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- PDB-4wzs: Crystal structure of the Mot1 N-terminal domain in complex with T... -

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Basic information

Entry
Database: PDB / ID: 4wzs
TitleCrystal structure of the Mot1 N-terminal domain in complex with TBP and NC2 bound to a promoter DNA fragment
Components
  • DNA (5'-D(P*CP*CP*AP*CP*CP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*CP*CP*T)-3')
  • DNA (5'-D(P*GP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*GP*GP*TP*GP*G)-3')
  • ECU04_1440 protein
  • ECU11_1470 protein
  • Similarity to HELICASE MOT1
  • TATA-binding protein-associated phosphoprotein
KeywordsTRANSCRIPTION / protein-DNA complex / Swi2/Snf2
Function / homology
Function and homology information


negative cofactor 2 complex / RNA polymerase II general transcription initiation factor activity / core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / DNA-templated transcription initiation / helicase activity / protein heterodimerization activity / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity ...negative cofactor 2 complex / RNA polymerase II general transcription initiation factor activity / core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / DNA-templated transcription initiation / helicase activity / protein heterodimerization activity / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
Negative cofactor 2 complex subunit beta / TATA-binding protein-associated factor Mot1 / : / Transcription factor CBF/NF-Y/archaeal histone domain / Histone-like transcription factor (CBF/NF-Y) and archaeal histone / TATA-Binding Protein / TATA-Binding Protein / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site ...Negative cofactor 2 complex subunit beta / TATA-binding protein-associated factor Mot1 / : / Transcription factor CBF/NF-Y/archaeal histone domain / Histone-like transcription factor (CBF/NF-Y) and archaeal histone / TATA-Binding Protein / TATA-Binding Protein / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / Histone, subunit A / Histone, subunit A / TBP domain superfamily / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / Histone-fold / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / TATA-binding protein-associated phosphoprotein / CLASS 2 TRANSCRIPTIONAL REPRESSOR similar NCB1_yeast / TRANSCRIPTION INITIATION FACTOR TFIID (TFIID-1) / Similarity to HELICASE MOT1
Similarity search - Component
Biological speciesEncephalitozoon cuniculi (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.78 Å
AuthorsButryn, A. / Hopfner, K.-P.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 646 Germany
CitationJournal: Elife / Year: 2015
Title: Structural basis for recognition and remodeling of the TBP:DNA:NC2 complex by Mot1.
Authors: Agata Butryn / Jan M Schuller / Gabriele Stoehr / Petra Runge-Wollmann / Friedrich Förster / David T Auble / Karl-Peter Hopfner /
Abstract: Swi2/Snf2 ATPases remodel substrates such as nucleosomes and transcription complexes to control a wide range of DNA-associated processes, but detailed structural information on the ATP-dependent ...Swi2/Snf2 ATPases remodel substrates such as nucleosomes and transcription complexes to control a wide range of DNA-associated processes, but detailed structural information on the ATP-dependent remodeling reactions is largely absent. The single subunit remodeler Mot1 (modifier of transcription 1) dissociates TATA box-binding protein (TBP):DNA complexes, offering a useful system to address the structural mechanisms of Swi2/Snf2 ATPases. Here, we report the crystal structure of the N-terminal domain of Mot1 in complex with TBP, DNA, and the transcription regulator negative cofactor 2 (NC2). Our data show that Mot1 reduces DNA:NC2 interactions and unbends DNA as compared to the TBP:DNA:NC2 state, suggesting that Mot1 primes TBP:NC2 displacement in an ATP-independent manner. Electron microscopy and cross-linking data suggest that the Swi2/Snf2 domain of Mot1 associates with the upstream DNA and the histone fold of NC2, thereby revealing parallels to some nucleosome remodelers. This study provides a structural framework for how a Swi2/Snf2 ATPase interacts with its substrate DNA:protein complex.
History
DepositionNov 20, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_radiation_wavelength / pdbx_audit_support / struct_conn
Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ECU11_1470 protein
B: TATA-binding protein-associated phosphoprotein
C: Similarity to HELICASE MOT1
D: ECU04_1440 protein
E: DNA (5'-D(P*CP*CP*AP*CP*CP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*CP*CP*T)-3')
F: DNA (5'-D(P*GP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*GP*GP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)156,8146
Polymers156,8146
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.629, 140.274, 90.778
Angle α, β, γ (deg.)90.00, 113.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein ECU11_1470 protein


Mass: 11173.392 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (strain GB-M1) (fungus)
Strain: GB-M1 / Gene: ECU11_1470 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8SQT6
#2: Protein TATA-binding protein-associated phosphoprotein


Mass: 17730.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Gene: ECU11_0730 / Production host: Escherichia coli (E. coli) / References: UniProt: M1K2J7
#3: Protein Similarity to HELICASE MOT1


Mass: 90408.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (strain GB-M1) (fungus)
Strain: GB-M1 / Gene: ECU03_1530 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8SVZ5
#4: Protein ECU04_1440 protein


Mass: 22760.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (strain GB-M1) (fungus)
Strain: GB-M1 / Gene: ECU04_1440 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ST28

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DNA chain , 2 types, 2 molecules EF

#5: DNA chain DNA (5'-D(P*CP*CP*AP*CP*CP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*CP*CP*T)-3')


Mass: 7176.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (5'-D(P*GP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*GP*GP*TP*GP*G)-3')


Mass: 7563.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 0.2M imidazole malate, PEG 4000 / PH range: 5.0-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.78→49.17 Å / Num. obs: 17169 / % possible obs: 98.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 128.05 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.3
Reflection shellResolution: 3.78→4 Å / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.49 / % possible all: 93.5

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
PHASER2.5.2phasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OC3

3oc3


Resolution: 3.78→49.17 Å / Cor.coef. Fo:Fc: 0.7009 / Cor.coef. Fo:Fc free: 0.6536 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.678
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 860 5.01 %RANDOM
Rwork0.2351 ---
obs0.2362 17163 98.87 %-
Displacement parametersBiso mean: 74.64 Å2
Baniso -1Baniso -2Baniso -3
1-12.7248 Å20 Å2-27.6534 Å2
2---43.1259 Å20 Å2
3---30.4011 Å2
Refine analyzeLuzzati coordinate error obs: 0.94 Å
Refinement stepCycle: LAST / Resolution: 3.78→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8238 799 0 0 9037
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0099268HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.7512688HARMONIC3
X-RAY DIFFRACTIONt_dihedral_angle_d3091SINUSOIDAL5
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes190HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1259HARMONIC7
X-RAY DIFFRACTIONt_it9268HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.56
X-RAY DIFFRACTIONt_other_torsion14.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1271SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9937SEMIHARMONIC4
LS refinement shellResolution: 3.78→4.01 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3018 135 5.06 %
Rwork0.2692 2533 -
all0.2709 2668 -
obs--98.87 %
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)
19.32072.3217-1.44016.31940.1189.06590.40580.0628-0.3577-0.09870.1629-0.14110.25180.2654-0.56870.7201-0.0432-0.3557-0.4279-0.20810.6366512.963517.0937227.8866
25.7268-2.349-1.75435.86442.14737.33220.0653-0.1467-0.2540.13050.78631.06730.3011-1.3265-0.85161.01130.1782-0.2911-0.0259-0.41670.6372495.414421.2486227.5061
313.1523-1.21750.573712.11077.662111.0570.15110.15670.1655-0.210.1578-0.0531-0.22240.1579-0.30880.86680.2104-0.2170.8157-0.36340.7301484.210311.2071218.5302
4-0.17221.62322.18853.75421.81898.6287-0.1240.76470.30450.03350.02650.05720.07030.18280.09750.9947-0.0409-0.27850.9119-0.33530.5793493.183912.8132215.2094
59.7064-1.659-13.38068.92778.019110.5915-0.5873-1.12971.08530.5274-0.44620.7361-0.7811-1.48841.0335-0.5538-0.1383-0.1746-0.2930.2871-0.415510.2676-14.184228.8831
68.02350.71582.9663.00220.28044.8639-0.22910.4123-0.1939-0.1807-0.2233-0.1720.13310.87240.4524-0.27020.01580.2052-0.52210.1591-0.124534.6452-13.9845222.2786
74.0342-1.6274-4.63660.52542.395514.6150.3256-0.39040.7042-0.523-0.3726-0.5137-0.93480.8480.0471-0.5045-0.2164-0.39280.48570.02240.409549.3484-6.479257.5689
83.59351.4799-1.46594.1848-0.25184.38620.1759-0.81080.68080.7397-0.27620.0651-0.86930.94790.1003-0.2113-0.038-0.18090.6267-0.19730.0749529.5406-3.3496283.1498
97.06920.77897.92851.7488-0.794516.21090.2437-0.1964-0.26511.0297-0.0611-0.1951.44770.5694-0.1826-0.84280.15380.17850.10250.045-0.1308501.5614-27.6519262.9148
104.6772-6.6336-4.300910.08926.6235-4.6772-0.6401-1.56330.72610.28290.25830.16930.0243-0.37420.3817-0.2229-0.3491-0.6721-0.9119-0.3390.3467533.499818.4154253.3344
119.34216.7853-6.73064.0329-2.14469.58850.0170.09440.6099-0.51950.1624-0.8424-0.57210.5989-0.17940.25660.05630.0027-0.4748-0.12320.1035538.271212.2269224.587
129.1421-0.7727-3.17997.05420.223214.3395-0.38-0.84070.5554-0.2136-0.4197-0.36230.2894-0.22710.7997-0.2053-0.2171-0.1885-0.9119-0.11120.0892534.677611.422236.2688
136.15780.2593-1.135907.6435-2.1524-0.26660.71220.9103-0.3544-1.2541-1.7651-0.64981.26011.52070.3962-0.1197-0.532-0.5075-0.14910.1358539.303118.1981243.3783
140.7744.48543.124516.7211.50442.59390.24680.79070.3048-0.1617-0.23980.5993-0.3713-0.3062-0.0070.1922-0.1378-0.01440.8797-0.14190.4916516.039132.8094260.047
158.29383.67931.26468.75540.023315.4316-0.1880.26210.52890.0281-0.1969-0.44030.317-0.61780.38480.0487-0.2369-0.2148-0.3265-0.59460.236527.615928.3558260.1105
161.07223.9296-0.2648.6784-1.45359.4653-0.1412-0.18390.23020.9372-0.08030.787-0.4529-0.15160.22160.8938-0.23790.04950.8425-0.1820.78527.857335.1352228.9099
178.5538-7.38053.20165.65036.295610.57350.3048-0.993-0.2860.51070.39380.9599-0.0666-1.6476-0.69860.3345-0.16430.19380.9119-0.25630.8605513.368517.0972248.6806
186.5089-1.5794-0.05325.1016-4.0377-1.3009-0.0450.344-0.9602-1.0221-0.40681.31321.0139-0.61960.45181.019-0.0486-0.0920.9119-0.37080.7752516.447121.0269245.561
191.9318-5.04584.43877.21233.90893.5247-0.01680.8377-0.0118-0.2194-0.74340.6301-0.2411-1.41540.76021.0753-0.0609-0.15030.53070.23290.7485528.133534.4748227.8054
2018.3685-4.1211-2.53932.09622.8187-0.4847-0.073-0.2736-0.43110.5541-0.5890.79650.4694-0.40080.6620.734-0.2342-0.42260.1698-0.60080.2724498.647813.9573226.7481
212.38024.7052-3.13441.757-2.904914.49580.23220.45870.4114-0.0525-0.05860.5731-0.75-0.805-0.17360.83210.40260.0734-0.0899-0.32120.9917505.189130.8812225.5174
2210.9822-3.5125-1.29578.733-0.983211.3747-0.21581.06530.10620.2761-0.31960.23680.09490.02990.53540.3713-0.32870.2263-0.3108-0.38550.3936529.708340.2114266.1164
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|15 - 33}
2X-RAY DIFFRACTION2{A|34 - 58}
3X-RAY DIFFRACTION3{A|59 - 78}
4X-RAY DIFFRACTION4{A|79 - 89}
5X-RAY DIFFRACTION5{C|1 - 67}
6X-RAY DIFFRACTION6{C|68 - 309}
7X-RAY DIFFRACTION7{C|310 - 446}
8X-RAY DIFFRACTION8{C|447 - 661}
9X-RAY DIFFRACTION9{C|662 - 778}
10X-RAY DIFFRACTION10{D|19 - 33}
11X-RAY DIFFRACTION11{D|34 - 46}
12X-RAY DIFFRACTION12{D|47 - 104}
13X-RAY DIFFRACTION13{D|105 - 123}
14X-RAY DIFFRACTION14{D|124 - 150}
15X-RAY DIFFRACTION15{D|151 - 196}
16X-RAY DIFFRACTION16{E|2 - 10}
17X-RAY DIFFRACTION17{E|11 - 21}
18X-RAY DIFFRACTION18{F|5 - 13}
19X-RAY DIFFRACTION19{F|14 - 23}
20X-RAY DIFFRACTION20{B|12 - 61}
21X-RAY DIFFRACTION21{B|62 - 101}
22X-RAY DIFFRACTION22{B|109 - 137}

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