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- PDB-3ndq: Structure of Human TFIIS Domain II -

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Basic information

Entry
Database: PDB / ID: 3ndq
TitleStructure of Human TFIIS Domain II
ComponentsTranscription elongation factor A protein 1
KeywordsTRANSCRIPTION / helix bundle
Function / homology
Function and homology information


transcription factor TFIID complex / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex ...transcription factor TFIID complex / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase II / DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / TFIIS helical bundle-like domain ...Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / TFIIS helical bundle-like domain / Transcription factor IIS, N-terminal / TFIIS N-terminal domain profile. / TFIIS/LEDGF domain superfamily / Zinc finger TFIIS-type signature. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger
Similarity search - Domain/homology
Transcription elongation factor A protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.933 Å
AuthorsHu, X.P. / Averell, G. / Ye, X.Y. / Hou, J. / Luo, H.
CitationJournal: To be Published
Title: Structure of Human TFIIS Domain II
Authors: Ye, X. / Gnatt, A. / Hu, X.P.
History
DepositionJun 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
A: Transcription elongation factor A protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1813
Polymers12,1351
Non-polymers462
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.270, 60.750, 61.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1229-

NA

21A-1339-

HOH

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Components

#1: Protein Transcription elongation factor A protein 1 / Transcription elongation factor S-II protein 1 / Transcription elongation factor TFIIS.o


Mass: 12134.657 Da / Num. of mol.: 1 / Fragment: TFIIS Domain II, residues 131-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2S, TCEA1, TFIIS / Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Plys / References: UniProt: P23193
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.0 M Ammonium sulphate, 0.1 M 2-(N-morpholino)ethanesulfonic acid , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97947 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 1, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.933→43.385 Å / Num. all: 8564 / Num. obs: 8564 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.933-2.0414.40.1151775812300.11100
2.04-2.1614.60.0966.11703711690.096100
2.16-2.3114.60.0857.11629511160.085100
2.31-2.514.60.0748.21527610490.074100
2.5-2.7314.50.0768137459460.076100
2.73-3.0614.50.0698.9126578740.069100
3.06-3.5314.30.0728.4111107780.072100
3.53-4.3213.60.0857.489406580.08598.7
4.32-6.1112.90.0758.166505150.07598.7
6.11-21.69110.06110.625082290.06174.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data processing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DME

2dme


Resolution: 1.933→21.693 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.14 / Isotropic thermal model: Isotropic / σ(F): 2.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.208 408 4.77 %
Rwork0.166 --
all0.168 8562 -
obs0.168 8562 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.798 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso max: 58.54 Å2 / Biso mean: 18.589 Å2 / Biso min: 6.24 Å2
Baniso -1Baniso -2Baniso -3
1--7.315 Å2-0 Å20 Å2
2---0.703 Å2-0 Å2
3---6.284 Å2
Refinement stepCycle: LAST / Resolution: 1.933→21.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms765 0 2 149 916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006792
X-RAY DIFFRACTIONf_angle_d0.8941066
X-RAY DIFFRACTIONf_chiral_restr0.065118
X-RAY DIFFRACTIONf_plane_restr0.003144
X-RAY DIFFRACTIONf_dihedral_angle_d10.656323
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.933-2.2130.2171350.15926822817100
2.213-2.7870.2031380.16227292867100
2.787-21.6940.2081350.1712743287897

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