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- PDB-4bit: solution structure of cerebral dopamine neurotrophic factor (CDNF) -

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Basic information

Entry
Database: PDB / ID: 4bit
Titlesolution structure of cerebral dopamine neurotrophic factor (CDNF)
ComponentsCEREBRAL DOPAMINE NEUROTROPHIC FACTOR
KeywordsSIGNALING PROTEIN / PARKINSON
Function / homology
Function and homology information


dopaminergic neuron differentiation / growth factor activity / neuron projection development / endoplasmic reticulum / extracellular space
Similarity search - Function
ARMET, C-terminal / ARMET, N-terminal / ARMET-like / ARMET, C-terminal / ARMET, N-terminal / SAP domain / Saposin-like / NK-Lysin / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / SAP domain superfamily ...ARMET, C-terminal / ARMET, N-terminal / ARMET-like / ARMET, C-terminal / ARMET, N-terminal / SAP domain / Saposin-like / NK-Lysin / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / SAP domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cerebral dopamine neurotrophic factor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / CNS USING RECOORD SCRIPTS
AuthorsLatge, C. / Cabral, K.M.S. / Raymundo, D.P. / Foguel, D. / Herrmann, T. / Almeida, M.S.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Solution Structure and Dynamics of Full-Length Human Cerebral Dopamine Neurotrophic Factor and its Neuroprotective Role Against Alpha-Synuclein Oligomers.
Authors: Latge, C. / Cabral, K.M.S. / De Oliveira, G.A.P. / Raymundo, D.P. / Freitas, J.A. / Johanson, L. / Romao, L.F. / Palhano, F.L. / Herrmann, T. / Almeida, M.S. / Foguel, D.
History
DepositionApr 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3May 4, 2016Group: Atomic model / Other
Revision 1.4Jan 24, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation / pdbx_nmr_spectrometer
Item: _audit_author.name / _citation.page_last ..._audit_author.name / _citation.page_last / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 1.5Jun 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_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CEREBRAL DOPAMINE NEUROTROPHIC FACTOR


Theoretical massNumber of molelcules
Total (without water)18,3541
Polymers18,3541
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein CEREBRAL DOPAMINE NEUROTROPHIC FACTOR / ARMET-LIKE PROTEIN 1 / CONSERVED DOPAMINE NEUROTROPHIC FACTOR


Mass: 18354.344 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: NEURON / Organ: BRAIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA B 4 / References: UniProt: Q49AH0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
221TOCSY
331HSQC
441COSY
551HN(CA)CB
661CBCA(CO)NH
771HBHA(CO)NH
881HNCO
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED CDNF.

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Sample preparation

DetailsContents: 20 MM MES, PH 6.0, 150 MM NACL, 5MM NAN3, 10% D20
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1150 mM6.0 1.0 atm298.0 K
2150 mM6.0 1.0 atm298.0 K
3150 mM6.0 1.0 atm298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE10001
Bruker AVANCEBrukerAVANCE8002
Bruker AVANCEBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3A.T.BRUNGER,P.D.ADAMS,G.M.CLORE,W.L. DELANO,P.GROS,R.W.GROSSE-KUNSTLEVE,J.-S. JIANG,J.KUSZEWSKI,M.NILGES,N.S.PANNU,R.J. READ,L.M.RICE,T.SIMONSON,G.L.WARRENrefinement
UNIO10structure solution
CNS1.3structure solution
RefinementMethod: CNS USING RECOORD SCRIPTS / Software ordinal: 1 / Details: USING RECOORD SCRIPTS.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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