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- PDB-1l5e: The domain-swapped dimer of CV-N in solution -

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Basic information

Entry
Database: PDB / ID: 1l5e
TitleThe domain-swapped dimer of CV-N in solution
ComponentsCyanovirin-N
KeywordsANTIVIRAL PROTEIN / 3D domain-swapping / cyanovirin-N / protein folding
Function / homology
Function and homology information


regulation of defense response to virus / carbohydrate binding
Similarity search - Function
HIV-inactivating Protein, Cyanovirin-n / Cyanovirin-N / Cyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesNostoc ellipsosporum (bacteria)
MethodSOLUTION NMR / Determination of the domain orientation for the solution structure of the dimer was carried out using a procedure analogous to the one described for determining the relative domain orientation in a two-domain protein fragment of a lectin.
AuthorsBarrientos, L.G. / Louis, J.M. / Botos, I. / Mori, T. / Han, Z. / O'Keefe, B.R. / Boyd, M.R. / Wlodawer, A. / Gronenborn, A.M.
CitationJournal: Structure / Year: 2002
Title: The domain-swapped dimer of cyanovirin-N is in a metastable folded state: reconciliation of X-ray and NMR structures.
Authors: Barrientos, L.G. / Louis, J.M. / Botos, I. / Mori, T. / Han, Z. / O'Keefe, B.R. / Boyd, M.R. / Wlodawer, A. / Gronenborn, A.M.
History
DepositionMar 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyanovirin-N
B: Cyanovirin-N


Theoretical massNumber of molelcules
Total (without water)22,0442
Polymers22,0442
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)1 / -
Representative

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Components

#1: Protein Cyanovirin-N / CV-N


Mass: 11022.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc ellipsosporum (bacteria) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P81180

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D IPAP [15N-1H]-HSQC
NMR detailsText: Residual dipolar couplings were measured in the presence of a colloidal phage solution of 11.5 mg/ml Pf1.

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Sample preparation

DetailsContents: 0.150 mM protein in 25 mM sodium phosphate buffer, pH 8.0 and 0.02 % NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.0 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1F.Delaglio, S.Grzesiek, G.W.Vuister, G.Zhu, J.Pfeifer, A.Baxprocessing
PALESM.Zweckstetter, A.Baxstructure solution
PALESM.Zweckstetter, A.Baxrefinement
RefinementMethod: Determination of the domain orientation for the solution structure of the dimer was carried out using a procedure analogous to the one described for determining the relative domain ...Method: Determination of the domain orientation for the solution structure of the dimer was carried out using a procedure analogous to the one described for determining the relative domain orientation in a two-domain protein fragment of a lectin.
Software ordinal: 1
Details: The coordinates of the individual domains of the domain swapped dimer CV-N were taken directly from the X-Ray coordinates, 3EZM and 1L5B. The only protons added are the HNE1 of W(49/150) and ...Details: The coordinates of the individual domains of the domain swapped dimer CV-N were taken directly from the X-Ray coordinates, 3EZM and 1L5B. The only protons added are the HNE1 of W(49/150) and all the backbone amide protons (HN), since domain-domain orientation was based only on HN/HNE1 residual dipolar couplings. The starting coordinates were those of two pseudo-monomer units (AB' and A'B) extracted from the refined trigonal 1.5 X-ray structure, in which proline 51 at the junction between A and B was removed, allowing for free rotation around this junction. We then treated AB' and A'B as two independent sub-domains. Assuming that the orientation of the two sub-domains is fixed in solution (at least to a first approximation), the principal axis systems, or alignment frames, of sub-domains AB' and A'B should be equivalent to the alignment system of the entire molecule and, vice versa, to each other. Using the residual dipolar couplings we calculated the order tensor principal axis systems for each domain. Rotation of pseudo sub-domain A'B around the hinge at amino acid position 51 until a superposition of the individual coordinate frames was obtained yielded the final model of the solution dimer.
NMR ensembleConformers submitted total number: 1

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