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- PDB-2lw4: Solution NMR Structure of Human Transcription Elongation Factor A... -

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Basic information

Entry
Database: PDB / ID: 2lw4
TitleSolution NMR Structure of Human Transcription Elongation Factor A protein 2, Central Domain, Northeast Structural Genomics Consortium (NESG) Target HR8682B
ComponentsTranscription elongation factor A protein 2
KeywordsTRANSCRIPTION / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


transcription elongation factor complex / transcription elongation factor activity / DNA-templated transcription elongation / regulation of DNA-templated transcription elongation / transcription elongation by RNA polymerase II / DNA binding / nucleoplasm / zinc ion binding / 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 superfamily / Transcription elongation factor S-II, central domain / 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 N-terminal domain profile. ...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 superfamily / Transcription elongation factor S-II, central domain / 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 N-terminal domain profile. / TFIIS helical bundle-like domain / Transcription factor IIS, N-terminal / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / Wang, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Human Transcription Elongation Factor A protein 2, Central Domain (CASP Target)
Authors: Eletsky, A. / Wang, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionJul 20, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription elongation factor A protein 2


Theoretical massNumber of molelcules
Total (without water)12,7371
Polymers12,7371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcription elongation factor A protein 2 / Testis-specific S-II / Transcription elongation factor S-II protein 2 / Transcription elongation ...Testis-specific S-II / Transcription elongation factor S-II protein 2 / Transcription elongation factor TFIIS.l


Mass: 12736.638 Da / Num. of mol.: 1 / Fragment: TFIIS central domain residues 130-239
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCEA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q15560

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C CT-HSQC aliphatic
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HN(CA)CO
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1813D (H)C(CO)NH-TOCSY
1913D HBHA(CO)NH
11013D (H)CCH-TOCSY
11112D 1H-13C CT-HSQC aromatic
11213D (H)CCH-COSY aliphatic
11311D 15N T1
11411D 15N T2
11522D 1H-13C CT-HSQC methyl

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] HR8682B.004, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM TRIS, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [5% 13C; U-100% 15N] HR8682B.004, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM TRIS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMHR8682B.004-1[U-100% 13C; U-100% 15N]1
100 mMNaCl-21
5 mMDTT-31
0.02 %NaN3-41
10 mMTRIS-51
1.0 mMHR8682B.004-6[5% 13C; U-100% 15N]2
100 mMNaCl-72
5 mMDTT-82
0.02 %NaN3-92
10 mMTRIS-102
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
ASDP1Huang, Tejero, Powers and Montelionedata analysis
ASDP1Huang, Tejero, Powers and Montelionerefinement
XEASY1.3.13Bartels et al.data analysis
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
VnmrJ2.2DVariancollection
PINE2Bahrami, Markley, Assadi, and Eghbalniachemical shift assignment
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PSVSBhattacharya, Montelionestructure validation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ASSIGNMENTS ...Details: STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ASSIGNMENTS WERE SELECTED AND USED IN ITERATIVE REFINEMENT WITH CYANA. THE 20 CONFORMERS OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY SIMULATED ANNEALING IN EXPLICIT WATER BATH USING THE PROGRAM CNS WITH PARAM19 FORCE FIELD
NMR constraintsNOE constraints total: 1402 / NOE intraresidue total count: 457 / NOE long range total count: 240 / NOE medium range total count: 326 / NOE sequential total count: 379 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 85 / Protein psi angle constraints total count: 85
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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