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- PDB-1wco: The solution structure of the nisin-lipid II complex -

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Entry
Database: PDB / ID: 1wco
TitleThe solution structure of the nisin-lipid II complex
Components
  • ALA-FGA-LYS-DAL-DAL PEPTIDE
  • Lantibiotic
KeywordsPEPTIDE/ANTIBIOTIC / PEPTIDE-ANTIBIOTIC COMPLEX / LANTIBIOTIC / ANTIMICROBIAL / BACTERIOCIN / THIOESTER / PORE FORMATION / PYROPHOSPHATE CAGE / FOOD PRESERVATIVE
Function / homology
Function and homology information


killing of cells of another organism / defense response to bacterium / signaling receptor binding / extracellular region
Similarity search - Function
Lantibiotic, Type A, Bacillales-type / Gallidermin
Similarity search - Domain/homology
Nisin A / Chem-FDF / Lantibiotic nisin-Z / Lantibiotic
Similarity search - Component
Biological speciesMONARTHROPALPUS FLAVUS (insect)
Lactococcus lactis (lactic acid bacteria)
MethodSOLUTION NMR / HADDOCK
AuthorsHsu, S.-T.D. / Breukink, E. / Tischenko, E. / Lutters, M.A.G. / de Kruijff, B. / Kaptein, R. / Bonvin, A.M.J.J. / van Nuland, N.A.J.
Citation
Journal: Nat. Struct. Mol. Biol. / Year: 2004
Title: The nisin-lipid II complex reveals a pyrophosphate cage that provides a blueprint for novel antibiotics.
Authors: Hsu, S.T. / Breukink, E. / Tischenko, E. / Lutters, M.A. / de Kruijff, B. / Kaptein, R. / Bonvin, A.M. / van Nuland, N.A.
#1: Journal: Biochemistry / Year: 2002
Title: Mapping the Targeted Membrane Pore Formation Mechanism by Solution NMR: The Nisin Z and Lipid II Interaction in Sds Micelles
Authors: Hsu, S.-T.D. / Breukink, E. / de Kruijff, B. / Kaptein, R. / Bonvin, A.M.J.J. / van Nuland, N.A.J.
#2: Journal: Science / Year: 1999
Title: Use of the Cell Wall Precursor Lipid II by a Pore- Forming Peptide Antibiotic
Authors: Breukink, E. / Wiedemann, I. / van Kraaij, C. / Kuipers, O.P. / Sahl, H.G. / de Kruijff, B.
#3: Journal: Proteins: Struct.,Funct., Genet. / Year: 2003
Title: Refinement of Protein Structures in Explicit Solvent
Authors: Linge, J. / Williams, M.A. / Spronk, C.A.E.M. / Bonvin, A.M.J.J. / Nilges, M.
#4: Journal: J.Am.Chem.Soc. / Year: 2003
Title: Haddock: A Protein-Protein Docking Approach Based on Biochemical or Biophysical Information
Authors: Dominguez, C. / Boelens, R. / Bonvin, A.M.J.J.
History
DepositionNov 19, 2004Deposition site: PDBE / Processing site: PDBE
SupersessionMar 7, 2005ID: 1UZT
Revision 1.0Mar 7, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 2.0Jan 17, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / citation_author / database_PDB_caveat / pdbx_nmr_spectrometer / pdbx_validate_polymer_linkage
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_atom_id / _atom_site.label_atom_id / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 3.0Jul 8, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site_gen
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.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_PDB_caveat.text / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_organism_scientific / _entity_src_nat.strain / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_mod_residue.details / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.db_code / _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.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id
Revision 4.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / 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_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
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.type_symbol / _chem_comp.name / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 5.0May 1, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity_poly / 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_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: ALA-FGA-LYS-DAL-DAL PEPTIDE
N: Lantibiotic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,7494
Polymers3,8352
Non-polymers9152
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1610 Å2
ΔGint3 kcal/mol
Surface area3620 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200RMSD CLUSTERING AND LOWEST TOTAL ENERGY
Representative

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Components

#1: Protein/peptide ALA-FGA-LYS-DAL-DAL PEPTIDE


Mass: 489.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MONARTHROPALPUS FLAVUS (insect)
#2: Protein/peptide Lantibiotic


Type: Polypeptide / Class: Lantibiotic / Mass: 3345.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Nisin Z is a heptacyclic peptide. Post Translational maturation of lantibiotics involves the enzymic conversion of Thr, and Ser into dehydrated AA and the formation of thioether bonds with ...Details: Nisin Z is a heptacyclic peptide. Post Translational maturation of lantibiotics involves the enzymic conversion of Thr, and Ser into dehydrated AA and the formation of thioether bonds with cysteine. Thioether bonds with cysteine result in five cyclic structures along the peptide chain. This is followed by membrane translocation and cleavage of the modified precursor.
Source: (natural) Lactococcus lactis (lactic acid bacteria) / References: UniProt: Q7BB86, Nisin A, UniProt: P29559*PLUS
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid


Type: oligosaccharide / Mass: 496.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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-FDF / (2E,6E)-12-fluoro-11-(fluoromethyl)-3,7-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate


Mass: 418.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26F2O7P2
Compound detailsNISIN Z IS A LANTIBIOTIC. THE LANTIBIOTICS ARE CHARACTERIZED BY LANTHIONINE AND/OR ...NISIN Z IS A LANTIBIOTIC. THE LANTIBIOTICS ARE CHARACTERIZED BY LANTHIONINE AND/OR METHYLLANTHIONINE NONPROTEINOGENIC AMINO ACIDS. HERE, NISIN Z IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: NISIN Z CHAIN: N COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 34 DESCRIPTION: NISIN Z IS A PENTACYCLIC PEPTIDE. THIOETHER BONDS WITH CYSTEINE RESULT IN FIVE CYCLIC STRUCTURES ALONG THE PEPTIDE CHAIN. CROSSLINK 3-7 METHYLLANTHIONINE (DAL-CYS) CROSSLINK 8-11 BETA-METHYLLANTHIONINE (DBB-CYS) CROSSLINK 13-19 BETA-METHYLLANTHIONINE (DBB-CYS) CROSSLINK 23-26 BETA-METHYLLANTHIONINE (DBB-CYS) CROSSLINK 25-28 BETA-METHYLLANTHIONINE (DBB-CYS)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-15N CT HSQC
12131P 1D
1311H-13C HSQC
1411H-13C HMBC
15131P 1D
1611H-15N-NOESY HSQC
1711H-1H NOESY
1811H-15N TOCSY- HSQC
1911H-1H TOCSY
11011H-1H COSY
11111H-15N-NOESY HSQC
11211H-1H NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING MULTIDIMENSIONAL NMR SPECTROSCOPY ON 15N-LABELLED NISIN IN COMPLEX WITH UNLABELLED 3-LIPID II. INTERMOLECULAR HYDROGEN BONDS WERE IDENTIFIED AND USED IN ...Text: THE STRUCTURE WAS DETERMINED USING MULTIDIMENSIONAL NMR SPECTROSCOPY ON 15N-LABELLED NISIN IN COMPLEX WITH UNLABELLED 3-LIPID II. INTERMOLECULAR HYDROGEN BONDS WERE IDENTIFIED AND USED IN STRUCTURAL CALCULATION BY 31P- EDITED 1H-15N CT HSQC.

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Sample preparation

DetailsContents: 100% D6-DMSO
Sample conditionsPressure: 1.0 atm / Temperature: 300.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE7503
Bruker AVANCEBrukerAVANCE9004

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
NMRViewVIEWstructure solution
CNSstructure solution
RefinementMethod: HADDOCK / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. THE ENSEMBLE OF STRUCTURES IS SUPERIMPOSED ON THE CA OF NISIN RESIDUES 1-12 (CHAIN N), THE HEAVY ATOMS OF MURNAC, PYROPHOSPHATE ...Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. THE ENSEMBLE OF STRUCTURES IS SUPERIMPOSED ON THE CA OF NISIN RESIDUES 1-12 (CHAIN N), THE HEAVY ATOMS OF MURNAC, PYROPHOSPHATE AND THE FIRST ISOPRENE OF 3-LIPID II (CHAIN L) AS THESE ARE THE ONLY SEGMENTS THAT HAVE SUFFICIENT DISTANCE RESTRAINTS TO DEFINE THE COMPLEX STRUCTURE. OTHER RESIDUES NAMELY RESIDUES 13-34 (ESPECIALLY RESIDUES 20-34) OF NISIN, THE PENTAPEPTIDE AND TERMINAL ISOPRENE UNITS OF 3-LIPID II ARE FLEXIBLE AS SUPPORTED BY DYNAMICS DATA. THE ATOM OCCUPANCY OF THE C- TERMINAL TAIL OF NISIN (RESIDUES 20-34) HAS BEEN MODIFIED TO BE 0.3 TO REFLECT THEIR DISORDER/FLEXIBILITY.
NMR ensembleConformer selection criteria: RMSD CLUSTERING AND LOWEST TOTAL ENERGY
Conformers calculated total number: 200 / Conformers submitted total number: 20

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