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- PDB-1y7k: NMR structure family of Human Agouti Signalling Protein (80-132: ... -

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Basic information

Entry
Database: PDB / ID: 1y7k
TitleNMR structure family of Human Agouti Signalling Protein (80-132: Q115Y, S124Y)
ComponentsAgouti Signaling Protein
KeywordsSIGNALING PROTEIN / Melanocortin / inhibitor / cystine knot / GPCR / endogenous antagonist / inverse agonist
Function / homology
Function and homology information


melanocortin receptor binding / type 3 melanocortin receptor binding / type 4 melanocortin receptor binding / positive regulation of melanin biosynthetic process / adult feeding behavior / melanin biosynthetic process / melanosome organization / melanosome transport / neuropeptide hormone activity / epigenetic programming in the zygotic pronuclei ...melanocortin receptor binding / type 3 melanocortin receptor binding / type 4 melanocortin receptor binding / positive regulation of melanin biosynthetic process / adult feeding behavior / melanin biosynthetic process / melanosome organization / melanosome transport / neuropeptide hormone activity / epigenetic programming in the zygotic pronuclei / hormone-mediated signaling pathway / generation of precursor metabolites and energy / cell-cell signaling / signaling receptor binding / signal transduction / 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-signaling protein
Similarity search - Component
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model type detailsminimized average
AuthorsMcNulty, J.C. / Jackson, P.J. / Thompson, D.A. / Chai, B. / Gantz, I. / Barsh, G.S. / Dawson, P.E. / Millhauser, G.L.
Citation
#1: Journal: Biochemistry / Year: 2001
Title: High-resolution NMR structure of the chemically-synthesized melanocortin receptor binding domain AGRP(87-132) of the agouti-related protein
Authors: McNulty, J.C. / Thompson, D.A. / Bolin, K.A. / Wilken, J. / Barsh, G.S. / Millhauser, G.L.
#2: Journal: Biochemistry / Year: 2002
Title: Design, pharmacology, and NMR structure of a minimized cystine knot with agouti-related protein activity
Authors: Jackson, P.J. / McNulty, J.C. / Yang, Y.K. / Thompson, D.A. / Chai, B. / Gantz, I. / Barsh, G.S. / Millhauser, G.L.
History
DepositionDec 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 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 viewerMolecule:
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Assembly

Deposited unit
A: Agouti Signaling Protein


Theoretical massNumber of molelcules
Total (without water)5,8241
Polymers5,8241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 1000target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein Agouti Signaling Protein / Agouti switch protein


Mass: 5823.997 Da / Num. of mol.: 1 / Fragment: residies 80-132 / Mutation: Q115Y, S124Y / Source method: obtained synthetically
Details: Sequence occurs naturally in humans, genes ASIP, AGTI, AGTIL, ASP
References: UniProt: P42127
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131DQF-COSY
2422D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques, in conjunction with a semi-automated assignment protocol.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM ASIP(80-132: Q115Y, S124Y), 100 mM d3-acetic acid/d3-sodium acetate, 90% H2O 10% D2O100 mM d3-acetic acid/d3-sodium acetate, 90% H2O 10% D2O
21 mM ASIP(80-132: Q115Y, S124Y), 100 mM d3-acetic acid/d3-sodium acetate, 100% D2O100 mM d3-acetic acid/d3-sodium acetate, 100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM d3-acetic acid/sodium acetate 5ambient 288 K
2100 mM d3-acetic acid/sodium acetate 4ambient 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS8001
Varian UNITYPLUSVarianUNITYPLUS8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.6Guentert, Herrmann, Mumenthaler, Wuthrichstructure solution
NMRPipe2.3Delaglioprocessing
VNMR6.1Ccollection
CYANA1.0.6Guentert, Herrmann, Mumenthaler, Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: This structure family represents one of two major conformers present in solution. The two conformers arise from the cis-trans proline isomerization of the Ala104-Pro105 peptide bond.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 1000 / Conformers submitted total number: 21
Distance constraint violation method: From the original family of twenty, the representative conformer had the lowest target function and was subjected to further minimization in water. The remaining ...Distance constraint violation method: From the original family of twenty, the representative conformer had the lowest target function and was subjected to further minimization in water. The remaining structures were obtained without explicit inclusion of solvent.

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