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- PDB-6l6y: Crystal Structure of Pluripotency Reprogramming Factor Sox17 muta... -

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Basic information

Entry
Database: PDB / ID: 6l6y
TitleCrystal Structure of Pluripotency Reprogramming Factor Sox17 mutant (Sox17EK) HMG Domain bound to DNA
Components
  • DNA (5'-D(*CP*CP*AP*GP*GP*AP*CP*AP*AP*TP*AP*GP*AP*GP*AP*C)-3')
  • DNA (5'-D(P*GP*GP*TP*CP*TP*CP*TP*AP*TP*TP*GP*TP*CP*CP*TP*G)-3')
  • Transcription factor SOX-17
KeywordsDNA BINDING PROTEIN/DNA / TRANSCRIPTION / HMG / Stem Cell Transcription Factor / Pluripotency Reprogramming Factor / DNA BINDING PROTEIN-DNA / TRANSCRIPTION complex
Function / homology
Function and homology information


cardiogenic plate morphogenesis / endodermal cell fate determination / regulation of cardiac cell fate specification / stem cell fate specification / endocardium formation / common bile duct development / ureter development / endodermal digestive tract morphogenesis / gallbladder development / inner cell mass cellular morphogenesis ...cardiogenic plate morphogenesis / endodermal cell fate determination / regulation of cardiac cell fate specification / stem cell fate specification / endocardium formation / common bile duct development / ureter development / endodermal digestive tract morphogenesis / gallbladder development / inner cell mass cellular morphogenesis / cardiac cell fate determination / endodermal cell fate specification / regulation of stem cell division / cell migration involved in gastrulation / Deactivation of the beta-catenin transactivating complex / endocardial cell differentiation / rostrocaudal neural tube patterning / positive regulation of endodermal cell differentiation / positive regulation of stem cell differentiation / embryonic foregut morphogenesis / regulation of stem cell proliferation / endoderm development / response to alkaloid / metanephros development / embryonic heart tube morphogenesis / embryonic heart tube development / signal transduction involved in regulation of gene expression / heart looping / negative regulation of Wnt signaling pathway / endodermal cell differentiation / regulation of cell differentiation / outflow tract morphogenesis / regulation of embryonic development / embryonic organ development / vasculogenesis / gastrulation / cellular response to leukemia inhibitory factor / stem cell differentiation / negative regulation of canonical Wnt signaling pathway / negative regulation of cell growth / beta-catenin binding / protein destabilization / Wnt signaling pathway / positive regulation of protein catabolic process / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / spermatogenesis / transcription regulator complex / gene expression / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / protein stabilization / DNA-binding transcription factor activity / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Sox, C-terminal / Sox 7/17/18, central domain / Sox 17/18 central domain / Sox C-terminal domain profile. / : / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor SOX-17
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBalasubramanian, M. / Kolatkar, P.R.
Funding supportQatar, 1items
OrganizationGrant numberCountry
Qatar FoundationIGP1 2014-004Qatar
Citation
Journal: To Be Published
Title: Crystal Structure of Pluripotency Reprogramming Factor Sox17 mutant (Sox17EK) HMG Domain bound to DNA
Authors: Balasubramanian, M. / Kolatkar, P.R.
#1: Journal: Bioinformatics / Year: 2019
Title: DeepCrystal: a deep learning framework for sequence-based protein crystallization prediction.
Authors: Elbasir, A. / Moovarkumudalvan, B. / Kunji, K. / Kolatkar, P.R. / Mall, R. / Bensmail, H.
History
DepositionOct 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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: DNA (5'-D(P*GP*GP*TP*CP*TP*CP*TP*AP*TP*TP*GP*TP*CP*CP*TP*G)-3')
B: DNA (5'-D(*CP*CP*AP*GP*GP*AP*CP*AP*AP*TP*AP*GP*AP*GP*AP*C)-3')
D: Transcription factor SOX-17
C: DNA (5'-D(P*GP*GP*TP*CP*TP*CP*TP*AP*TP*TP*GP*TP*CP*CP*TP*G)-3')
E: DNA (5'-D(*CP*CP*AP*GP*GP*AP*CP*AP*AP*TP*AP*GP*AP*GP*AP*C)-3')
F: Transcription factor SOX-17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8587
Polymers39,7626
Non-polymers961
Water23413
1
A: DNA (5'-D(P*GP*GP*TP*CP*TP*CP*TP*AP*TP*TP*GP*TP*CP*CP*TP*G)-3')
B: DNA (5'-D(*CP*CP*AP*GP*GP*AP*CP*AP*AP*TP*AP*GP*AP*GP*AP*C)-3')
D: Transcription factor SOX-17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9774
Polymers19,8813
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-20 kcal/mol
Surface area10910 Å2
MethodPISA
2
C: DNA (5'-D(P*GP*GP*TP*CP*TP*CP*TP*AP*TP*TP*GP*TP*CP*CP*TP*G)-3')
E: DNA (5'-D(*CP*CP*AP*GP*GP*AP*CP*AP*AP*TP*AP*GP*AP*GP*AP*C)-3')
F: Transcription factor SOX-17


Theoretical massNumber of molelcules
Total (without water)19,8813
Polymers19,8813
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-10 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.040, 73.205, 81.952
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: DNA chain DNA (5'-D(P*GP*GP*TP*CP*TP*CP*TP*AP*TP*TP*GP*TP*CP*CP*TP*G)-3')


Mass: 4871.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*CP*CP*AP*GP*GP*AP*CP*AP*AP*TP*AP*GP*AP*GP*AP*C)-3')


Mass: 4925.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein Transcription factor SOX-17


Mass: 10084.753 Da / Num. of mol.: 2 / Mutation: E122K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sox17, Sox-17 / Plasmid: PETG20A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q61473
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 0.2 M Ammonium Sulfate, 30% PEG 4000, 0.1 M Tris pH 8.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Details: Bruker D8 Venture / Wavelength: 1.5418 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Jul 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.99→20.97 Å / Num. obs: 16478 / % possible obs: 99.1 % / Redundancy: 9.61 % / Biso Wilson estimate: 32.63 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 11.02
Reflection shellResolution: 2.99→3.09 Å / Redundancy: 7.04 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.74 / Num. unique obs: 839 / % possible all: 95.3

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Processing

Software
NameVersionClassificationNB
PHENIX1.17_3644refinement
PROTEUMdata reduction
SADABSdata scaling
PHENIX1.17_3644phasing
PROTEUMdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F27

3f27


Resolution: 3→20.97 Å / SU ML: 0.3848 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8894
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2537 1632 9.9 %
Rwork0.1896 --
obs0.1961 16478 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.15 Å2
Refinement stepCycle: LAST / Resolution: 3→20.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1356 1306 5 13 2680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01232854
X-RAY DIFFRACTIONf_angle_d1.25594110
X-RAY DIFFRACTIONf_chiral_restr0.0681436
X-RAY DIFFRACTIONf_plane_restr0.0071306
X-RAY DIFFRACTIONf_dihedral_angle_d33.1596810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.090.37971270.29821252X-RAY DIFFRACTION99.78
3.09-3.190.27351450.24021248X-RAY DIFFRACTION100
3.19-3.30.30081360.23381213X-RAY DIFFRACTION100
3.3-3.430.30391490.21341225X-RAY DIFFRACTION99.85
3.43-3.590.27231290.20731244X-RAY DIFFRACTION100
3.59-3.780.30911320.19181232X-RAY DIFFRACTION100
3.78-4.010.22781320.17471240X-RAY DIFFRACTION100
4.01-4.320.21541320.15561251X-RAY DIFFRACTION100
4.32-4.750.20591340.16441230X-RAY DIFFRACTION100
4.75-5.420.23681390.17711249X-RAY DIFFRACTION100
5.43-6.80.21791330.16851241X-RAY DIFFRACTION100
6.8-20.970.22021440.15621221X-RAY DIFFRACTION99.49
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)
11.44982504552-0.0150346654562-0.6480569604822.25765565865-1.529155126742.830916513660.05282521572580.1463135739010.489274339754-0.20774250325-0.00422218395787-0.449917777407-0.3914595239890.3910715027240.01403787030620.209476289746-0.1607621757560.05900339163330.3733622696410.06552770394950.25239855113721.843774519720.39712480574.88275088704
21.762991680260.203021953739-0.08278971996671.781951642750.3752252145841.739580149090.0242071320967-0.3679748275980.1699468295060.3346766519650.103623306543-0.159786837526-0.206043935362-0.1272457272190.3698891614660.245123905460.0145623904739-0.1018632140060.2874451425310.1667637997020.082867908941419.423507468621.30704235115.53088221862
32.067123501670.283275261156-0.5543414343020.582324483088-0.3127917427580.8358164864010.0400795302131-0.358335055964-0.350178716297-0.0910798323139-0.0464137635876-0.143619857260.1594792847290.1241744592370.02645299844150.108441713512-0.01098910246630.05376928722790.1558771691760.08484567131850.18068071810219.82260521667.773766230727.78369420734
40.7275499093141.017877737810.3396526254981.440864328140.4200372100191.24534652741-0.101315056721-0.651911187469-0.2037914271110.5457035527630.171265769599-0.4373985406160.6493743841190.7410057929380.07768044978410.6421958987380.38081384458-0.03872607976380.860072998395-0.1129929039430.2961730630237.3555776798-8.42136322885-5.15487968827
51.696089398810.8188165920570.3271572970941.600698186740.8364938674170.4452606743620.1200554746-0.558546616841-0.6560643317740.4445768426780.248529664527-0.4696737998610.8698524245020.551685691657-0.03519572463990.7344516429630.395790368146-0.04321311523780.8743717020130.04018365536230.42923546260436.9649978261-10.8735281099-5.6298263526
62.193676581190.8455989357641.253907044972.189764560961.01467807632.452069661480.166685519333-0.176848027398-0.4254975175830.318824308849-0.104637570242-0.2824459973820.757825895525-0.11144782675-0.0551560018030.306109874075-0.06682250167010.03006187426840.363722795351-0.1299674028640.25323271531325.8671400928-3.28937488941-6.61224228081
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 15)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 16)
3X-RAY DIFFRACTION3(chain 'D' and resid 62 through 141)
4X-RAY DIFFRACTION4(chain 'C' and resid 0 through 15)
5X-RAY DIFFRACTION5(chain 'E' and resid 1 through 16)
6X-RAY DIFFRACTION6(chain 'F' and resid 62 through 141)

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