A. / Cramer, P.
History
DepositionNov 10, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionNov 24, 2010ID: 3OR8
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5997
Polymers47,1682
Non-polymers4315
Water8,719484
1
A: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7023
Polymers23,5841
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8974
Polymers23,5841
Non-polymers3133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Transcription elongation factor SPT6
B: Transcription elongation factor SPT6
hetero molecules

A: Transcription elongation factor SPT6
B: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,19814
Polymers94,3364
Non-polymers86310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10670 Å2
ΔGint-29 kcal/mol
Surface area35920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.240, 57.020, 87.970
Angle α, β, γ (deg.)90.000, 126.140, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 23583.877 Da / Num. of mol.: 2 / Fragment: tandem SH2 domain, UNP residues 1250-1444
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Gene: CAGL0L04774g, SPT6 / Plasmid: pET28B / Production host: Escherichia coli (E. coli) / References: UniProt: Q6FLB1
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22-24% PEG 8000, 50MM MES, 0.2M SODIUM ACETATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91881 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91881 Å / Relative weight: 1
ReflectionResolution: 1.6→71.043 Å / Num. all: 58807 / Num. obs: 56066 / Redundancy: 2.12 % / Rsym value: 0.032 / Net I/σ(I): 13.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→35.04 Å / Occupancy max: 1 / Occupancy min: 0.49 / SU ML: 0.25 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 2837 5.06 %
Rwork0.198 --
obs0.2 56064 95.4 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.54 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso max: 89.3 Å2 / Biso mean: 27.0281 Å2 / Biso min: 6.91 Å2
Baniso -1Baniso -2Baniso -3
1--4.2441 Å2-0 Å21.5096 Å2
2---8.2926 Å20 Å2
3---12.5367 Å2
Refinement stepCycle: LAST / Resolution: 1.6→35.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 28 484 3788
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.994
X-RAY DIFFRACTIONf_dihedral_angle_d13.115
X-RAY DIFFRACTIONf_chiral_restr0.075
X-RAY DIFFRACTIONf_plane_restr0.004
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.62760.38171370.33252653279096
1.6276-1.65720.37711360.31832655279196
1.6572-1.68910.34141370.29142669280696
1.6891-1.72360.32871280.27892641276996
1.7236-1.76110.27891520.25832640279295
1.7611-1.8020.31761490.25662646279596
1.802-1.84710.27571250.24982682280796
1.8471-1.8970.32071540.21522663281796
1.897-1.95280.26491300.21722673280395
1.9528-2.01590.29681320.21042680281296
2.0159-2.08790.23351520.21482657280996
2.0879-2.17150.24131490.20092623277296
2.1715-2.27030.22621520.19042636278895
2.2703-2.390.21861500.18682668281896
2.39-2.53970.24181430.19722667281096
2.5397-2.73570.22191310.19052682281395
2.7357-3.01090.25591490.19522662281195
3.0109-3.44620.23211390.18892648278795
3.4462-4.34060.20371470.15982620276793
4.3406-35.0490.2031450.18072762290795
Refinement TLS params.Method: refined / Origin x: -0.0948 Å / Origin y: 25.6258 Å / Origin z: 15.7248 Å
111213212223313233
T0.0797 Å2-0.0234 Å20.0038 Å2-0.0901 Å2-0.0063 Å2--0.0786 Å2
L0.1079 °2-0.571 °20.0829 °2-0.6636 °2-0.1028 °2--0.1475 °2
S-0.0214 Å °-0.0622 Å °-0.0081 Å °0.0925 Å °0.0096 Å °0.0015 Å °-0.0018 Å °-0.0061 Å °0.0009 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1251 - 1444
2X-RAY DIFFRACTION1ALLB1250 - 1444
3X-RAY DIFFRACTION1ALLA1445 - 1446
4X-RAY DIFFRACTION1ALLB1445 - 1447
5X-RAY DIFFRACTION1ALLA1447 - 1707
6X-RAY DIFFRACTION1ALLB1448 - 1670

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