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- PDB-6t78: Structure of human Sox11 transcription factor in complex with a s... -

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Basic information

Entry
Database: PDB / ID: 6t78
TitleStructure of human Sox11 transcription factor in complex with a short DNA fragment
Components
  • DNA (5'-D(*AP*AP*CP*AP*AP*AP*AP*TP*AP*AP*AP*CP*AP*AP*TP*A)-3')
  • DNA (5'-D(*TP*AP*TP*TP*GP*TP*TP*TP*AP*TP*TP*TP*TP*GP*TP*T)-3')
  • Transcription factor SOX-11
KeywordsNUCLEAR PROTEIN / Sox11 / transcription factor / pioneer factor / DNA
Function / homology
Function and homology information


closure of optic fissure / positive regulation of lens epithelial cell proliferation / soft palate development / cornea development in camera-type eye / positive regulation of hippo signaling / noradrenergic neuron differentiation / negative regulation of transcription regulatory region DNA binding / negative regulation of lymphocyte proliferation / hard palate development / lens morphogenesis in camera-type eye ...closure of optic fissure / positive regulation of lens epithelial cell proliferation / soft palate development / cornea development in camera-type eye / positive regulation of hippo signaling / noradrenergic neuron differentiation / negative regulation of transcription regulatory region DNA binding / negative regulation of lymphocyte proliferation / hard palate development / lens morphogenesis in camera-type eye / embryonic skeletal system morphogenesis / regulation of transforming growth factor beta receptor signaling pathway / embryonic digestive tract morphogenesis / neuroepithelial cell differentiation / oligodendrocyte development / sympathetic nervous system development / positive regulation of hormone secretion / positive regulation of BMP signaling pathway / positive regulation of ossification / positive regulation of neurogenesis / negative regulation of glial cell proliferation / spinal cord development / ventricular septum morphogenesis / lung morphogenesis / positive regulation of stem cell proliferation / eyelid development in camera-type eye / outflow tract morphogenesis / skeletal muscle cell differentiation / anatomical structure morphogenesis / glial cell proliferation / positive regulation of osteoblast differentiation / positive regulation of neuron differentiation / kidney development / neuron differentiation / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
Transcription factor SOX-12/11/4 / High mobility group box domain / DNA Binding (I), subunit A / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor SOX-11
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.504 Å
AuthorsDodonova, S.O. / Zhu, F. / Dienemann, C. / Taipale, J. / Cramer, P.
Funding support Germany, 3items
OrganizationGrant numberCountry
European Research Council693023 Germany
European Molecular Biology OrganizationALTF-949-2016 Germany
Volkswagen Foundation Germany
CitationJournal: Nature / Year: 2020
Title: Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function.
Authors: Svetlana O Dodonova / Fangjie Zhu / Christian Dienemann / Jussi Taipale / Patrick Cramer /
Abstract: 'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions ...'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions of the genome with closed chromatin. SOX2 is a prominent pioneer factor that is essential for pluripotency and self-renewal of embryonic stem cells. Here we report cryo-electron microscopy structures of the DNA-binding domains of SOX2 and its close homologue SOX11 bound to nucleosomes. The structures show that SOX factors can bind and locally distort DNA at superhelical location 2. The factors also facilitate detachment of terminal nucleosomal DNA from the histone octamer, which increases DNA accessibility. SOX-factor binding to the nucleosome can also lead to a repositioning of the N-terminal tail of histone H4 that includes residue lysine 16. We speculate that this repositioning is incompatible with higher-order nucleosome stacking, which involves contacts of the H4 tail with a neighbouring nucleosome. Our results indicate that pioneer transcription factors can use binding energy to initiate chromatin opening, and thereby facilitate nucleosome remodelling and subsequent transcription.
History
DepositionOct 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor SOX-11
B: Transcription factor SOX-11
C: DNA (5'-D(*TP*AP*TP*TP*GP*TP*TP*TP*AP*TP*TP*TP*TP*GP*TP*T)-3')
D: DNA (5'-D(*AP*AP*CP*AP*AP*AP*AP*TP*AP*AP*AP*CP*AP*AP*TP*A)-3')
F: DNA (5'-D(*TP*AP*TP*TP*GP*TP*TP*TP*AP*TP*TP*TP*TP*GP*TP*T)-3')
G: DNA (5'-D(*AP*AP*CP*AP*AP*AP*AP*TP*AP*AP*AP*CP*AP*AP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)45,2956
Polymers45,2956
Non-polymers00
Water1086
1
A: Transcription factor SOX-11
F: DNA (5'-D(*TP*AP*TP*TP*GP*TP*TP*TP*AP*TP*TP*TP*TP*GP*TP*T)-3')
G: DNA (5'-D(*AP*AP*CP*AP*AP*AP*AP*TP*AP*AP*AP*CP*AP*AP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)22,6473
Polymers22,6473
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-15 kcal/mol
Surface area9090 Å2
MethodPISA
2
B: Transcription factor SOX-11
C: DNA (5'-D(*TP*AP*TP*TP*GP*TP*TP*TP*AP*TP*TP*TP*TP*GP*TP*T)-3')
D: DNA (5'-D(*AP*AP*CP*AP*AP*AP*AP*TP*AP*AP*AP*CP*AP*AP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)22,6473
Polymers22,6473
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-15 kcal/mol
Surface area9200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.130, 106.130, 76.890
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 48 through 121)
21chain B
12(chain C and resid 1 through 14)
22chain F
13(chain D and resid 3 through 16)
23chain G

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 48 through 121)A48 - 121
211chain BB48 - 121
112(chain C and resid 1 through 14)C1 - 14
212chain FF1 - 12
113(chain D and resid 3 through 16)D3 - 16
213chain GG5 - 16

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Transcription factor SOX-11


Mass: 12856.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOX11 / Plasmid: LIC-1B (MacroLabs) / Production host: Escherichia coli (E. coli) / References: UniProt: P35716
#2: DNA chain DNA (5'-D(*TP*AP*TP*TP*GP*TP*TP*TP*AP*TP*TP*TP*TP*GP*TP*T)-3')


Mass: 4890.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*AP*CP*AP*AP*AP*AP*TP*AP*AP*AP*CP*AP*AP*TP*A)-3')


Mass: 4900.273 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Sodium Acetate 100 mM pH 4.5, Calcium Acetate Hydrate 200 mM, 15-18 % PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.5→45.956 Å / Num. obs: 17066 / % possible obs: 99.9 % / Redundancy: 20.55 % / Biso Wilson estimate: 75.835 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.129 / Χ2: 1.052 / Net I/σ(I): 16.54 / Num. measured all: 350700 / Scaling rejects: 96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.5719.9732.7860.8725266127512650.662.85899.2
2.57-2.6421.0562.3251.2525352120512040.7752.38399.9
2.64-2.7220.7121.8021.6824564118811860.8041.84899.8
2.72-2.819.6011.3182.3622913116911690.9051.353100
2.8-2.8920.7520.9073.5423118111411140.9450.929100
2.89-2.9921.5040.7114.5723310108510840.9750.72899.9
2.99-3.1121.1830.5446.1322327105410540.9790.557100
3.11-3.2320.6330.3739.2720777100710070.9880.383100
3.23-3.3819.910.27112.34191149609600.9940.278100
3.38-3.5419.5690.20715.53183759399390.9960.213100
3.54-3.7321.3420.14422.16185258688680.9980.148100
3.73-3.9621.1460.11326.23178478448440.9990.116100
3.96-4.2320.9390.09631.22164377857850.9980.099100
4.23-4.5719.4220.08234.55141207277270.9990.084100
4.57-5.0121.2310.07437.96145436856850.9990.075100
5.01-5.621.1540.07639.33129046106100.9990.077100
5.6-6.4720.1710.06839.81108725395390.9990.07100
6.47-7.9220.0660.05251.7191704574570.9990.053100
7.92-11.220.3250.0464.21737836336310.041100
11.2-45.95618.3880.03670.02378820920610.03798.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.66 Å45.96 Å
Translation2.66 Å45.96 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.7.16phasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GT0

1gt0


Resolution: 2.504→45.956 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.88
RfactorNum. reflection% reflection
Rfree0.2578 853 5.01 %
Rwork0.2269 --
obs0.2284 17031 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 215.77 Å2 / Biso mean: 96.3747 Å2 / Biso min: 48.08 Å2
Refinement stepCycle: final / Resolution: 2.504→45.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1307 1019 0 6 2332
Biso mean---65.63 -
Num. residues----201
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A782X-RAY DIFFRACTION6.231TORSIONAL
12B782X-RAY DIFFRACTION6.231TORSIONAL
21C272X-RAY DIFFRACTION6.231TORSIONAL
22F272X-RAY DIFFRACTION6.231TORSIONAL
31D274X-RAY DIFFRACTION6.231TORSIONAL
32G274X-RAY DIFFRACTION6.231TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5045-2.66140.43941420.388266999
2.6614-2.86680.37921410.3212678100
2.8668-3.15530.2961410.29862672100
3.1553-3.61170.23921420.22912700100
3.6117-4.54970.26791430.20732710100
4.5497-45.90.22021440.19942749100
Refinement TLS params.Method: refined / Origin x: 29.4328 Å / Origin y: 55.5287 Å / Origin z: 23.2924 Å
111213212223313233
T0.6846 Å2-0.0374 Å2-0.0556 Å2-0.7261 Å20.0727 Å2--0.7415 Å2
L4.4731 °2-2.7281 °2-0.7697 °2-1.5084 °20.4089 °2--0.7618 °2
S-0.0085 Å °0.0747 Å °0.9103 Å °-0.0526 Å °0.0559 Å °-0.5252 Å °-0.4133 Å °0.3464 Å °-0.0989 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA46 - 122
2X-RAY DIFFRACTION1allB48 - 121
3X-RAY DIFFRACTION1allC1 - 13
4X-RAY DIFFRACTION1allD4 - 16
5X-RAY DIFFRACTION1allF1 - 12
6X-RAY DIFFRACTION1allG5 - 16
7X-RAY DIFFRACTION1allS1 - 6

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