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- PDB-2rrh: NMR structure of vasoactive intestinal peptide in Methanol -

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Basic information

Entry
Database: PDB / ID: 2rrh
TitleNMR structure of vasoactive intestinal peptide in Methanol
ComponentsVIP peptides
KeywordsHORMONE / peptide hormone
Function / homology
Function and homology information


epinephrine secretion / prolactin secretion / body fluid secretion / neuropeptide hormone activity / mRNA stabilization / peptide hormone receptor binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / Glucagon-type ligand receptors / positive regulation of protein catabolic process ...epinephrine secretion / prolactin secretion / body fluid secretion / neuropeptide hormone activity / mRNA stabilization / peptide hormone receptor binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / Glucagon-type ligand receptors / positive regulation of protein catabolic process / regulation of protein localization / G alpha (s) signalling events / neuron projection / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / extracellular region
Similarity search - Function
: / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsUmetsu, Y. / Tenno, T. / Goda, N. / Ikegami, T. / Hiroaki, H.
CitationJournal: Biochim.Biophys.Acta / Year: 2011
Title: Structural difference of vasoactive intestinal peptide in two distinct membrane-mimicking environments.
Authors: Umetsu, Y. / Tenno, T. / Goda, N. / Shirakawa, M. / Ikegami, T. / Hiroaki, H.
History
DepositionNov 12, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 1, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: citation / pdbx_nmr_sample_details ...citation / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VIP peptides


Theoretical massNumber of molelcules
Total (without water)3,3901
Polymers3,3901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3150 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide VIP peptides / Intestinal peptide PHV-42 / Intestinal peptide PHM-27 / Peptide histidine methioninamide 27 / ...Intestinal peptide PHV-42 / Intestinal peptide PHM-27 / Peptide histidine methioninamide 27 / Vasoactive intestinal peptide / VIP / Vasoactive intestinal polypeptide


Mass: 3389.883 Da / Num. of mol.: 1
Fragment: Vasoactive intestinal peptide, residues in UNP 125-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VIP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01282

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D C(CO)NH
1713D H(CCO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] VIP-1, 20 mM TRIS-2, 50 % [U-2H] methanol-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMVIP-1[U-13C; U-15N]1
20 mMTRIS-21
50 %methanol-3[U-2H]1
Sample conditionspH: 7.4 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe5.2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.11Goddardchemical shift assignment
Sparky3.11Goddardpeak picking
CYANA2.0.17Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.0.17Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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