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- PDB-1cit: DNA-BINDING MECHANISM OF THE MONOMERIC ORPHAN NUCLEAR RECEPTOR NGFI-B -

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Basic information

Entry
Database: PDB / ID: 1cit
TitleDNA-BINDING MECHANISM OF THE MONOMERIC ORPHAN NUCLEAR RECEPTOR NGFI-B
Components
  • DNA (5'-D(*CP*CP*GP*AP*AP*AP*AP*GP*GP*TP*CP*AP*TP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*AP*TP*GP*AP*CP*CP*TP*TP*TP*TP*CP*GP*G)-3')
  • PROTEIN (ORPHAN NUCLEAR RECEPTOR NGFI-B)
KeywordsTRANSCRIPTION/DNA / ORPHAN NUCLEAR RECEPTOR / EARLY IMMEDIATE RESPONSE GENE PRODUCT / TRANSCRIPTION FACTOR / MONOMERIC PROTEIN-DNA COMPLEX / MINOR GROOVE INTERACTIONS / PROTEIN/DNA / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


AKT phosphorylates targets in the nucleus / neurotransmitter secretion involved in regulation of skeletal muscle contraction / cellular response to corticotropin-releasing hormone stimulus / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / endothelial cell chemotaxis / Nuclear Receptor transcription pathway / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus ...AKT phosphorylates targets in the nucleus / neurotransmitter secretion involved in regulation of skeletal muscle contraction / cellular response to corticotropin-releasing hormone stimulus / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / endothelial cell chemotaxis / Nuclear Receptor transcription pathway / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis / transcription factor binding / fat cell differentiation / skeletal muscle cell differentiation / negative regulation of cell cycle / cellular response to vascular endothelial growth factor stimulus / response to electrical stimulus / positive regulation of endothelial cell proliferation / response to amphetamine / lipopolysaccharide binding / nuclear receptor activity / sequence-specific double-stranded DNA binding / presynapse / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / sequence-specific DNA binding / transcription regulator complex / transcription by RNA polymerase II / response to lipopolysaccharide / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / positive regulation of apoptotic process / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Orphan nuclear receptor, HMR type / Orphan nuclear receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Orphan nuclear receptor, HMR type / Orphan nuclear receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear receptor subfamily 4 group A member 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMeinke, G. / Sigler, P.B.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: DNA-binding mechanism of the monomeric orphan nuclear receptor NGFI-B.
Authors: Meinke, G. / Sigler, P.B.
History
DepositionApr 5, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 3, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*CP*CP*GP*AP*AP*AP*AP*GP*GP*TP*CP*AP*TP*GP*CP*G)-3')
C: DNA (5'-D(*CP*GP*CP*AP*TP*GP*AP*CP*CP*TP*TP*TP*TP*CP*GP*G)-3')
A: PROTEIN (ORPHAN NUCLEAR RECEPTOR NGFI-B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0275
Polymers19,8963
Non-polymers1312
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.420, 34.240, 56.260
Angle α, β, γ (deg.)90.00, 109.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain DNA (5'-D(*CP*CP*GP*AP*AP*AP*AP*GP*GP*TP*CP*AP*TP*GP*CP*G)-3')


Mass: 4932.218 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*GP*CP*AP*TP*GP*AP*CP*CP*TP*TP*TP*TP*CP*GP*G)-3')


Mass: 4865.152 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (ORPHAN NUCLEAR RECEPTOR NGFI-B) / NGFI-B


Mass: 10098.962 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN AND C-TERMINAL EXTENSION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: NUCLEUS / Organ: BRAIN / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22829
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 53 %
Crystal growpH: 7
Details: PROTEIN/DNA COMPLEX CRYSTALS WERE GROWN USING THE VAPOR DIFFUSION METHOD AT 27 DEGREES CELSIUS. THE RESEVOIR CONTAINS 50 MM MORPHOLINO-SULFONIC ACID PH7.0, 250MM AMMONIUM CHLORIDE, 30 % PEG ...Details: PROTEIN/DNA COMPLEX CRYSTALS WERE GROWN USING THE VAPOR DIFFUSION METHOD AT 27 DEGREES CELSIUS. THE RESEVOIR CONTAINS 50 MM MORPHOLINO-SULFONIC ACID PH7.0, 250MM AMMONIUM CHLORIDE, 30 % PEG 4000, 5 MM DTT. THE DROPS CONTAINED A 1:1 RATIO OF PROTEIN-COMPLEX TO RESEVOIR.
Crystal grow
*PLUS
Temperature: 27 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: drop consists of 1:1 mixture of well and protein solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
210 mMTris-HCl1drop
350 mM1dropNaCl
41 mMdithiothreitol1drop
550 mMMops1reservoir
60.25 M1reservoirNH4Cl
729-30 %PEG40001reservoir
85 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→18 Å / Num. obs: 5200 / % possible obs: 95 % / Observed criterion σ(I): 3 / Redundancy: 2.3 % / Biso Wilson estimate: 80.3 Å2 / Rsym value: 0.073 / Net I/σ(I): 14.5
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.368 / % possible all: 96.9
Reflection
*PLUS
Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 96.9 % / Rmerge(I) obs: 0.368

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
MLPHAREphasing
CNS0.5refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HCQ

1hcq


Resolution: 2.7→18 Å / Rfactor Rfree error: 0.012 / Data cutoff high rms absF: 401381.9 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.295 568 10.9 %RANDOM
Rwork0.219 ---
obs-5200 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.7→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms690 650 2 38 1380
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
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_deg2.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.061.5
X-RAY DIFFRACTIONc_mcangle_it4.832
X-RAY DIFFRACTIONc_scbond_it4.362
X-RAY DIFFRACTIONc_scangle_it6.342.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.42 97 11 %
Rwork0.35 787 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.78

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