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- PDB-9ijw: Serine protease inhibitor HCIQ2c1 from Heteractis crispa with TRP... -

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Basic information

Entry
Database: PDB / ID: 9ijw
TitleSerine protease inhibitor HCIQ2c1 from Heteractis crispa with TRPA1 mediated antinociceptive activity
ComponentsPI-stichotoxin-Hcr2i
KeywordsTOXIN / Kunitz / TRPA1 / inhibitor
Function / homology
Function and homology information


nematocyst / ion channel regulator activity / negative regulation of peptidase activity / serine-type endopeptidase inhibitor activity / toxin activity / extracellular region
Similarity search - Function
: / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily
Similarity search - Domain/homology
PI-stichotoxin-Hcr2i
Similarity search - Component
Biological speciesRadianthus crispa (leathery sea anemone)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsOreshkov, S.D. / Mironov, P.A. / Menshov, A.S. / Paramonov, A.S. / Leychenko, E.V. / Shenkarev, Z.O. / Lyukmanova, E.N.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: Mar Drugs / Year: 2024
Title: Sea Anemone Kunitz Peptide HCIQ2c1: Structure, Modulation of TRPA1 Channel, and Suppression of Nociceptive Reaction In Vivo.
Authors: Kvetkina, A.N. / Oreshkov, S.D. / Mironov, P.A. / Zaigraev, M.M. / Klimovich, A.A. / Deriavko, Y.V. / Menshov, A.S. / Kulbatskii, D.S. / Logashina, Y.A. / Andreev, Y.A. / Chugunov, A.O. / ...Authors: Kvetkina, A.N. / Oreshkov, S.D. / Mironov, P.A. / Zaigraev, M.M. / Klimovich, A.A. / Deriavko, Y.V. / Menshov, A.S. / Kulbatskii, D.S. / Logashina, Y.A. / Andreev, Y.A. / Chugunov, A.O. / Kirpichnikov, M.P. / Lyukmanova, E.N. / Leychenko, E.V. / Shenkarev, Z.O.
History
DepositionJun 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PI-stichotoxin-Hcr2i


Theoretical massNumber of molelcules
Total (without water)6,3451
Polymers6,3451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1target function

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Components

#1: Protein PI-stichotoxin-Hcr2i / PI-SHTX-Hcr2i / Kunitz-peptide HCIQ2c1


Mass: 6345.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Radianthus crispa (leathery sea anemone)
Gene: iq2c1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6B7FBD3
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
211isotropic1NOESY
221isotropic12D 1H-1H TOCSY
232isotropic13D 1H-15N TOCSY
242isotropic13D 1H-15N TOCSY
252isotropic22D 1H-15N HSQC
262isotropic13D HNHA
272isotropic13D HNHB

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.31 mM HCIQ2c1, 95% H2O/5% D2Oc95% H2O/5% D2O
solution20.08 mM [U-100% 15N] HCIQ2c1, 95% H2O/5% D2Oh95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.31 mMHCIQ2c1natural abundance1
0.08 mMHCIQ2c1[U-100% 15N]2
Sample conditionsIonic strength: 0.1 M / Label: 1 / pH: 4.5 / Pressure: AMBIENT Pa / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert, Mumenthaler and Wuthrichrefinement
TopSpinBruker Biospincollection
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.9.1.7Keller and Wuthrichchemical shift assignment
CARA1.9.1.7Keller and Wuthrichpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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