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- PDB-1hyk: AGOUTI-RELATED PROTEIN (87-132) (AC-AGRP(87-132)) -

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Basic information

Entry
Database: PDB / ID: 1hyk
TitleAGOUTI-RELATED PROTEIN (87-132) (AC-AGRP(87-132))
ComponentsAGOUTI RELATED PROTEIN
KeywordsSIGNALING PROTEIN / CYSTEINE RICH / DISULFIDE BOND / ICK / INHIBITOR CYSTINE KNOT / MELANOCORTIN ANTAGONISTS / AGOUTI / AGOUTI-RELATED / AGRP / ENDOGENOUS ANTAGONIST
Function / homology
Function and homology information


long-day photoperiodism / type 1 melanocortin receptor binding / positive regulation of feeding behavior / adult feeding behavior / regulation of feeding behavior / neuropeptide hormone activity / feeding behavior / eating behavior / neuropeptide signaling pathway / maternal process involved in female pregnancy ...long-day photoperiodism / type 1 melanocortin receptor binding / positive regulation of feeding behavior / adult feeding behavior / regulation of feeding behavior / neuropeptide hormone activity / feeding behavior / eating behavior / neuropeptide signaling pathway / maternal process involved in female pregnancy / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / hormone-mediated signaling pathway / response to insulin / Golgi lumen / circadian rhythm / signaling receptor binding / neuronal cell body / extracellular space
Similarity search - Function
Agouti Related Protein; Chain A / Agouti domain / Agouti / Agouti domain / Agouti domain superfamily / Agouti protein / Agouti domain profile. / Agouti domain signature. / Agouti protein / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Agouti-related protein
Similarity search - Component
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBolin, K.A. / Anderson, D.J. / Trulson, J.A. / Thompson, D.A. / Wilken, J. / Kent, S.B.H. / Millhauser, G.L.
Citation
Journal: FEBS Lett. / Year: 1999
Title: NMR structure of a minimized human agouti related protein prepared by total chemical synthesis.
Authors: Bolin, K.A. / Anderson, D.J. / Trulson, J.A. / Thompson, D.A. / Wilken, J. / Kent, S.B. / Gantz, I. / Millhauser, G.L.
#1: Journal: Mol.Endocrinol. / Year: 1999
Title: Characterization of Agouti-Related Protein Binding to Melanocortin Receptors.
Authors: Yang, Y.K. / Thompson, D.A. / Dickinson, C.J. / Wilken, J. / Barsh, G.S. / Kent, S.B. / Gantz, I.
#2: Journal: Biochemistry / Year: 1998
Title: Determination of Disulfide Structure in Agouti-Related Protein (Agrp) by Stepwise Reduction and Alkylation
Authors: Bures, E.J. / Hui, J.O. / Young, Y. / Chow, D.T. / Katta, V. / Rohde, M.F. / Zeni, L. / Rosenfeld, R.D. / Stark, K.L. / Haniu, M.
History
DepositionJan 19, 2001Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 7, 2001ID: 1QU8
Revision 1.0Feb 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AGOUTI RELATED PROTEIN


Theoretical massNumber of molelcules
Total (without water)5,2071
Polymers5,2071
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 40see refinement method and details
RepresentativeModel #10lowest energy

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Components

#1: Protein/peptide AGOUTI RELATED PROTEIN


Mass: 5207.157 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN AC-AGRP(87-132) / Source method: obtained synthetically
Details: This sequence is the native sequence for the cystine-rich C-terminal domain of the human agouti-related protein. The N-terminal acetylation at residue 87 (the first residue of the sequence) ...Details: This sequence is the native sequence for the cystine-rich C-terminal domain of the human agouti-related protein. The N-terminal acetylation at residue 87 (the first residue of the sequence) is non-native and done only to prevent a non-native positively charged amino terminus in the synthetic fragment. Synthesis was by means of standard BOC-based solid-phase peptide synthesis followed by refolding and oxidation of cysteines to cystines.
References: UniProt: O00253
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-NOESY
121DQF-COSY
131E-COSY
NMR detailsText: STANDARD 2D HOMONUCLEAR TECHNIQUES WERE USED TO ASSIGN SPECTRA ACQUIRED OVER THE TEMPERATURE RANGE 288- 303 K. A SUBSET OF UNAMBIGUOUSLY ASSIGNED NOE PEAKS TAKEN FROM DATA ACQUIRED AT 288 K ...Text: STANDARD 2D HOMONUCLEAR TECHNIQUES WERE USED TO ASSIGN SPECTRA ACQUIRED OVER THE TEMPERATURE RANGE 288- 303 K. A SUBSET OF UNAMBIGUOUSLY ASSIGNED NOE PEAKS TAKEN FROM DATA ACQUIRED AT 288 K WITH AN 150 MS MIXING TIME WERE USED IN STRUCTURE CALCULATIONS, AS WERE 34 PHI BACKBONE ANGLE RESTRAINTS DERIVED FROM FITTING OF DQF- COSY CROSSPEAKS. BOTH CARRIER PRESATURATION AND Z- GRADIENT WET TECHNIQUES WERE USED FOR SOLVENT SUPPRESSION. New experiments from 1qu8 are E-COSY at 500 MHz and 150 msec 2D-NOESY at 800 MHz, 288K.

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Sample preparation

DetailsContents: 1.9 MM Ac-AGRP(87-132) (same as 1.9 MM MARP of 1qu8)
Solvent system: 50 MM PHOSPHATE BUFFER PH 5.0 (pH is changed from pH=4.2 in 1qu8)
Sample conditionsIonic strength: 50mM PHOSPHATE / pH: 5 / Pressure: 1 atm / Temperature: 288.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1A.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
VNMR5.2F. Vosman, D. Iverson, S. Patt, S. Chetham, R. Lasater, P. Hornung, G. Brissey, E. Williams, B. John, C. H. Yoder, B. L. Buckwaltercollection
MNMR940501M. Kjear, K.V. Andersoen, C. Rischelprocessing
XEASY1.2T. Xia, C. Bartelsdata analysis
DYANA1.5P. Guntert, C. Mumenthaler, T. Herrmannstructure solution
PROCHECK3.4.4Laskowski R. A., MacArthur M. W., Moss D. S., Thornton J. M., Rullmann J. A. C.processing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The preliminary structure calculation and restraint quality assessment was performed in DYANA v 1.5, so that out of 200 structures the 20 with the lowest target functions would have target ...Details: The preliminary structure calculation and restraint quality assessment was performed in DYANA v 1.5, so that out of 200 structures the 20 with the lowest target functions would have target function vaules of < 3.0 square angstroms. The lowest target function structure of this family was then submitted as a pre-folded structure in CNS v. 1.0, and 40 structures calculated under cool (< 288K) simulated annealing and conjugate gradient energy minimization. These calculations were carried out in the presence of experimnetal NOE and J-coupling restraints as well as assigned hydrogen bonds consistent with HX protection. DYANA 1.5: 799 unique NOE's from 800 MHz data, 444 resulting distance restraints after pseudoatom calculation/replacement and removal of NOE's between atoms separated by only two or three bonds. 35 alpha-H to amide-H 3-bond J-coupling constants and 44 alpha-H to beta-H 3-bond J-coupling constants from ECOSY data were also included. Disulfides and seven hydrogen bonds as determinied from surrounding NOE's and HX data were included as pseudo-NOE restraints. CNS 1.0, patch level 0: 504 distance restraints from 800 MHz NOE data, corresponding to the same upper limit restraints as used in the final round of DYANA 1.5 calulations (conversion using AQUA 2.0 in PROCHECK_NMR, and modified lower limit of 1.6 angstroms was imposed on all NOE restraints while keeping upper bounds). Disulfide map was incorporated into the covalent structure of the molecule and thereby strictly enforced in this step. The seven hydrogen bonds were included in a separate restraint file. 34 alpha-H to amide-H 3-bond J-coupling constants (not including CYS-87 amide mesurement) were also included. 40 structures were so calculated and all are deposited here.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: see refinement method and details
Conformers calculated total number: 40 / Conformers submitted total number: 40

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