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- PDB-4a3n: Crystal Structure of HMG-BOX of Human SOX17 -

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Basic information

Entry
Database: PDB / ID: 4a3n
TitleCrystal Structure of HMG-BOX of Human SOX17
ComponentsTRANSCRIPTION FACTOR SOX-17
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


cardiogenic plate morphogenesis / regulation of cardiac cell fate specification / heart formation / endocardium formation / endodermal digestive tract morphogenesis / ureter development / endoderm formation / cardiac cell fate determination / embryonic foregut morphogenesis / endodermal cell fate specification ...cardiogenic plate morphogenesis / regulation of cardiac cell fate specification / heart formation / endocardium formation / endodermal digestive tract morphogenesis / ureter development / endoderm formation / cardiac cell fate determination / embryonic foregut morphogenesis / endodermal cell fate specification / endocardial cell differentiation / Specification of primordial germ cells / metanephros development / Developmental Lineage of Multipotent Pancreatic Progenitor Cells / embryonic heart tube development / embryonic heart tube morphogenesis / Formation of definitive endoderm / response to alkaloid / heart looping / outflow tract morphogenesis / vasculogenesis / regulation of embryonic development / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / protein destabilization / negative regulation of cell growth / Deactivation of the beta-catenin transactivating complex / beta-catenin binding / heart development / positive regulation of protein catabolic process / transcription regulator complex / angiogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein stabilization / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / nucleoplasm / 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 ...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
Transcription factor SOX-17
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGao, N. / Gao, H. / Qian, H. / Si, S. / Xie, Y.
Citation
Journal: Protein Pept.Lett. / Year: 2013
Title: Structural Basis of Human Transcription Factor Sry-Related Box 17 Binding to DNA.
Authors: Gao, N. / Jiang, W. / Gao, H. / Cheng, Z. / Qian, H. / Si, S. / Xie, Y.
#1: Journal: J.Mol.Biol. / Year: 2009
Title: The Structure of Sox17 Bound to DNA Reveals a Conserved Bending Topology But Selective Protein Interaction Platforms.
Authors: Palasingam, P. / Jauch, R. / Ng, C.K.L. / Kolatkar, P.R.
History
DepositionOct 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Mar 20, 2013Group: Data collection / Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: TRANSCRIPTION FACTOR SOX-17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6424
Polymers8,4461
Non-polymers1963
Water1,29772
1
A: TRANSCRIPTION FACTOR SOX-17
hetero molecules

A: TRANSCRIPTION FACTOR SOX-17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2848
Polymers16,8922
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1410 Å2
ΔGint-180.6 kcal/mol
Surface area9370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.281, 22.525, 66.668
Angle α, β, γ (deg.)90.00, 129.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRANSCRIPTION FACTOR SOX-17


Mass: 8445.764 Da / Num. of mol.: 1 / Fragment: HMG-BOX, RESIDUES 68-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H6I2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.25 Å3/Da / Density % sol: 62.19 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 4389 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 23.4 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F27

3f27


Resolution: 2.4→23.66 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1313405.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.267 453 10.5 %RANDOM
Rwork0.202 ---
obs0.202 4319 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.9136 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 44.7 Å2
Baniso -1Baniso -2Baniso -3
1-16.34 Å20 Å2-12.99 Å2
2---13.86 Å20 Å2
3----2.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.4→23.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms534 0 3 72 609
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 64 8.9 %
Rwork0.255 653 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP

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