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- PDB-5l85: Solution structure of the complex between human ZNHIT3 and NUFIP1... -

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Basic information

Entry
Database: PDB / ID: 5l85
TitleSolution structure of the complex between human ZNHIT3 and NUFIP1 proteins
Components
  • Nuclear fragile X mental retardation-interacting protein 1
  • Zinc finger HIT domain-containing protein 3
KeywordsSIGNALING PROTEIN / Pac-Hit fold jaw helices
Function / homology
Function and homology information


snoRNA localization / pre-snoRNP complex / perichromatin fibrils / box C/D snoRNP assembly / nuclear thyroid hormone receptor binding / presynaptic active zone / RNA processing / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / transcription elongation factor complex / fibrillar center ...snoRNA localization / pre-snoRNP complex / perichromatin fibrils / box C/D snoRNP assembly / nuclear thyroid hormone receptor binding / presynaptic active zone / RNA processing / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / transcription elongation factor complex / fibrillar center / nuclear matrix / protein-macromolecule adaptor activity / ATPase binding / nucleolus / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
NUFIP1-like / : / Zinc finger HIT domain-containing protein 3, C-terminal domain / FMR1-interacting protein 1, conserved domain / FMR1-interacting protein 1 (NUFIP1) / HIT zinc finger / Zinc finger HIT-type profile. / Zinc finger, HIT-type / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding ...NUFIP1-like / : / Zinc finger HIT domain-containing protein 3, C-terminal domain / FMR1-interacting protein 1, conserved domain / FMR1-interacting protein 1 (NUFIP1) / HIT zinc finger / Zinc finger HIT-type profile. / Zinc finger, HIT-type / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Zinc finger HIT domain-containing protein 3 / Nuclear fragile X mental retardation-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsQuinternet, M. / Chagot, M.-E. / Manival, X.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-BSV8-01503 France
CitationJournal: Structure / Year: 2016
Title: Structural Features of the Box C/D snoRNP Pre-assembly Process Are Conserved through Species.
Authors: Quinternet, M. / Chagot, M.E. / Rothe, B. / Tiotiu, D. / Charpentier, B. / Manival, X.
History
DepositionJun 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Oct 19, 2016Group: Database references
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.6Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger HIT domain-containing protein 3
B: Nuclear fragile X mental retardation-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)12,5232
Polymers12,5232
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1970 Å2
ΔGint-23 kcal/mol
Surface area7630 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 160structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Zinc finger HIT domain-containing protein 3 / HNF-4a coactivator / Thyroid hormone receptor interactor 3 / Thyroid receptor-interacting protein 3 / TRIP-3


Mass: 8492.720 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNHIT3, TRIP3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15649
#2: Protein/peptide Nuclear fragile X mental retardation-interacting protein 1 / Nuclear FMRP-interacting protein 1


Mass: 4030.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUFIP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UHK0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY aliphatic
121isotropic13D 1H-13C NOESY aromatic
131isotropic13D 1H-15N NOESY
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
191isotropic13D HNCA
181isotropic13D HN(CA)CB
171isotropic13D HN(CA)CO
161isotropic13D (H)CCH-TOCSY
1111isotropic12D 1H-15N HSQC
1101isotropic12D 1H-13C HSQC aliphatic
1121isotropic12D 1H-13C HSQC aromatic
1131isotropic12D 1H-1H NOESY
1141isotropic13D HBHA(CO)NH

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] ZNHIT3, 1 mM [U-13C; U-15N] NUFIP1, 95% H2O/5% D2O
Label: sample_1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMZNHIT3[U-13C; U-15N]1
1 mMNUFIP1[U-13C; U-15N]1
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 6.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
TopSpin3.2Bruker Biospincollection
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 160 / Conformers submitted total number: 20

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