title: Orphan nuclear receptor NGFI-B forms dimers with nonclassical interface.
abstract: The orphan receptor nerve growth factor-induced B (NGFI-B) is a member of the nuclear receptor's subfamily 4A (Nr4a). NGFI-B was shown to be capable of binding both as a monomer to an extended half-site containing a single AAAGGTCA motif and also as a homodimer to a widely separated everted repeat, as opposed to a large number of nuclear receptors that recognize and bind specific DNA sequences predominantly as homo- and/or heterodimers. To unveil the structural organization of NGFI-B in solution, we determined the quaternary structure of the NGFI-B LBD by a combination of ab initio procedures from small-angle X-ray scattering (SAXS) data and hydrogen-deuterium exchange followed by mass spectrometry. Here we report that the protein forms dimers in solution with a radius of gyration of 2.9 nm and maximum dimension of 9.0 nm. We also show that the NGFI-B LBD dimer is V-shaped, with the opening angle significantly larger than that of classical dimer's exemplified by estrogen receptor (ER) or retinoid X receptor (RXR). Surprisingly, NGFI-B dimers formation does not occur via the classical nuclear receptor dimerization interface exemplified by ER and RXR, but instead, involves an extended surface area composed of the loop between helices 3 and 4 and C-terminal fraction of the helix 3. Remarkably, the NGFI-B dimer interface is similar to the dimerization interface earlier revealed for glucocorticoid nuclear receptor (GR), which might be relevant to the recognition of cognate DNA response elements by NGFI-B and to antagonism of NGFI-B-dependent transcription exercised by GR in cells.
authors.affiliation: Instituto de Física de São Carlos, Departamento de Física e Informática, Universidade de São Paulo, CEP 13566-590 São Carlos, São Paulo, Brazil.
authors.forename: Marcos R
authors.initials: MR
authors.lastname: Calgaro
authors.forename: Mario de Oliveira
authors.initials: Mde O
authors.lastname: Neto
authors.forename: Ana Carolina M
authors.initials: AC
authors.lastname: Figueira
authors.forename: Maria A M
authors.initials: MA
authors.lastname: Santos
authors.forename: Rodrigo V
authors.initials: RV
authors.lastname: Portugal
authors.forename: Carolina A
authors.initials: CA
authors.lastname: Guzzi
authors.forename: Daniel M
authors.initials: DM
authors.lastname: Saidemberg
authors.forename: Lucas
authors.initials: L
authors.lastname: Bleicher
authors.forename: Javier
authors.initials: J
authors.lastname: Vernal
authors.forename: Pablo
authors.initials: P
authors.lastname: Fernandez
authors.forename: Hernán
authors.initials: H
authors.lastname: Terenzi
authors.forename: Mario Sergio
authors.initials: MS
authors.lastname: Palma
authors.forename: Igor
authors.initials: I
authors.lastname: Polikarpov
mesh_terms: D002942:Circular Dichroism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification; D019281:Dimerization; D013058:Mass Spectrometry; D008954:Models, Biological; D008958:Models, Molecular; D057105:Nuclear Receptor Subfamily 4, Group A, Member 1; D017433:Protein Structure, Secondary; D018160:Receptors, Cytoplasmic and Nuclear / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification; D011965:Receptors, Glucocorticoid / Q000737:chemistry; D011987:Receptors, Steroid / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification; D053838:Scattering, Small Angle; D012996:Solutions; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification
chemical_list: D004268:DNA-Binding Proteins; D057105:Nuclear Receptor Subfamily 4, Group A, Member 1; D018160:Receptors, Cytoplasmic and Nuclear; D011965:Receptors, Glucocorticoid; D011987:Receptors, Steroid; D012996:Solutions; D014157:Transcription Factors