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- PDB-4fqg: Crystal structure of the TCERG1 FF4-6 tandem repeat domain -

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Basic information

Entry
Database: PDB / ID: 4fqg
TitleCrystal structure of the TCERG1 FF4-6 tandem repeat domain
ComponentsTranscription elongation regulator 1
KeywordsTRANSCRIPTION / FF domain / tandem repeat domain / PCTD-binding domain
Function / homology
Function and homology information


transcription elongation factor activity / ubiquitin-like protein conjugating enzyme binding / RNA polymerase binding / negative regulation of transcription elongation by RNA polymerase II / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / mRNA processing / transcription corepressor activity ...transcription elongation factor activity / ubiquitin-like protein conjugating enzyme binding / RNA polymerase binding / negative regulation of transcription elongation by RNA polymerase II / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / mRNA processing / transcription corepressor activity / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / nuclear speck / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
FF domain / Transcription elongation regulator 1-like / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily ...FF domain / Transcription elongation regulator 1-like / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Transcription elongation regulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsLiu, J. / Fan, S. / Lee, C.J. / Greenleaf, A.L. / Zhou, P.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Specific Interaction of the Transcription Elongation Regulator TCERG1 with RNA Polymerase II Requires Simultaneous Phosphorylation at Ser2, Ser5, and Ser7 within the Carboxyl-terminal Domain Repeat.
Authors: Liu, J. / Fan, S. / Lee, C.J. / Greenleaf, A.L. / Zhou, P.
History
DepositionJun 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription elongation regulator 1
B: Transcription elongation regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3285
Polymers46,1752
Non-polymers1533
Water9,044502
1
A: Transcription elongation regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1462
Polymers23,0871
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcription elongation regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1823
Polymers23,0871
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.919, 77.087, 95.179
Angle α, β, γ (deg.)90.00, 96.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transcription elongation regulator 1 / TATA box-binding protein-associated factor 2S / Transcription factor CA150


Mass: 23087.490 Da / Num. of mol.: 2
Fragment: TCERG1 FF4-6 tandem repeat domain (unp residues 895:1081)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCERG1, CA150, TAF2S / Plasmid: plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)STAR / References: UniProt: O14776
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.016 M NiCl2, 0.1 M Tris-HCl, 16% polyethylene glycol monomethyl ether 2000, and 0.13 M glycine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-BM11.0001
SYNCHROTRONAPS 22-BM20.9719
SYNCHROTRONAPS 22-BM30.9794
SYNCHROTRONAPS 22-BM40.9796
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDApr 12, 2010
MARMOSAIC 225 mm CCD2CCDDec 17, 2009
3
4
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray1
3x-ray1
4x-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.00011
20.97191
30.97941
40.97961
ReflectionResolution: 2→50 Å / Num. all: 27256 / Num. obs: 26788 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 11.7 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
SOLVEphasing
REFMAC5.5.0072refinement
DENZOdata reduction
HKL-2000data scaling
HKL-2000data collection
RefinementMethod to determine structure: MAD / Resolution: 2→24.797 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / SU ML: 0.26 / σ(F): 0 / Phase error: 24.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 1314 5 %
Rwork0.1892 --
obs0.1919 26272 96.45 %
all-27256 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.111 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2353 Å2-0 Å20.3241 Å2
2---5.1785 Å20 Å2
3---4.9432 Å2
Refinement stepCycle: LAST / Resolution: 2→24.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3193 0 3 502 3698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063241
X-RAY DIFFRACTIONf_angle_d0.9174328
X-RAY DIFFRACTIONf_dihedral_angle_d12.9251302
X-RAY DIFFRACTIONf_chiral_restr0.065472
X-RAY DIFFRACTIONf_plane_restr0.003545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9972-2.07720.2881330.19572693X-RAY DIFFRACTION96
2.0772-2.17160.23061490.17852804X-RAY DIFFRACTION97
2.1716-2.28610.27821090.20252509X-RAY DIFFRACTION87
2.2861-2.42920.2421400.18622774X-RAY DIFFRACTION97
2.4292-2.61650.24351530.20572849X-RAY DIFFRACTION99
2.6165-2.87950.24861440.20872859X-RAY DIFFRACTION99
2.8795-3.29530.23861540.19882868X-RAY DIFFRACTION100
3.2953-4.14860.24091540.17282709X-RAY DIFFRACTION94
4.1486-24.79910.21881780.17792893X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 4.6242 Å / Origin y: -18.6353 Å / Origin z: 23.2696 Å
111213212223313233
T0.0602 Å2-0.0006 Å2-0.0041 Å2-0.066 Å2-0.006 Å2--0.0614 Å2
L0.0011 °20.0014 °2-0.0134 °2-0.0384 °20.038 °2--0.0122 °2
S-0.0001 Å °-0.0207 Å °0.0081 Å °0.0224 Å °-0.0118 Å °0.0041 Å °0.0067 Å °-0.0071 Å °0.0037 Å °
Refinement TLS groupSelection details: all

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