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- PDB-5aim: Crystal structure of T138 central eWH domain -

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Basic information

Entry
Database: PDB / ID: 5aim
TitleCrystal structure of T138 central eWH domain
ComponentsTRANSCRIPTION FACTOR TAU 138 KDA SUBUNIT
KeywordsTRANSCRIPTION / TFIIIC / T138
Function / homology
Function and homology information


5S class rRNA transcription by RNA polymerase III / transcription factor TFIIIC complex / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcription initiation at RNA polymerase III promoter / transcription by RNA polymerase III / protein localization to chromatin / mitochondrion / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Transcription factor tau subunit sfc3/Tfc3, C-terminal / : / Family of unknown function (DUF6581) / Transcription factor tau 138 kDa subunit, extended winged helix / B-block binding subunit of TFIIIC / Tfc3, extended winged-helix domain / Transcription facto Tfc3-like / B-block binding subunit of TFIIIC
Similarity search - Domain/homology
Transcription factor tau 138 kDa subunit
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 Å
AuthorsMale, G. / Glatt, S. / Mueller, C.W.
CitationJournal: Nat Commun / Year: 2015
Title: Architecture of TFIIIC and its role in RNA polymerase III pre-initiation complex assembly.
Authors: Male, G. / von Appen, A. / Glatt, S. / Taylor, N.M. / Cristovao, M. / Groetsch, H. / Beck, M. / Muller, C.W.
History
DepositionFeb 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 2.0Feb 14, 2018Group: Advisory / Atomic model / Database references
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 2.1May 1, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 FACTOR TAU 138 KDA SUBUNIT
B: TRANSCRIPTION FACTOR TAU 138 KDA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5324
Polymers22,3482
Non-polymers1842
Water3,549197
1
A: TRANSCRIPTION FACTOR TAU 138 KDA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2662
Polymers11,1741
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRANSCRIPTION FACTOR TAU 138 KDA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2662
Polymers11,1741
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.090, 129.090, 68.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2079-

HOH

21A-2101-

HOH

31B-2072-

HOH

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Components

#1: Protein TRANSCRIPTION FACTOR TAU 138 KDA SUBUNIT / TFIIIC 138 KDA SUBUNIT / TRANSCRIPTION FACTOR C SUBUNIT 3


Mass: 11173.905 Da / Num. of mol.: 2 / Fragment: CENTRAL EWH DOMAIN, RESIDUES 546-641
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P34111
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.61 % / Description: NONE
Crystal growDetails: 1.15 M NA CITRATE PH 6.2, 0.1 M NA CACODYLATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 42553 / % possible obs: 99.9 % / Observed criterion σ(I): 1.7 / Redundancy: 10.1 % / Biso Wilson estimate: 20.37 Å2 / Rmerge(I) obs: 0.05
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 9.4 % / Rmerge(I) obs: 1.38 / Mean I/σ(I) obs: 1.7 / % possible all: 99.3

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURE OF THIS PROTEIN BY SULPHUR-SAD

Resolution: 1.401→43.191 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 22.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1975 2127 5 %
Rwork0.1752 --
obs0.1763 42552 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.401→43.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 12 197 1727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061614
X-RAY DIFFRACTIONf_angle_d0.9472167
X-RAY DIFFRACTIONf_dihedral_angle_d13.102657
X-RAY DIFFRACTIONf_chiral_restr0.054247
X-RAY DIFFRACTIONf_plane_restr0.003275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.401-1.43360.34451390.39892651X-RAY DIFFRACTION99
1.4336-1.46950.30671420.29042683X-RAY DIFFRACTION100
1.4695-1.50920.2381410.25322682X-RAY DIFFRACTION100
1.5092-1.55360.31031410.22232677X-RAY DIFFRACTION100
1.5536-1.60380.22991410.21462680X-RAY DIFFRACTION100
1.6038-1.66110.22491410.21572681X-RAY DIFFRACTION100
1.6611-1.72760.22351410.20152683X-RAY DIFFRACTION100
1.7276-1.80620.22121410.20852688X-RAY DIFFRACTION100
1.8062-1.90150.22051420.19782684X-RAY DIFFRACTION100
1.9015-2.02060.20471410.18992689X-RAY DIFFRACTION100
2.0206-2.17660.19561430.17952703X-RAY DIFFRACTION100
2.1766-2.39560.1981410.17112690X-RAY DIFFRACTION100
2.3956-2.74220.20871430.17262714X-RAY DIFFRACTION100
2.7422-3.45470.19741430.16292723X-RAY DIFFRACTION100
3.4547-43.21170.15831470.14532797X-RAY DIFFRACTION100
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)
11.32980.017-0.08584.89995.156.93440.1207-0.10230.04010.2477-0.0885-0.1516-0.226-0.0782-0.02370.2146-0.0050.03220.1580.01320.2449-15.9505-2.9693-15.09
27.24072.17063.20423.50180.99997.04840.1878-0.54440.08780.1696-0.1746-0.19960.1225-0.1509-0.02440.1518-0.02020.00580.16080.00680.1728-18.0485-15.4764-13.0871
34.56644.4039-4.23664.4827-3.23797.2393-0.0151-2.5231-0.07881.8668-0.34230.2001-0.54840.6370.21230.826-0.01690.07090.61720.03250.5259-13.5868-10.0802-4.5155
42.40393.22530.92035.43940.56812.01630.2881-0.19590.14270.6516-0.24130.54980.1022-0.5855-0.16660.2267-0.05280.0830.2273-0.01940.2785-26.8394-7.5022-16.5185
56.98415.9197-5.60165.5408-5.33454.43720.0474-0.3042-0.0062-0.3749-0.09590.21110.3907-0.078-0.08110.2201-0.05980.00980.24560.00990.1993-28.3647-17.1253-20.6854
63.0154-3.28713.79083.5868-3.88534.47130.3384-0.1281-0.4888-0.3852-0.05940.28561.2264-0.5212-0.14780.4037-0.1236-0.0150.2427-0.0130.2028-26.5333-24.7147-23.4513
74.57953.2556-3.66182.1281-2.20395.0621-0.07040.24840.1885-0.05410.07820.09190.05660.1245-0.03240.16680.0011-0.03630.17230.02940.25073.4628-16.2614-22.7768
83.45580.6222-0.36564.7937-0.28096.2565-0.02850.3227-0.0112-0.28520.0021-0.08080.2041-0.15670.00840.13910.01480.02130.1451-0.0020.2266-8.7409-22.4977-23.6519
91.2948-1.3386-0.10971.5110.72333.43380.51161.16790.32250.0007-0.6876-0.02510.35850.14770.21480.5937-0.15640.3251.0439-0.01350.6708-4.6596-21.2857-32.8012
109.04822.70181.18168.685-3.08422.11480.05840.7641-0.851-0.54660.0603-0.21450.60940.3336-0.06920.2290.0281-0.01610.2251-0.05190.43733.7469-25.9139-22.7641
117.48076.82090.6695.13441.29170.5020.1432-0.0493-0.44890.3091-0.2062-0.42970.31160.1530.02560.33110.0049-0.04760.16010.03790.4141-3.3808-33.7113-15.0718
126.01981.5866-2.81754.12482.00376.9592-0.1519-0.2233-0.42730.1823-0.01680.19470.09280.33540.05920.29810.026-0.03080.16350.05390.2861-4.1693-27.9445-11.3969
133.42611.25492.59023.3302-1.93315.2262-0.0767-0.2222-0.13360.5157-0.0830.53860.8097-0.52750.17860.4016-0.03430.10720.21010.01110.3508-13.6785-32.1934-10.3229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN B AND (RESID 543 THROUGH 566 )
2X-RAY DIFFRACTION2CHAIN B AND (RESID 567 THROUGH 584 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 585 THROUGH 591 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 592 THROUGH 613 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 614 THROUGH 627 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 628 THROUGH 640 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 543 THROUGH 566 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 567 THROUGH 584 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 585 THROUGH 592 )
10X-RAY DIFFRACTION10CHAIN A AND (RESID 593 THROUGH 604 )
11X-RAY DIFFRACTION11CHAIN A AND (RESID 605 THROUGH 618 )
12X-RAY DIFFRACTION12CHAIN A AND (RESID 619 THROUGH 627 )
13X-RAY DIFFRACTION13CHAIN A AND (RESID 628 THROUGH 639 )

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