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- PDB-1h0t: An affibody in complex with a target protein: structure and coupl... -

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Basic information

Entry
Database: PDB / ID: 1h0t
TitleAn affibody in complex with a target protein: structure and coupled folding
Components
  • IMMUNOGLOBULIN G BINDING PROTEIN A
  • ZSPA-1 AFFIBODY
KeywordsIMMUNE SYSTEM / PROTEIN-PROTEIN INTERACTIONS / PROTEIN ENGINEERING / MOLECULAR RECOGNITION / NMR SPECTROSCOPY / MOLTEN GLOBULE / INDUCED FIT / COUPLED PROTEIN FOLDING / AFFIBODY / IGG BINDING PROTEIN A
Function / homology
Function and homology information


symbiont-mediated suppression of host signal transduction pathway via antagonism of host cell surface receptor / IgG binding / extracellular region
Similarity search - Function
Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodSOLUTION NMR / SIMULATED ANEALING
AuthorsWahlberg, E. / Lendel, C. / Helgstrand, M. / Allard, P. / Dincbas-Renqvist, V. / Hedqvist, A. / Berglund, H. / Nygren, P.-A. / Hard, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: An Affibody in Complex with a Target Protein: Structure and Coupled Folding
Authors: Wahlberg, E. / Lendel, C. / Helgstrand, M. / Allard, P. / Dincbas-Renqvist, V. / Hedqvist, A. / Berglund, H. / Nygren, P.-A. / Hard, T.
History
DepositionJun 27, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2003Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Derived calculations / Other ...Derived calculations / Other / Source and taxonomy / Version format compliance
Revision 1.2Jan 17, 2018Group: Database references / Category: citation / Item: _citation.page_last
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMMUNOGLOBULIN G BINDING PROTEIN A
B: ZSPA-1 AFFIBODY


Theoretical massNumber of molelcules
Total (without water)13,0962
Polymers13,0962
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 100LEAST RESTRAINT VIOLATION AND GOOD RAMACHANDRAN PLOTS
RepresentativeModel #1

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Components

#1: Antibody IMMUNOGLOBULIN G BINDING PROTEIN A / IGG BINDING PROTEIN A


Mass: 6648.316 Da / Num. of mol.: 1 / Fragment: RESIDUES 213-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Plasmid: PET28A(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02976
#2: Protein ZSPA-1 AFFIBODY


Mass: 6447.263 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PET28A(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED PROTEINS. ONE OF THE SUBUNITS WAS LABELED THE OTHER SUBUNIT WAS KEPT UNLABELED.

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Sample preparation

Sample conditionspH: 5.6 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIHBRUNGERrefinement
XwinNMRstructure solution
NMRPipestructure solution
ANSIGWINDOWSstructure solution
X-PLORstructure solution
RefinementMethod: SIMULATED ANEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION AND GOOD RAMACHANDRAN PLOTS
Conformers calculated total number: 100 / Conformers submitted total number: 40

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