[English] 日本語
Yorodumi
- PDB-4a3n: Crystal Structure of HMG-BOX of Human SOX17 -

+
Open data


ID or keywords:

Loading...

-
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 / endodermal cell fate determination / regulation of cardiac cell fate specification / stem cell fate specification / endocardium formation / common bile duct development / endodermal digestive tract morphogenesis / ureter development / 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 / endodermal digestive tract morphogenesis / ureter development / gallbladder development / inner cell mass cellular morphogenesis / heart formation / cardiac cell fate determination / regulation of stem cell division / rostrocaudal neural tube patterning / endodermal cell fate specification / endoderm formation / cell migration involved in gastrulation / Specification of primordial germ cells / endocardial cell differentiation / positive regulation of endodermal cell differentiation / positive regulation of stem cell differentiation / embryonic foregut morphogenesis / regulation of stem cell proliferation / signal transduction involved in regulation of gene expression / Formation of definitive endoderm / metanephros development / embryonic heart tube development / embryonic heart tube morphogenesis / heart looping / outflow tract morphogenesis / regulation of embryonic development / anatomical structure morphogenesis / vasculogenesis / cellular response to leukemia inhibitory factor / Deactivation of the beta-catenin transactivating complex / negative regulation of canonical Wnt signaling pathway / protein destabilization / negative regulation of cell growth / beta-catenin binding / Wnt signaling pathway / positive regulation of protein catabolic process / gene expression / heart development / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / protein stabilization / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / 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 / 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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.19 % / Description: NONE

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more