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- PDB-9gi4: TFIIIC5 DNA binding domain -

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Basic information

Entry
Database: PDB / ID: 9gi4
TitleTFIIIC5 DNA binding domain
ComponentsGeneral transcription factor 3C polypeptide 5
KeywordsDNA BINDING PROTEIN / TFIIIC / Transcription / Pol III
Function / homology
Function and homology information


5S class rRNA transcription by RNA polymerase III / transcription factor TFIIIC complex / RNA polymerase III general transcription initiation factor activity / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Abortive And Retractive Initiation / transcription initiation at RNA polymerase III promoter / transcription by RNA polymerase III / skeletal muscle cell differentiation / tRNA transcription by RNA polymerase III ...5S class rRNA transcription by RNA polymerase III / transcription factor TFIIIC complex / RNA polymerase III general transcription initiation factor activity / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Abortive And Retractive Initiation / transcription initiation at RNA polymerase III promoter / transcription by RNA polymerase III / skeletal muscle cell differentiation / tRNA transcription by RNA polymerase III / DNA binding / nucleoplasm
Similarity search - Function
Transcription factor IIIC subunit 5, HTH 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 / Tau95 Triple barrel domain
Similarity search - Domain/homology
PHOSPHATE ION / General transcription factor 3C polypeptide 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsLeen, E. / Bayliss, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V029975/1 United Kingdom
CitationJournal: To Be Published
Title: N-myc interacts with TFIIIC via the DNA binding interface of TFIIIC5.
Authors: Leen, E. / Bayliss, R.
History
DepositionAug 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: General transcription factor 3C polypeptide 5
B: General transcription factor 3C polypeptide 5
C: General transcription factor 3C polypeptide 5
D: General transcription factor 3C polypeptide 5
E: General transcription factor 3C polypeptide 5
F: General transcription factor 3C polypeptide 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,70313
Polymers168,0386
Non-polymers6657
Water54030
1
A: General transcription factor 3C polypeptide 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1012
Polymers28,0061
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: General transcription factor 3C polypeptide 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1012
Polymers28,0061
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: General transcription factor 3C polypeptide 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1012
Polymers28,0061
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: General transcription factor 3C polypeptide 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1963
Polymers28,0061
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: General transcription factor 3C polypeptide 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1012
Polymers28,0061
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: General transcription factor 3C polypeptide 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1012
Polymers28,0061
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.524, 37.644, 276.677
Angle α, β, γ (deg.)90.010, 90.020, 59.900
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
General transcription factor 3C polypeptide 5 / TF3C-epsilon / Transcription factor IIIC 63 kDa subunit / TFIIIC 63 kDa subunit / TFIIIC63 / ...TF3C-epsilon / Transcription factor IIIC 63 kDa subunit / TFIIIC 63 kDa subunit / TFIIIC63 / Transcription factor IIIC subunit epsilon


Mass: 28006.293 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Modified human TFIIIC5 protein sequence (UniProt Q9Y5Q8). 208-470 Delta 345-366 inclusive. The construct has a non-native Glycine at the N-terminus.
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF3C5, CDABP0017 / Plasmid: pET30TEV
Details (production host): pET vector with an N-terminal TEV cleavable 6xHis tag
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q9Y5Q8
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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

Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 0.1 M Phosphate/Citrate pH 4.2, 40% PEG 300.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.63→46.11 Å / Num. obs: 38159 / % possible obs: 97.91 % / Redundancy: 3.6 % / Biso Wilson estimate: 67.74 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.07 / Net I/σ(I): 10
Reflection shellResolution: 2.67→2.742 Å / Num. unique obs: 3706 / Rpim(I) all: 0.692 / % possible all: 93.68

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→46.11 Å / SU ML: 0.485 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.1286
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2996 1825 4.78 %Random selection
Rwork0.2437 36334 --
obs0.2463 38159 97.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.6 Å2
Refinement stepCycle: LAST / Resolution: 2.63→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9225 0 35 30 9290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029507
X-RAY DIFFRACTIONf_angle_d0.486212915
X-RAY DIFFRACTIONf_chiral_restr0.04021389
X-RAY DIFFRACTIONf_plane_restr0.00361660
X-RAY DIFFRACTIONf_dihedral_angle_d3.59781267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.70.35311390.32592729X-RAY DIFFRACTION91.22
2.7-2.780.32991280.33662610X-RAY DIFFRACTION97.54
2.78-2.870.4464520.33033043X-RAY DIFFRACTION98.16
2.87-2.970.40961930.29922645X-RAY DIFFRACTION98.13
2.97-3.090.39361980.28562855X-RAY DIFFRACTION98.01
3.09-3.230.27371000.28772729X-RAY DIFFRACTION98.09
3.23-3.40.25661120.25452961X-RAY DIFFRACTION98.68
3.4-3.610.28921640.23622659X-RAY DIFFRACTION98.26
3.61-3.890.3664960.24622865X-RAY DIFFRACTION98.8
3.89-4.290.31271940.21412828X-RAY DIFFRACTION99.15
4.29-4.90.23291100.20132819X-RAY DIFFRACTION99.09
4.9-6.180.27891820.24482876X-RAY DIFFRACTION99.25
6.18-46.110.28821570.23042715X-RAY DIFFRACTION97.22

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