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- PDB-3nr5: Crystal structure of human Maf1 -

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Basic information

Entry
Database: PDB / ID: 3nr5
TitleCrystal structure of human Maf1
ComponentsRepressor of RNA polymerase III transcription MAF1 homolog
KeywordsTRANSCRIPTION / RNA-Pol III transcriptional repressor / RNA-Pol III
Function / homology
Function and homology information


intracellular anatomical structure / negative regulation of transcription by RNA polymerase III / RNA polymerase III core binding / RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / inhibitory synapse / RNA polymerase III type 3 promoter sequence-specific DNA binding / GABA receptor binding / negative regulation of transcription by RNA polymerase I / Regulation of PTEN gene transcription ...intracellular anatomical structure / negative regulation of transcription by RNA polymerase III / RNA polymerase III core binding / RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / inhibitory synapse / RNA polymerase III type 3 promoter sequence-specific DNA binding / GABA receptor binding / negative regulation of transcription by RNA polymerase I / Regulation of PTEN gene transcription / axon / intracellular membrane-bounded organelle / dendrite / nucleolus / perinuclear region of cytoplasm / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Repressor of RNA polymerase III transcription Maf1 / Repressor of RNA polymerase III transcription Maf1 / Repressor of RNA polymerase III transcription Maf1 superfamily / Maf1 regulator / Protein Transport Mog1p; Chain A / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Repressor of RNA polymerase III transcription MAF1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsRingel, R. / Vannini, A. / Kusser, A.G. / Berninghausen, O. / Kassavetis, G.A. / Cramer, P.
CitationJournal: Cell / Year: 2010
Title: Molecular basis of RNA polymerase III transcription repression by Maf1.
Authors: Alessandro Vannini / Rieke Ringel / Anselm G Kusser / Otto Berninghausen / George A Kassavetis / Patrick Cramer /
Abstract: RNA polymerase III (Pol III) transcribes short RNAs required for cell growth. Under stress conditions, the conserved protein Maf1 rapidly represses Pol III transcription. We report the crystal ...RNA polymerase III (Pol III) transcribes short RNAs required for cell growth. Under stress conditions, the conserved protein Maf1 rapidly represses Pol III transcription. We report the crystal structure of Maf1 and cryo-electron microscopic structures of Pol III, an active Pol III-DNA-RNA complex, and a repressive Pol III-Maf1 complex. Binding of DNA and RNA causes ordering of the Pol III-specific subcomplex C82/34/31 that is required for transcription initiation. Maf1 binds the Pol III clamp and rearranges C82/34/31 at the rim of the active center cleft. This impairs recruitment of Pol III to a complex of promoter DNA with the initiation factors Brf1 and TBP and thus prevents closed complex formation. Maf1 does however not impair binding of a DNA-RNA scaffold and RNA synthesis. These results explain how Maf1 specifically represses transcription initiation from Pol III promoters and indicate that Maf1 also prevents reinitiation by binding Pol III during transcription elongation.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Repressor of RNA polymerase III transcription MAF1 homolog


Theoretical massNumber of molelcules
Total (without water)19,1591
Polymers19,1591
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.398, 48.816, 79.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Repressor of RNA polymerase III transcription MAF1 homolog / Maf1


Mass: 19159.357 Da / Num. of mol.: 1 / Fragment: residues in UNP 1-35, 83-205 / Mutation: Deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAF1 / Plasmid: pET 28b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H063
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4549.7
2
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50mM MES, 175mM sodium oxalate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06DA10.9187
SYNCHROTRONSLS X06DA20.9196, 0.9211, 0.92
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELNov 23, 2008
PSI PILATUS 6M2PIXELNov 23, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1graphiteSINGLE WAVELENGTHMx-ray1
2graphiteMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.91871
20.91961
30.92111
40.921
ReflectionResolution: 1.55→26 Å / Num. all: 26137 / Num. obs: 26137 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.55→25.974 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8404 / SU ML: 0.25 / σ(F): 0 / Phase error: 22.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2115 1344 5.14 %RANDOM
Rwork0.1881 ---
all0.1895 ---
obs0.1895 26137 93.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.129 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso max: 104.56 Å2 / Biso min: 14.08 Å2
Baniso -1Baniso -2Baniso -3
1-6.4102 Å2-0 Å2-0 Å2
2---2.9435 Å2-0 Å2
3----3.4667 Å2
Refinement stepCycle: LAST / Resolution: 1.55→25.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1290 0 0 141 1431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061352
X-RAY DIFFRACTIONf_angle_d0.9591837
X-RAY DIFFRACTIONf_chiral_restr0.074194
X-RAY DIFFRACTIONf_plane_restr0.004239
X-RAY DIFFRACTIONf_dihedral_angle_d17.16495
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.60540.37771210.33532191231284
1.6054-1.66970.29541150.27352431254693
1.6697-1.74570.27271320.23622521265396
1.7457-1.83770.23391370.20252544268197
1.8377-1.95280.21581490.18422486263595
1.9528-2.10350.21921300.17082509263995
2.1035-2.3150.23671440.18432509265395
2.315-2.64970.21931400.19092523266395
2.6497-3.33730.20611450.17952525267094
3.3373-25.97760.17151310.16772554268590
Refinement TLS params.Method: refined / Origin x: 6.4165 Å / Origin y: 13.7151 Å / Origin z: 12.0462 Å
111213212223313233
T0.1504 Å2-0.0041 Å2-0.0133 Å2-0.1401 Å20.0067 Å2--0.1695 Å2
L2.2588 °20.3293 °2-0.5321 °2-1.7282 °20.2143 °2--2.3036 °2
S0.0145 Å °-0.0029 Å °0.0653 Å °-0.0032 Å °-0.0085 Å °-0.0143 Å °-0.0889 Å °0.069 Å °-0.0001 Å °
Refinement TLS groupSelection details: chain A

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