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- PDB-4bjj: Sfc1-Sfc7 dimerization module -

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Basic information

Entry
Database: PDB / ID: 4bjj
TitleSfc1-Sfc7 dimerization module
Components
  • TRANSCRIPTION FACTOR TAU SUBUNIT SFC1
  • TRANSCRIPTION FACTOR TAU SUBUNIT SFC7
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


RNA polymerase III cis-regulatory region sequence-specific DNA binding / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcription factor TFIIIC complex / RNA polymerase III general transcription initiation factor activity / transcription initiation at RNA polymerase III promoter / transcription by RNA polymerase III / DNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Immunoglobulin-like - #4370 / TFIIIC, subcomplex tauA, subunit Sfc1, barrel domain / TFIIIC subunit GTF3C6-like / Transcription factor IIIC subunit 5, HTH domain / Transcription factor TFIIIC, triple barrel domain / Transcription factor IIIC subunit Tfc1/Sfc1 / Transcription factor IIIC subunit Tfc1/Sfc1, triple barrel domain / TFIIIC, subcomplex tauA subunit Sfc1, triple barrel domain superfamily / RNA polymerase III transcription factor (TF)IIIC subunit HTH domain / TFIIIC subunit triple barrel domain ...Immunoglobulin-like - #4370 / TFIIIC, subcomplex tauA, subunit Sfc1, barrel domain / TFIIIC subunit GTF3C6-like / Transcription factor IIIC subunit 5, HTH domain / Transcription factor TFIIIC, triple barrel domain / Transcription factor IIIC subunit Tfc1/Sfc1 / Transcription factor IIIC subunit Tfc1/Sfc1, triple barrel domain / TFIIIC, subcomplex tauA subunit Sfc1, triple barrel domain superfamily / RNA polymerase III transcription factor (TF)IIIC subunit HTH domain / TFIIIC subunit triple barrel domain / Tau95 Triple barrel domain / Phosphorylase Kinase; domain 1 / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Transcription factor tau subunit sfc7 / Transcription factor tau subunit sfc1
Similarity search - Component
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsTaylor, N.M.I. / Baudin, F. / von Scheven, G. / Muller, C.W.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: RNA Polymerase III-Specific General Transcription Factor Iiic Contains a Heterodimer Resembling Tfiif RAP30/RAP74.
Authors: Taylor, N.M.I. / Baudin, F. / Von Scheven, G. / Muller, C.W.
History
DepositionApr 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references / Other
Revision 1.2Nov 6, 2013Group: Database references
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_conn.ptnr2_label_seq_id / _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 SUBUNIT SFC1
B: TRANSCRIPTION FACTOR TAU SUBUNIT SFC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3004
Polymers23,8992
Non-polymers4012
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-69 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.245, 85.245, 154.108
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein TRANSCRIPTION FACTOR TAU SUBUNIT SFC1 / TFIIIC SUBUNIT SFC1 / TRANSCRIPTION FACTOR C SUBUNIT 1


Mass: 12688.354 Da / Num. of mol.: 1 / Fragment: SFC7-INTERACTING DOMAIN, RESIDUES 1-110 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Strain: 972 / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIPL / References: UniProt: O14229
#2: Protein TRANSCRIPTION FACTOR TAU SUBUNIT SFC7 / TFIIIC SUBUNIT SFC7 / TRANSCRIPTION FACTOR C SUBUNIT 7


Mass: 11210.533 Da / Num. of mol.: 1 / Fragment: SFC1-INTERACTING DOMAIN, RESIDUES 2-101
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Strain: 972 / Plasmid: PCDF-MCN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIPL / References: UniProt: A6X980
#3: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.25 Å3/Da / Density % sol: 62.12 % / Description: NONE
Crystal growpH: 7 / Details: 1.4 M AMSO4, 0.1 M HEPES PH 7, 0.1 M KCL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.00685
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2010 / Details: BENT CYLINDRICAL MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00685 Å / Relative weight: 1
ReflectionResolution: 2.4→42.62 Å / Num. obs: 13629 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 49.71 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.4→33.29 Å / SU ML: 0.32 / σ(F): 0.91 / Phase error: 24.17 / Stereochemistry target values: ML
Details: THE HYDROGEN ATOMS ON THE SULPHUR ATOMS O OF MERCURY-BOUND CYSTEINES HAVE BEEN REMOVED AFTER REFINEMENT AS THEY DO NOT MAKE SENSE CHEMICALLY.
RfactorNum. reflection% reflection
Rfree0.2236 1223 5 %
Rwork0.1809 --
obs0.183 13591 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.97 Å2
Refinement stepCycle: LAST / Resolution: 2.4→33.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 0 2 42 1575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111566
X-RAY DIFFRACTIONf_angle_d1.2372113
X-RAY DIFFRACTIONf_dihedral_angle_d15.234588
X-RAY DIFFRACTIONf_chiral_restr0.074235
X-RAY DIFFRACTIONf_plane_restr0.006279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.49610.31181200.28362595X-RAY DIFFRACTION99
2.4961-2.60960.31711420.26382573X-RAY DIFFRACTION100
2.6096-2.74710.27131530.22592582X-RAY DIFFRACTION100
2.7471-2.91920.30711310.21412584X-RAY DIFFRACTION100
2.9192-3.14440.2491270.18682607X-RAY DIFFRACTION100
3.1444-3.46050.23961630.17522539X-RAY DIFFRACTION100
3.4605-3.96060.18631280.16062603X-RAY DIFFRACTION100
3.9606-4.98720.17761460.14362584X-RAY DIFFRACTION100
4.9872-33.29280.21721130.18522613X-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)
10.0062-0.0430.03090.0195-0.00940.0236-0.2313-0.55890.5021-0.0953-0.28880.0054-0.08390.01460.00070.4575-0.0737-0.04670.51930.04810.58889.916919.003416.2428
20.24260.2145-0.00370.1853-0.13930.28670.05510.0919-0.279-0.2038-0.04240.09740.44330.13640.00010.49010.0757-0.03630.38570.01010.474332.6146.717421.9338
30.11290.0115-0.06920.0211-0.03390.0445-0.3161-0.1996-0.08130.71750.3771-0.36290.4608-0.5415-0.00040.3798-0.1144-0.01350.5334-0.0120.463424.8359.770632.1804
4-0.0060.0315-0.05650.0489-0.0405-0.009-0.1249-0.2917-0.0671-0.17070.37720.1774-0.2435-0.274-00.44550.06740.00070.4350.00710.487331.210615.764333.5008
5-0.0165-0.0490.010.04010.02120.00760.2065-0.22930.0462-0.1429-0.2958-0.43860.0557-0.06660.00030.3719-0.0607-0.08010.34730.01020.481545.45214.045126.6265
60.0191-0.00990.01320.034-0.0165-0.0051-0.063-0.02730.2396-0.14160.0555-0.1901-0.1185-0.2047-0.00020.43450.0413-0.0330.4911-0.02520.425747.290210.203830.2506
70.0325-0.0149-0.01490.1031-0.00970.0016-0.06820.2970.222-0.1418-0.0328-0.4226-0.05480.1272-0.00010.39680.0704-0.05130.45280.01570.384328.431123.451623.566
80.00580.04660.0250.01220.07610.03430.42360.5045-0.1169-0.50720.1345-0.60610.3401-0.2648-00.6712-0.0527-0.14150.4739-0.07070.466116.491911.30776.98
90.0504-0.14390.06780.2791-0.11780.026-0.08680.17530.07590.02860.1270.13790.0890.00160.00010.3546-0.0644-0.04990.4190.03630.449720.223917.307919.1751
10-0.0056-0.0003-0.05760.0054-0.03680.027-0.74940.02780.17820.1557-0.4495-0.8383-0.229-0.26350.00160.46860.0199-0.05080.51070.0930.642142.317917.344319.2485
112.10560.88070.54252.0311.1932.2821-0.020.2624-0.08260.12060.13720.16870.32790.0686-0.17580.3843-0.0263-0.06230.4450.02730.402119.55720.606110.7177
120.06840.34360.93510.1424-0.10160.735-0.01140.1712-0.0263-0.1014-0.0952-0.01180.00330.02650.00010.46910.0214-0.01030.43260.01840.423224.533621.190110.0452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 3 THROUGH 9 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 10 THROUGH 32 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 33 THROUGH 45 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 46 THROUGH 54 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 55 THROUGH 59 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 60 THROUGH 68 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 69 THROUGH 75 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 76 THROUGH 85 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 86 THROUGH 98 )
10X-RAY DIFFRACTION10CHAIN A AND (RESID 99 THROUGH 108 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 7 THROUGH 51 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 52 THROUGH 100 )

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