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- PDB-4y60: Structure of SOX18-HMG/PROX1-DNA -

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Basic information

Entry
Database: PDB / ID: 4y60
TitleStructure of SOX18-HMG/PROX1-DNA
Components
  • DNA (5'-D(*CP*AP*CP*TP*AP*GP*CP*AP*TP*TP*GP*TP*CP*TP*GP*GP*G)-3')
  • DNA (5'-D(*GP*CP*CP*CP*AP*GP*AP*CP*AP*AP*TP*GP*CP*TP*AP*GP*T)-3')
  • Transcription factor SOX-18
KeywordsTRANSCRIPTION/DNA / Transcription factor / SOX / protein-DNA / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


stem cell fate specification / endocardium formation / lymphatic endothelial cell differentiation / hair cycle process / endocardial cell differentiation / lymphangiogenesis / blood vessel endothelial cell migration / chromatin => GO:0000785 / lymph vessel development / regulation of stem cell proliferation ...stem cell fate specification / endocardium formation / lymphatic endothelial cell differentiation / hair cycle process / endocardial cell differentiation / lymphangiogenesis / blood vessel endothelial cell migration / chromatin => GO:0000785 / lymph vessel development / regulation of stem cell proliferation / embryonic heart tube development / vasculature development / establishment of endothelial barrier / blood vessel development / hair follicle development / anatomical structure morphogenesis / vasculogenesis / cell maturation / sequence-specific double-stranded DNA binding / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / in utero embryonic development / transcription regulator complex / sequence-specific DNA binding / cell differentiation / 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 DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Sox, C-terminal / Sox 7/17/18, central domain / Sox 17/18 central domain / Sox C-terminal domain profile. / 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 ...Sox, C-terminal / Sox 7/17/18, central domain / Sox 17/18 central domain / Sox C-terminal domain profile. / 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-18
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsNarasimhan, K. / Prokoph, N. / Kolatkar, P. / Robinson, H. / Jauch, R.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structure and decoy-mediated inhibition of the SOX18/Prox1-DNA interaction.
Authors: Klaus, M. / Prokoph, N. / Girbig, M. / Wang, X. / Huang, Y.H. / Srivastava, Y. / Hou, L. / Narasimhan, K. / Kolatkar, P.R. / Francois, M. / Jauch, R.
History
DepositionFeb 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Transcription factor SOX-18
A: DNA (5'-D(*CP*AP*CP*TP*AP*GP*CP*AP*TP*TP*GP*TP*CP*TP*GP*GP*G)-3')
B: DNA (5'-D(*GP*CP*CP*CP*AP*GP*AP*CP*AP*AP*TP*GP*CP*TP*AP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)20,1863
Polymers20,1863
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-17 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.942, 111.942, 32.417
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Transcription factor SOX-18


Mass: 9771.423 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 77-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sox18, Sox-18 / Production host: Escherichia coli (E. coli) / References: UniProt: P43680
#2: DNA chain DNA (5'-D(*CP*AP*CP*TP*AP*GP*CP*AP*TP*TP*GP*TP*CP*TP*GP*GP*G)-3')


Mass: 5218.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: DNA chain DNA (5'-D(*GP*CP*CP*CP*AP*GP*AP*CP*AP*AP*TP*GP*CP*TP*AP*GP*T)-3')


Mass: 5196.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M MMT buffer pH 5.0, 25% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Oct 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 23871 / % possible obs: 100 % / Redundancy: 24 % / Net I/σ(I): 19.94

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementResolution: 1.75→36.642 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1989 1222 5.12 %
Rwork0.1737 --
obs0.175 23869 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→36.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms648 675 0 194 1517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011419
X-RAY DIFFRACTIONf_angle_d1.9042053
X-RAY DIFFRACTIONf_dihedral_angle_d25.873593
X-RAY DIFFRACTIONf_chiral_restr0.163219
X-RAY DIFFRACTIONf_plane_restr0.007150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7495-1.81950.26811190.22632516X-RAY DIFFRACTION100
1.8195-1.90230.23811450.21062490X-RAY DIFFRACTION100
1.9023-2.00260.22251240.2072481X-RAY DIFFRACTION100
2.0026-2.12810.23031550.20322468X-RAY DIFFRACTION100
2.1281-2.29240.21191170.19112530X-RAY DIFFRACTION100
2.2924-2.5230.23181340.18862506X-RAY DIFFRACTION100
2.523-2.8880.21341360.19782509X-RAY DIFFRACTION100
2.888-3.6380.17511370.1562550X-RAY DIFFRACTION100
3.638-36.64960.18431550.1552597X-RAY DIFFRACTION100
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)
14.60070.0689-0.61564.49142.88992.3345-0.26350.4416-0.4959-0.91030.38550.06180.6430.7896-0.23760.4115-0.02410.0020.367-0.10160.328343.7358-53.5221-8.5248
29.13184.45910.6812.5151-0.70673.18690.305-0.4019-0.40010.0141-0.3935-0.35290.309-0.12050.10210.1882-0.0052-0.01960.2425-0.02680.22846.9666-42.17010.7304
32.21421.68851.35147.4392-1.60588.43880.50970.29490.7611-0.2843-0.55590.0127-0.80950.0751-0.06990.33930.04270.05610.27210.02580.366456.8974-36.9179-1.0854
47.02576.7111-1.92356.5008-2.35627.05420.0960.0517-0.3484-0.1695-0.1599-0.468-0.03440.59780.08570.24690.02470.01060.34760.00490.332763.4311-41.65632.8042
59.6784-5.18970.74527.02161.0353.574-0.337-0.7734-0.28420.75070.16160.09790.1796-0.09810.12440.2798-0.02360.0130.2619-0.00450.203452.3525-41.17219.0612
64.5841-3.7796-1.22684.5995-1.11393.37460.0075-1.20890.97010.7502-0.145-0.3643-0.20860.24450.2940.2995-0.04810.0070.375-0.11930.318643.8997-32.75159.6205
72.52982.82192.21774.91434.96137.2477-0.14010.0190.1294-0.5558-0.29290.847-0.0681-0.63140.47150.2425-0.0131-0.04080.3491-0.02890.336635.5592-43.44-4.3259
86.6185-6.80885.34047.5208-6.18845.23560.85160.4083-2.16840.05370.46161.0351.7943-0.1539-1.31990.6741-0.11830.00220.403-0.08160.552238.5565-61.2848-3.6421
98.0968-0.0921-3.1982.8489-1.20593.0672-0.1480.6882.7291-0.92150.32110.52191.2278-1.2954-0.15370.45430.0963-0.05810.88750.05240.516464.4751-60.3535-13.5233
105.1386-5.3261-5.24435.57315.58535.7754-0.27690.6582-0.70130.872-0.1012-0.47361.8328-0.72570.44470.52970.04760.09210.45970.040.507259.2438-56.39791.8433
114.26342.5825-1.56299.94431.1755.84450.2893-0.4281-0.26350.414-0.63850.35210.2495-0.1770.30290.217-0.04860.03430.3093-0.01820.249743.999-50.00726.4153
125.11061.9826-3.22055.5875-5.76156.7929-0.5192-0.0466-0.677-1.14970.45970.60681.97230.321-0.09720.6065-0.13840.1240.4839-0.01150.493936.0281-66.07087.8025
137.76331.0531-2.24993.95343.13683.8142-1.03770.11360.0159-0.75570.64580.02170.09920.57570.32620.4052-0.05060.09040.56410.02190.495133.2235-60.739214.9938
147.74312.3717-5.99922.9687-2.29694.7086-0.2031-0.90180.12040.1308-0.0470.20310.69691.20590.29980.30880.04310.07440.39160.02590.40145.7169-60.25866.7221
152.0662-0.21851.74072.62080.8062.71750.08311.0614-0.0988-0.3591-0.0525-0.12110.33080.2819-0.10710.2374-0.00260.02780.31080.02320.235552.7785-49.0363-3.8176
163.131-3.00111.26844.79050.76762.58670.06350.7850.02990.98810.0161-1.05560.54120.6418-0.30770.30640.17360.00770.5094-0.01210.457967.615-55.1307-3.2853
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain C and resid 0:7)
2X-RAY DIFFRACTION2(chain C and resid 8:15)
3X-RAY DIFFRACTION3(chain C and resid 16:23)
4X-RAY DIFFRACTION4(chain C and resid 24:33)
5X-RAY DIFFRACTION5(chain C and resid 34:42)
6X-RAY DIFFRACTION6(chain C and resid 43:48)
7X-RAY DIFFRACTION7(chain C and resid 49:68)
8X-RAY DIFFRACTION8(chain C and resid 69:75)
9X-RAY DIFFRACTION9(chain A and resid 0:3)
10X-RAY DIFFRACTION10(chain A and resid 4:7)
11X-RAY DIFFRACTION11(chain A and resid 8:12)
12X-RAY DIFFRACTION12(chain A and resid 13:16)
13X-RAY DIFFRACTION13(chain B and resid 0:3)
14X-RAY DIFFRACTION14(chain B and resid 4:7)
15X-RAY DIFFRACTION15(chain B and resid 8:11)
16X-RAY DIFFRACTION16(chain B and resid 12:15)

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