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- PDB-1au7: PIT-1 MUTANT/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1au7
TitlePIT-1 MUTANT/DNA COMPLEX
Components
  • CONSENSUS DNA 25-MER
  • DNA (5'-D(*CP*TP*TP*CP*CP*TP*CP*AP*TP*GP*TP*AP*TP*AP*TP*AP*C P*AP*TP*GP*AP*GP* GP*A)-3')
  • PROTEIN PIT-1
KeywordsTRANSCRIPTION/DNA / COMPLEX (DNA-BINDING PROTEIN-DNA) / PITUITARY / CPHD / POU DOMAIN / TRANSCRIPTION FACTOR / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


somatotropin secreting cell development / somatotropin secreting cell differentiation / regulation of insulin-like growth factor receptor signaling pathway / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / positive regulation of inositol trisphosphate biosynthetic process / adenohypophysis development / pituitary gland development / positive regulation of multicellular organism growth / cell fate specification ...somatotropin secreting cell development / somatotropin secreting cell differentiation / regulation of insulin-like growth factor receptor signaling pathway / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / positive regulation of inositol trisphosphate biosynthetic process / adenohypophysis development / pituitary gland development / positive regulation of multicellular organism growth / cell fate specification / B cell differentiation / determination of adult lifespan / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / positive regulation of cell population proliferation / 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
Pituitary-specific positive transcription factor 1 / POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / Homeobox, conserved site / 'Homeobox' domain signature. ...Pituitary-specific positive transcription factor 1 / POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / lambda repressor-like DNA-binding domains / Homeobox domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Pituitary-specific positive transcription factor 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJacobson, E.M. / Li, P. / Leon-Del-Rio, A. / Rosenfeld, M.G. / Aggarwal, A.K.
CitationJournal: Genes Dev. / Year: 1997
Title: Structure of Pit-1 POU domain bound to DNA as a dimer: unexpected arrangement and flexibility.
Authors: Jacobson, E.M. / Li, P. / Leon-del-Rio, A. / Rosenfeld, M.G. / Aggarwal, A.K.
History
DepositionSep 12, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: CONSENSUS DNA 25-MER
D: DNA (5'-D(*CP*TP*TP*CP*CP*TP*CP*AP*TP*GP*TP*AP*TP*AP*TP*AP*C P*AP*TP*GP*AP*GP* GP*A)-3')
A: PROTEIN PIT-1
B: PROTEIN PIT-1


Theoretical massNumber of molelcules
Total (without water)49,0734
Polymers49,0734
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.500, 50.100, 55.800
Angle α, β, γ (deg.)76.70, 79.30, 67.20
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.388765, -0.637872, 0.664816), (-0.664442, -0.693985, -0.277312), (0.638262, -0.333923, -0.693626)
Vector: -1.92157, 58.74348, 62.81211)

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Components

#1: DNA chain CONSENSUS DNA 25-MER


Mass: 7722.009 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*TP*TP*CP*CP*TP*CP*AP*TP*GP*TP*AP*TP*AP*TP*AP*C P*AP*TP*GP*AP*GP* GP*A)-3')


Mass: 7343.766 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN PIT-1 / GHF-1


Mass: 17003.570 Da / Num. of mol.: 2 / Mutation: E5G, I6M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: SPRAGUE-DAWLEY / Tissue: ENDOCRINE / Cell: LACTOTROPES, SOMATOTROPES / Cellular location: NUCLEAR / Gene: PIT-1 / Organ: PITUITARY GLAND / Plasmid: 14B / Species (production host): Escherichia coli / Cellular location (production host): INCLUSION BODIES / Gene (production host): PIT-1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Keywords: MUTATIONS E5G, I6M / References: UniProt: P10037
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Compound detailsLINKERS CONNECTING POU SPECIFIC DOMAIN AND POU HOMEO DOMAIN ARE DISORDERED IN THE STRUCTURE AND NOT ...LINKERS CONNECTING POU SPECIFIC DOMAIN AND POU HOMEO DOMAIN ARE DISORDERED IN THE STRUCTURE AND NOT VISIBLE IN THE ELECTRON DENSITY MAP.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 33 % / Description: BROMO-URACIL MAD EXPERIMENT
Crystal growMethod: vapor diffusion, hanging drop / pH: 4
Details: A 28 BP DNA DUPLEX (10MG/ML) WAS ADDED TO THE PROTEIN IN A 1:2 MOLAR RATIO. CRYSTALS WERE GROWN BY VAPOR DIFFUSION USING HANGING DROPS OF 1 UL. OF PROTEIN/DNA SOLUTION MIXED 1 UL. OF ...Details: A 28 BP DNA DUPLEX (10MG/ML) WAS ADDED TO THE PROTEIN IN A 1:2 MOLAR RATIO. CRYSTALS WERE GROWN BY VAPOR DIFFUSION USING HANGING DROPS OF 1 UL. OF PROTEIN/DNA SOLUTION MIXED 1 UL. OF RESERVOIR SOLUTION. THE BEST CRYSTALS WERE OBTAINED WITH RESERVOIRS CONTAINING 400-600 MM PHOSPHORIC ACID ADJUSTED TO PH 4.0 - 4.3 WITH TRIETHYLAMINE., pH 4.00, vapor diffusion - hanging drop
PH range: 4.0-4.3
Components of the solutions
IDNameCrystal-IDSol-ID
1PHOSPHORIC ACID11
2TRIETHYLAMINE11

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Data collection

DiffractionMean temperature: 111 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Aug 1, 1994 / Details: DUAL SLITS
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 10021 / % possible obs: 87.2 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.058 / Rsym value: 5.8 / Net I/σ(I): 18
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 7 / Rsym value: 18.9 / % possible all: 73

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Processing

Software
NameVersionClassification
PHASITmodel building
X-PLOR3.1Frefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASITphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.3→6 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.302 -5 %RANDOM
Rwork0.23 ---
obs-14575 84.7 %-
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 1094 0 528 4275
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.71
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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