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- PDB-3oc3: Crystal structure of the Mot1 N-terminal domain in complex with TBP -

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Basic information

Entry
Database: PDB / ID: 3oc3
TitleCrystal structure of the Mot1 N-terminal domain in complex with TBP
Components
  • HELICASE MOT1
  • TRANSCRIPTION INITIATION FACTOR TFIID (TFIID-1)
KeywordsHYDROLASE/TRANSCRIPTION / Transcription / Regulation of Transcription / HYDROLASE-TRANSCRIPTION complex
Function / homology
Function and homology information


ATP-dependent chromatin remodeler activity / TBP-class protein binding / helicase activity / DNA-templated transcription initiation / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
TATA-binding protein-associated factor Mot1 / TATA-Binding Protein / TATA-box binding protein, eukaryotic / TATA-Binding Protein / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal ...TATA-binding protein-associated factor Mot1 / TATA-Binding Protein / TATA-box binding protein, eukaryotic / TATA-Binding Protein / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / TBP domain superfamily / Helicase conserved C-terminal domain / Armadillo-like helical / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TRANSCRIPTION INITIATION FACTOR TFIID (TFIID-1) / Similarity to HELICASE MOT1
Similarity search - Component
Biological speciesEncephalitozoon cuniculi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsWollmann, P. / Cui, S. / Viswanathan, R. / Berninghausen, O. / Wells, M.N. / Moldt, M. / Witte, G. / Butryn, A. / Wendler, P. / Beckmann, R. ...Wollmann, P. / Cui, S. / Viswanathan, R. / Berninghausen, O. / Wells, M.N. / Moldt, M. / Witte, G. / Butryn, A. / Wendler, P. / Beckmann, R. / Auble, D.T. / Hopfner, K.-P.
CitationJournal: Nature / Year: 2011
Title: Structure and mechanism of the Swi2/Snf2 remodeller Mot1 in complex with its substrate TBP.
Authors: Wollmann, P. / Cui, S. / Viswanathan, R. / Berninghausen, O. / Wells, M.N. / Moldt, M. / Witte, G. / Butryn, A. / Wendler, P. / Beckmann, R. / Auble, D.T. / Hopfner, K.P.
History
DepositionAug 9, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2011Group: Structure summary
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _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: HELICASE MOT1
B: HELICASE MOT1
C: TRANSCRIPTION INITIATION FACTOR TFIID (TFIID-1)
D: TRANSCRIPTION INITIATION FACTOR TFIID (TFIID-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,3586
Polymers232,9684
Non-polymers3902
Water52229
1
A: HELICASE MOT1
C: TRANSCRIPTION INITIATION FACTOR TFIID (TFIID-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6793
Polymers116,4842
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-19 kcal/mol
Surface area46260 Å2
MethodPISA
2
B: HELICASE MOT1
D: TRANSCRIPTION INITIATION FACTOR TFIID (TFIID-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6793
Polymers116,4842
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-18 kcal/mol
Surface area45990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.260, 147.820, 103.440
Angle α, β, γ (deg.)90.00, 94.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HELICASE MOT1 / Mot1


Mass: 91981.445 Da / Num. of mol.: 2 / Fragment: HEAT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Gene: ECU03_1530 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8SVZ5
#2: Protein TRANSCRIPTION INITIATION FACTOR TFIID (TFIID-1) / TBP / TATA box binding protein


Mass: 24502.486 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Gene: ECU04_1440 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ST28
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 3.26 Å3/Da / Density % sol: 62.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50mM Mes pH 6, 200mM Ammoniumacetate, 5% MPD, 4% PEG 3350, 200mM NDSB-201, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 10, 2009
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 54019 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.1→3.2 Å / % possible all: 97.2

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Processing

Software
NameVersionClassification
DNAdata collection
SHARPphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.1→47.276 Å / SU ML: 0.4 / σ(F): 2 / Phase error: 24.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2421 2700 5 %RANDOM
Rwork0.1871 ---
obs0.1899 54011 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.11 Å2 / ksol: 0.269 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5993 Å20 Å2-2.3321 Å2
2--3.7942 Å2-0 Å2
3----3.1948 Å2
Refinement stepCycle: LAST / Resolution: 3.1→47.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14968 0 24 29 15021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515294
X-RAY DIFFRACTIONf_angle_d0.86620628
X-RAY DIFFRACTIONf_dihedral_angle_d16.385792
X-RAY DIFFRACTIONf_chiral_restr0.0632351
X-RAY DIFFRACTIONf_plane_restr0.0032605
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0972-3.15350.34811340.2941256896
3.1535-3.21410.38761430.26462721100
3.2141-3.27970.30841420.24882690100
3.2797-3.3510.35231420.24312700100
3.351-3.42890.2761420.22422701100
3.4289-3.51470.28021400.2142668100
3.5147-3.60970.28571430.21052709100
3.6097-3.71580.24991420.19442708100
3.7158-3.83570.25181420.19482697100
3.8357-3.97280.25921430.18662710100
3.9728-4.13170.25451420.17912697100
4.1317-4.31960.21551420.1632692100
4.3196-4.54720.22821420.15352702100
4.5472-4.83190.18221410.14742693100
4.8319-5.20450.21631440.15982725100
5.2045-5.72740.25081430.18752720100
5.7274-6.55430.28031430.21162726100
6.5543-8.25060.25331440.18162733100
8.2506-47.28150.16811460.1691275199

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