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- PDB-2jm2: Structure of the N-terminal subdomain of insulin-like growth fact... -

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Basic information

Entry
Database: PDB / ID: 2jm2
TitleStructure of the N-terminal subdomain of insulin-like growth factor (IGF) binding protein-6 and its interactions with IGFs
ComponentsInsulin-like growth factor-binding protein 6
KeywordsHORMONE/GROWTH FACTOR / Insulin like growth factor binding protein / Growth Factor / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


insulin-like growth factor binary complex / regulation of insulin-like growth factor receptor signaling pathway / positive regulation of stress-activated MAPK cascade / insulin-like growth factor II binding / insulin-like growth factor I binding / fibronectin binding / negative regulation of canonical Wnt signaling pathway / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cell migration / positive regulation of MAPK cascade ...insulin-like growth factor binary complex / regulation of insulin-like growth factor receptor signaling pathway / positive regulation of stress-activated MAPK cascade / insulin-like growth factor II binding / insulin-like growth factor I binding / fibronectin binding / negative regulation of canonical Wnt signaling pathway / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cell migration / positive regulation of MAPK cascade / negative regulation of cell population proliferation / signaling receptor binding / signal transduction / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin-like growth factor-binding protein 6 / Insulin-like growth factor-binding protein family 1-6, chordata / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. ...Insulin-like growth factor-binding protein 6 / Insulin-like growth factor-binding protein family 1-6, chordata / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / Growth factor receptor cysteine-rich domain superfamily
Similarity search - Domain/homology
Insulin-like growth factor-binding protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsChandrashekaran, I.R. / Yao, S. / Wang, C.C. / Bansal, P.S. / Alewood, P.F. / Forbes, B.E. / Wallace, J.C. / Bach, L.A. / Norton, R.S.
CitationJournal: Biochemistry / Year: 2007
Title: The N-Terminal Subdomain of Insulin-like Growth Factor (IGF) Binding Protein 6. Structure and Interaction with IGFs
Authors: Chandrashekaran, I.R. / Yao, S. / Wang, C.C. / Bansal, P.S. / Alewood, P.F. / Forbes, B.E. / Wallace, J.C. / Bach, L.A. / Norton, R.S.
History
DepositionSep 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other / Source and taxonomy
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_entity_src_syn / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_entity_src_syn.details ..._pdbx_database_status.status_code_cs / _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_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Oct 5, 2022Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Refinement description / Source and taxonomy / Structure summary
Category: database_2 / diffrn ...database_2 / diffrn / diffrn_radiation / diffrn_radiation_wavelength / entity_name_com / pdbx_entity_src_syn / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_nmr_spectrometer / struct_ref / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_name_com.name / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_nmr_exptl_sample_conditions.label / _pdbx_nmr_exptl_sample_conditions.pH_units / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_spectrometer.type / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.5Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.6Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.7Nov 20, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin-like growth factor-binding protein 6


Theoretical massNumber of molelcules
Total (without water)4,3691
Polymers4,3691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Insulin-like growth factor-binding protein 6 / IBP-6 / IGF-binding protein 6 / IGFBP-6


Mass: 4368.759 Da / Num. of mol.: 1 / Fragment: N-terminal subdomain of IGFBP-6, residues 25-69 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P24592
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1312D DQF-COSY

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Sample preparation

DetailsType: solution / Contents: 1.1 mM IGFBP-6, 95% H2O/5% D2O / Label: 1 / Solvent system: 95% H2O/5% D2O
SampleConc.: 1.1 mM / Component: IGFBP-6 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 10 / Label: 1 / pH: 4.3 Not defined / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker DRXBrukerDRX6002
Bruker AVANCEBrukerAVANCE5003

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Processing

NMR software
NameDeveloperClassification
CYANAP Guntert, C Mumenthaler and K Wuthrichstructure solution
X-PLOR NIHCD Schwieters, JJ Kuszewski, N Tjandra and GM Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 2
Details: The structures are based on a total of 446 restraints, 428 are noe-derived distance constraints, 18 dihedral angle restraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: lowest energy / Conformers calculated total number: 50 / Conformers submitted total number: 20

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