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- PDB-2rqf: Solution structure of juvenile hormone binding protein from silkw... -

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Basic information

Entry
Database: PDB / ID: 2rqf
TitleSolution structure of juvenile hormone binding protein from silkworm in complex with JH III
ComponentsHemolymph juvenile hormone binding protein
KeywordsHormone Binding Protein / juvenile hormone
Function / homology
Function and homology information


TULIP domain / Haemolymph juvenile hormone binding / Takeout superfamily / Haemolymph juvenile hormone binding protein (JHBP) / Juvenile hormone binding protein domains in insects. / Bactericidal permeability-increasing protein; domain 1 / Super Roll / Alpha Beta
Similarity search - Domain/homology
Chem-JH3 / Hemolymph juvenile hormone binding protein
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsSuzuki, R. / Fujimoto, Z. / Shiotsuki, T. / Momma, M. / Tase, A. / Yamazaki, T.
Citation
Journal: Sci Rep / Year: 2011
Title: Structural mechanism of JH delivery in hemolymph by JHBP of silkworm, Bombyx mori
Authors: Suzuki, R. / Fujimoto, Z. / Shiotsuki, T. / Tsuchiya, W. / Momma, M. / Tase, A. / Miyazawa, M. / Yamazaki, T.
#1: Journal: To be Published
Title: NMR assignments of juvenile hormone binding protein in complex with JH III
Authors: Suzuki, R. / Tase, A. / Fujimoto, Z. / Shiotsuki, T. / Yamazaki, T.
History
DepositionApr 27, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 15, 2012Group: Database references
Revision 1.3Jun 19, 2013Group: Database references
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _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

Downloads & links

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Assembly

Deposited unit
A: Hemolymph juvenile hormone binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0472
Polymers24,7811
Non-polymers2661
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Hemolymph juvenile hormone binding protein / hJHBP


Mass: 24781.092 Da / Num. of mol.: 1 / Fragment: UNP residues 19-243
Source method: isolated from a genetically manipulated source
Details: The numbering in the PDB file and the constraint files are differ. This is because the program Sparky does not accept minus residue numbers.
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9U556
#2: Chemical ChemComp-JH3 / methyl (2E,6E)-9-[(2R)-3,3-dimethyloxiran-2-yl]-3,7-dimethylnona-2,6-dienoate / JH III / juvenile hormone III


Mass: 266.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26O3 / Comment: hormone*YM
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-15N HSQC
1332D 1H-13C HSQC
1423D HNCO
1523D CBCA(CO)NH
1623D HNCA
1733D HCABGCO
1833D (H)CCH-TOCSY
1913D 15N-separated HOHAHA-HSQC
11013D 15N-separated NOESY-HSQC
11133D 13C/15N-separated NOESY-HSQC
11233D 13C-separated NOESY-HSQC
11333D 13C/13C-separated NOESY-HSQC
11432D 13C-filtered COSY
11532D 13C-filtered NOESY
11633D 13C-filtered/13C-selected NOESY-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6-1.0 mM [U-15N] hJHBP-1, 0.6-1.0 mM JH III-2, 45 mM sodium phosphate-3, 90 % H2O-4, 10 % D2O-5, 90% H2O/10% D2O90% H2O/10% D2O
20.6-1.0 mM [U-13C; U-15N] hJHBP-6, 0.6-1.0 mM JH III-7, 45 mM sodium phosphate-8, 90 % H2O-9, 10 % D2O-10, 90% H2O/10% D2O90% H2O/10% D2O
30.6-1.0 mM [U-13C; U-15N] hJHBP-11, 0.6-1.0 mM JH III-12, 45 mM sodium phosphate-13, 100 % D2O-14, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMhJHBP-1[U-15N]0.6-1.01
mMJH III-20.6-1.01
45 mMsodium phosphate-31
90 %H2O-41
10 %D2O-51
mMhJHBP-6[U-13C; U-15N]0.6-1.02
mMJH III-70.6-1.02
45 mMsodium phosphate-82
90 %H2O-92
10 %D2O-102
mMhJHBP-11[U-13C; U-15N]0.6-1.03
mMJH III-120.6-1.03
45 mMsodium phosphate-133
100 %D2O-143
Sample conditionspH: 6 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Bruker Biospincollection
NMRPipereleased at Feb 10, 2006Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddardpeak picking
Sparky3.113Goddardchemical shift assignment
TALOS2003.027.13.05Cornilescu, Delaglio and Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
AQUA3.2Rullmann, Doreleijers and Kapteindata analysis
ProcheckNMR3.5.4Laskowski and MacArthurdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 11742 / NOE intraresidue total count: 1848 / NOE long range total count: 5147 / NOE medium range total count: 2339 / NOE sequential total count: 2408 / Disulfide bond constraints total count: 2 / Hydrogen bond constraints total count: 89 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 147 / Protein psi angle constraints total count: 147
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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