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- PDB-7r0r: Solution structure of the designed Armadillo repeat protein N(A4)... -

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Basic information

Entry
Database: PDB / ID: 7r0r
TitleSolution structure of the designed Armadillo repeat protein N(A4)M4C(AII) refined by pseudocontact shifts
ComponentsDesigned Armadillo Repeat Protein N(A4)M4C(AII)
KeywordsPEPTIDE BINDING PROTEIN / repeat protein / designed Armadillo repeat protein
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsCucuzza, S. / Zerbe, O.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation122686 Switzerland
CitationJournal: Biochemistry / Year: 2023
Title: Improved Repeat Protein Stability by Combined Consensus and Computational Protein Design.
Authors: Michel, E. / Cucuzza, S. / Mittl, P.R.E. / Zerbe, O. / Pluckthun, A.
History
DepositionFeb 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Designed Armadillo Repeat Protein N(A4)M4C(AII)


Theoretical massNumber of molelcules
Total (without water)61,9071
Polymers61,9071
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)3 / 400structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Designed Armadillo Repeat Protein N(A4)M4C(AII)


Mass: 61907.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-15N HSQC
133isotropic12D 1H-15N HSQC
155isotropic12D 1H-15N HSQC
1126isotropic12D 1H-15N HSQC
1117isotropic12D 1H-15N HSQC
1810isotropic12D 1H-15N HSQC
1711isotropic12D 1H-15N HSQC
11313isotropic12D 1H-15N HSQC
1142isotropic13D 1H-15N NOESY
1156isotropic13D 1H-15N NOESY
11610isotropic13D 1H-15N NOESY
1171isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution120 mM sodium phosphate, 2 mM TMSP, 300 uM [U-15N] A4M4C, 90% H2O/10% D2Owt-A4M4C15N_sample_wt90% H2O/10% D2O
solution220 mM sodium phosphate, 2 mM TMSP, 150 uM [U-100% 15N] A4M4C, 90% H2O/10% D2O(C-Cap)S21C mutant coupled to the metal chelator Tm-4R4S-DOTA-M8 loaded with the diamagnetic Lutetium ion15N_sample_mut1a90% H2O/10% D2O
solution320 mM sodium phosphate, 2 mM TMSP, 150 uM [U-100% 15N] A4M4C, 90% H2O/10% D2O(C-Cap)S21C mutant coupled to the metal chelator Tm-4R4S-DOTA-M8 loaded with the paramagnetic Tulium ion15N_sample_mut1b90% H2O/10% D2O
solution520 mM sodium phosphate, 2 mM TMSP, 150 uM 15N-Leu A4M4C, 90% H2O/10% D2O(C-Cap)S21C mutant coupled to the metal chelator Tm-4R4S-DOTA-M8 loaded with the paramagnetic Tulium ion15N_sample_mut1c90% H2O/10% D2O
solution620 mM sodium phosphate, 2 mM TMSP, 150 uM [U-15N] A4M4C, 90% H2O/10% D2O(M2)Q18C mutant coupled to the metal chelator Tm-4R4S-DOTA-M8 loaded with the diamagnetic Lutetium ion15N_sample_mut2a90% H2O/10% D2O
solution720 mM sodium phosphate, 2 mM TMSP, 150 uM [U-15N] A4M4C, 90% H2O/10% D2O(M2)Q18C mutant coupled to the metal chelator Tm-4R4S-DOTA-M8 loaded with the paramagnetic Tulium ion15N_sample_mut2b90% H2O/10% D2O
solution1020 mM sodium phosphate, 2 mM TMSP, 150 uM [U-15N] A4M4C, 90% H2O/10% D2O(NA)E15C mutant coupled to the metal chelator Tm-4R4S-DOTA-M8 loaded with the diamagnetic Lutetium ion15N_sample_mut3a90% H2O/10% D2O
solution1120 mM sodium phosphate, 2 mM TMSP, 150 uM [U-15N] A4M4C, 90% H2O/10% D2O(NA)E15C mutant coupled to the metal chelator Tm-4R4S-DOTA-M8 loaded with the paramagnetic Tulium ion15N_sample_mut3b90% H2O/10% D2O
solution1320 mM sodium phosphate, 2 mM TMSP, 150 uM 15N-Leu A4M4C, 90% H2O/10% D2O(NA)E15C mutant coupled to the metal chelator Tm-4R4S-DOTA-M8 loaded with the paramagnetic Tulium ion15N_sample_mut3c90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphatenone1
2 mMTMSPnone1
300 uMA4M4C[U-15N]1
20 mMsodium phosphatenone2
2 mMTMSPnone2
150 uMA4M4C[U-100% 15N]2
20 mMsodium phosphatenone3
2 mMTMSPnone3
150 uMA4M4C[U-100% 15N]3
20 mMsodium phosphatenone5
2 mMTMSPnone5
150 uMA4M4C15N-Leu5
20 mMsodium phosphatenone6
2 mMTMSPnone6
150 uMA4M4C[U-15N]6
20 mMsodium phosphatenone7
2 mMTMSPnone7
150 uMA4M4C[U-15N]7
20 mMsodium phosphatenone10
2 mMTMSPnone10
150 uMA4M4C[U-15N]10
20 mMsodium phosphatenone11
2 mMTMSPnone11
150 uMA4M4C[U-15N]11
20 mMsodium phosphatenone13
2 mMTMSPnone13
150 uMA4M4C15N-Leu13
Sample conditionsIonic strength: 20 mM / Label: 15N_sample / pH: 7 / Pressure: AMBIENT atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AV600 Neo / Manufacturer: Bruker / Model: AV600 Neo / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Peter Guntertrefinement
CARAKeller and Wuthrichchemical shift assignment
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: PCS were determined for 3 different attachment sites. During the refinement the tensor is updatexd in an iterative fashion as described by Cucuzza et al., JNMR 2020. Scaffold restraints are ...Details: PCS were determined for 3 different attachment sites. During the refinement the tensor is updatexd in an iterative fashion as described by Cucuzza et al., JNMR 2020. Scaffold restraints are supplied by the regularization macro from CYANA. Three differnt starting sdtrucutres were refined, and for each, the strucutre with the lowest Q factor is submitted
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 400 / Conformers submitted total number: 3

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