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- PDB-1d6g: MOLECULAR COMPLEX OF CHOLECYSTOKININ-8 AND N-TERMINUS OF THE CHOL... -

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Basic information

Entry
Database: PDB / ID: 1d6g
TitleMOLECULAR COMPLEX OF CHOLECYSTOKININ-8 AND N-TERMINUS OF THE CHOLECYSTOKININ A RECEPTOR BY NMR SPECTROSCOPY
Components
  • cholecystokinin type a receptor
  • cholecystokinin-8
KeywordsHORMONE/GROWTH FACTOR / alpha-helix / beta-sheet / complex GPCR-ligand / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


cholecystokinin receptor activity / cholecystokinin signaling pathway / regulation of hormone secretion / neuropeptide receptor activity / peptide hormone binding / forebrain development / cellular response to hormone stimulus / Peptide ligand-binding receptors / axonogenesis / peptide binding ...cholecystokinin receptor activity / cholecystokinin signaling pathway / regulation of hormone secretion / neuropeptide receptor activity / peptide hormone binding / forebrain development / cellular response to hormone stimulus / Peptide ligand-binding receptors / axonogenesis / peptide binding / neuron migration / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / G protein-coupled receptor signaling pathway / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Cholecystokinin Type A Receptor; Chain A / Cholecystokinin A receptor, N-terminal domain / Cholecystokinin receptor type A / Cholecystokinin A receptor, N-terminal / Cholecystokinin A receptor, N-terminal domain superfamily / Cholecystokinin A receptor, N-terminal / Cholecystokinin receptor / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Cholecystokinin Type A Receptor; Chain A / Cholecystokinin A receptor, N-terminal domain / Cholecystokinin receptor type A / Cholecystokinin A receptor, N-terminal / Cholecystokinin A receptor, N-terminal domain superfamily / Cholecystokinin A receptor, N-terminal / Cholecystokinin receptor / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / Few Secondary Structures / Irregular / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Cholecystokinin receptor type A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics
AuthorsPellegrini, M. / Mierke, D.F.
CitationJournal: Biochemistry / Year: 1999
Title: Molecular complex of cholecystokinin-8 and N-terminus of the cholecystokinin A receptor by NMR spectroscopy.
Authors: Pellegrini, M. / Mierke, D.F.
History
DepositionOct 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 7, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Source and taxonomy
Category: diffrn / diffrn_radiation ...diffrn / diffrn_radiation / diffrn_radiation_wavelength / pdbx_entity_src_syn / pdbx_nmr_ensemble / pdbx_nmr_exptl / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_sample_details / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_ensemble.conformers_calculated_total_number / _pdbx_nmr_exptl.conditions_id / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cholecystokinin type a receptor
B: cholecystokinin-8


Theoretical massNumber of molelcules
Total (without water)6,2882
Polymers6,2882
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area790 Å2
ΔGint-4 kcal/mol
Surface area4640 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 90
Representativelowest energy

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Components

#1: Protein/peptide cholecystokinin type a receptor / CCK-A-RECEPTOR


Mass: 5225.963 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN (1-47) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P32238
#2: Protein/peptide cholecystokinin-8 / CCK-8


Mass: 1062.199 Da / Num. of mol.: 1 / Fragment: C-TERMINAL FRAGMENT / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
3342D NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.6mM CCK-A_R(1-47), 171 mM DPC-d38, 90% H2O/10% D2Osample 190% H2O/10% D2O
solution21.5mM CCK-8, 137mM DPC-d38, 90% H2O/10% D2Osample 290% H2O/10% D2O
solution30.8mM CCK-A-R(1-47) + 0.37-3mM CCK-8, 171 mM DPC-d38, 100% D2Osample 3100% D2O
solution41.6mM CCK-A-R(1-47) + 3mM CCK-8, 171 mM DPC-d38, 100% D2O or 90% H2O, 10% D2Osample 4100% D2O or 90% H2O, 10% D2O
Sample conditions
Conditions-IDLabelpHPressure (kPa)Temperature (K)
1conditions 16.5 Not definedambient 285 K
2conditions 26.5 Not definedambient 298 K
3conditions 36.5 Not definedambient 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY5001
Bruker AVANCE DRXBrukerAVANCE DRX6002
Varian UNITYVarianUNITY7503

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Processing

NMR software
NameVersionDeveloperClassification
GROMACS1.6van der Spoel, D.; van Buuren, A.R.; Apol, E.; Meulenhoff, P.J.; Tielman, D.P.; Sijbers, A.L.T.M.; van Drunen, R.; Berendsen, H.J.C.refinement
Distance Geometryhome writtenMierke, D.F.structure solution
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
Details: The structures of CCK-A-R(1-47) and CCK-8 were calculated separately. The complex was calculated using intra- and intermolecular NOEs using simulated annealing and molecular dynamics ...Details: The structures of CCK-A-R(1-47) and CCK-8 were calculated separately. The complex was calculated using intra- and intermolecular NOEs using simulated annealing and molecular dynamics calculations. The calculations utilized explicit solvent, as a decane/water simulation cell.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers calculated total number: 90 / Conformers submitted total number: 1

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