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- PDB-6yfy: Solid-state NMR structure of the D-Arg4,L10-teixobactin - Lipid I... -

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Basic information

Entry
Database: PDB / ID: 6yfy
TitleSolid-state NMR structure of the D-Arg4,L10-teixobactin - Lipid II complex in lipid bilayers.
Components
  • D-Arg4,Leu10-Teixobactin
  • Lipid II
KeywordsANTIBIOTIC / teixobactin Lipid II Complex antimicrobial peptide
Function / homologyD-Arg4,Leu10-Teixobactin / Lipid II / PHOSPHONATE / 3-methylbut-2-en-1-ol / polypeptide(D)
Function and homology information
Biological speciesStaphylococcus simulans (bacteria)
Eleftheria terrae (bacteria)
MethodSOLID-STATE NMR / torsion angle dynamics
AuthorsWeingarth, M.H. / Shukla, R.
Funding support Netherlands, 4items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)723.014.003 Netherlands
Netherlands Organisation for Scientific Research (NWO)711.018.001 Netherlands
Netherlands Organisation for Scientific Research (NWO)700.26.121 Netherlands
Netherlands Organisation for Scientific Research (NWO)700.10.443 Netherlands
CitationJournal: Nat Commun / Year: 2020
Title: Mode of action of teixobactins in cellular membranes.
Authors: Shukla, R. / Medeiros-Silva, J. / Parmar, A. / Vermeulen, B.J.A. / Das, S. / Paioni, A.L. / Jekhmane, S. / Lorent, J. / Bonvin, A.M.J.J. / Baldus, M. / Lelli, M. / Veldhuizen, E.J.A. / ...Authors: Shukla, R. / Medeiros-Silva, J. / Parmar, A. / Vermeulen, B.J.A. / Das, S. / Paioni, A.L. / Jekhmane, S. / Lorent, J. / Bonvin, A.M.J.J. / Baldus, M. / Lelli, M. / Veldhuizen, E.J.A. / Breukink, E. / Singh, I. / Weingarth, M.
History
DepositionMar 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list ..._chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Aug 19, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / citation_author / pdbx_entry_details / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_rmsd_bond / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.compound_details / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_prop.value / _pdbx_validate_rmsd_bond.auth_atom_id_2 / _struct_asym.entity_id
Revision 3.1Sep 15, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_validate_polymer_linkage / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.2May 17, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 4.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 5.0Aug 7, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-Arg4,Leu10-Teixobactin
B: D-Arg4,Leu10-Teixobactin
E: D-Arg4,Leu10-Teixobactin
F: D-Arg4,Leu10-Teixobactin
C: Lipid II
D: Lipid II
G: Lipid II
H: Lipid II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,61232
Polymers6,9528
Non-polymers3,65924
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Excimer Fluorescence with tagged Lipid II, microscopy, Fluorescence microscopy with tagged Lipid II
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area8730 Å2
ΔGint-31 kcal/mol
Surface area5130 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)26 / 26all calculated structures submitted
RepresentativeModel #1medoid

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Components

#1: Protein/peptide
D-Arg4,Leu10-Teixobactin


Type: Polypeptide / Class: Antibiotic / Mass: 1248.536 Da / Num. of mol.: 4 / Mutation: D-Glu4D-Arg, L-allo-End10Leu / Source method: obtained synthetically / Source: (synth.) Eleftheria terrae (bacteria) / References: D-Arg4,Leu10-Teixobactin
#2: Polypeptide(D)
Lipid II


Class: Glycan component / Mass: 489.542 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Staphylococcus simulans (bacteria) / References: Lipid II
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid


Type: oligosaccharide / Class: Glycan component / Mass: 496.463 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
References: Lipid II
DescriptorTypeProgram
DGlcpNAcb1-4MurNAc1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O_3*OC^RCO/4=O/3C][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][<C3O1>]{}[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Chemical
ChemComp-2PO / PHOSPHONATE


Class: Glycan component / Mass: 79.980 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: HO3P / References: Lipid II
#5: Chemical
ChemComp-P1W / 3-methylbut-2-en-1-ol


Class: Glycan component / Mass: 86.132 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C5H10O / References: Lipid II
Compound detailsLipid II is a precursor molecule in the synthesis of the cell wall of bacteria
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D NH
121anisotropic12D CC
131anisotropic12D TOBSY
141anisotropic13D HNCO
161anisotropic13D HNCA
NMR detailsText: All the structures are aligned to chains A,B,E,F of model 5. Residues 1-5 and 9-12 in chains C,D,G,H are highly flexible (no NMR restraints were applied).Alignment was performed in PyMol using ...Text: All the structures are aligned to chains A,B,E,F of model 5. Residues 1-5 and 9-12 in chains C,D,G,H are highly flexible (no NMR restraints were applied).Alignment was performed in PyMol using the alignto command, and we converted the pdb file to a cif file using the online convertor provided by wwPDB.

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Sample preparation

DetailsType: liposome
Contents: 25 mM sodium chloride, 40 mM sodium phosphate, 1.6 mM [U-99% 13C; U-99% 15N] D-Arg,Leu10-teixobactin, 0.8 mM [U-99% 13C; U-99% 15N] Lipid II, 1.6 mM [U-99% 13C; U-99% 15N] Leu10- ...Contents: 25 mM sodium chloride, 40 mM sodium phosphate, 1.6 mM [U-99% 13C; U-99% 15N] D-Arg,Leu10-teixobactin, 0.8 mM [U-99% 13C; U-99% 15N] Lipid II, 1.6 mM [U-99% 13C; U-99% 15N] Leu10-teixobactin, 40mM Phosphate 25mM NaCl
Label: 13C15N_TeixoLII / Solvent system: 40mM Phosphate 25mM NaCl
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMsodium chloridenone1
40 mMsodium phosphatenone1
1.6 mMD-Arg,Leu10-teixobactin[U-99% 13C; U-99% 15N]1
0.8 mMLipid II[U-99% 13C; U-99% 15N]1
1.6 mMLeu10-teixobactin[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength: 40 mM / Label: NMR Buffer / pH: 7 / PH err: 0.2 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.5

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9501
Bruker AVANCE IIIBrukerAVANCE III7002
Bruker AVANCE IIIBrukerAVANCE III8003
Bruker AVANCE IIIBrukerAVANCE III5004

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
HADDOCKBonvinstructure calculation
SparkyGoddardchemical shift assignment
TopSpinBruker Biospinpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 26 / Conformers submitted total number: 26

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