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- PDB-1ul4: Solution structure of the DNA-binding domain of squamosa promoter... -

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Basic information

Entry
Database: PDB / ID: 1ul4
TitleSolution structure of the DNA-binding domain of squamosa promoter binding protein-like 4
Componentssquamosa promoter binding protein-like 4
KeywordsDNA BINDING PROTEIN / Transcription factor / SBP / Flower development / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of vegetative phase change / flower development / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Squamosa promoter-binding protein / DNA-binding domain of squamosa promoter binding protein-like 12 (lacking the second zinc- binding site) / Transcription factor, SBP-box domain / SBP domain / SBP domain superfamily / SBP domain / Zinc finger SBP-type profile. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Squamosa promoter-binding-like protein 4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing
AuthorsYamasaki, K. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2004
Title: A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors.
Authors: Yamasaki, K. / Kigawa, T. / Inoue, M. / Tateno, M. / Yamasaki, T. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Nunokawa, E. / Ishizuka, Y. / Terada, T. / Shirouzu, M. / Osanai, T. / ...Authors: Yamasaki, K. / Kigawa, T. / Inoue, M. / Tateno, M. / Yamasaki, T. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Nunokawa, E. / Ishizuka, Y. / Terada, T. / Shirouzu, M. / Osanai, T. / Tanaka, A. / Seki, M. / Shinozaki, K. / Yokoyama, S.
History
DepositionSep 9, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: squamosa promoter binding protein-like 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7533
Polymers10,6221
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations, structures with the lowest energy
Representative

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Components

#1: Protein squamosa promoter binding protein-like 4 / SPL4


Mass: 10621.970 Da / Num. of mol.: 1 / Fragment: DNA-binding domain (SBP domain)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: cell-free synthesis / Gene: SPL4 / Plasmid: pCR2.1 / References: UniProt: Q9S7A9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 13C-separated NOESY
1413D 15N-separated NOESY
151HMQC-J
161DQF-COSY

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Sample preparation

DetailsContents: 0.02mM ZNCL2
Sample conditionsIonic strength: 20mM KPi, 300mM KCl / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionClassification
CNS1.1structure solution
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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