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- PDB-7mdx: LolCDE nucleotide-free -

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Basic information

Entry
Database: PDB / ID: 7mdx
TitleLolCDE nucleotide-free
Components
  • (Lipoprotein-releasing system transmembrane protein ...) x 2
  • Lipoprotein-releasing system ATP-binding protein LolD
  • Triacyl-lipoprotein
KeywordsMEMBRANE PROTEIN / ATP binding cassette transporter / ABC transporter / inner membrane / protein transport
Function / homology
Function and homology information


lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / lipoprotein transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space ...lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / lipoprotein transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Lipoprotein releasing system, ATP-binding protein / Lipoprotein-releasing system transmembrane protein LolE, gammaproteobacteria type / Lipoprotein release ATP-binding protein lolD family profile. / Lipoprotein-releasing system transmembrane protein LolC/E / : / MacB-like periplasmic core domain / MacB-like periplasmic core domain / MacB, ATP-binding domain / ABC transporter, lipoprotein release, LolD / ABC3 transporter permease protein domain ...Lipoprotein releasing system, ATP-binding protein / Lipoprotein-releasing system transmembrane protein LolE, gammaproteobacteria type / Lipoprotein release ATP-binding protein lolD family profile. / Lipoprotein-releasing system transmembrane protein LolC/E / : / MacB-like periplasmic core domain / MacB-like periplasmic core domain / MacB, ATP-binding domain / ABC transporter, lipoprotein release, LolD / ABC3 transporter permease protein domain / FtsX-like permease family / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PENTADECANOIC ACID / : / polypeptide(D) / Lipoprotein-releasing system transmembrane protein LolC / Lipoprotein-releasing system ATP-binding protein LolD / Lipoprotein-releasing system transmembrane protein LolE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSharma, S. / Liao, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2021
Title: Mechanism of LolCDE as a molecular extruder of bacterial triacylated lipoproteins.
Authors: Stuti Sharma / Ruoyu Zhou / Li Wan / Shan Feng / KangKang Song / Chen Xu / Yanyan Li / Maofu Liao /
Abstract: Lipoproteins are important for bacterial growth and antibiotic resistance. These proteins use lipid acyl chains attached to the N-terminal cysteine residue to anchor on the outer surface of ...Lipoproteins are important for bacterial growth and antibiotic resistance. These proteins use lipid acyl chains attached to the N-terminal cysteine residue to anchor on the outer surface of cytoplasmic membrane. In Gram-negative bacteria, many lipoproteins are transported to the outer membrane (OM), a process dependent on the ATP-binding cassette (ABC) transporter LolCDE which extracts the OM-targeted lipoproteins from the cytoplasmic membrane. Lipid-anchored proteins pose a unique challenge for transport machinery as they have both hydrophobic lipid moieties and soluble protein component, and the underlying mechanism is poorly understood. Here we determined the cryo-EM structures of nanodisc-embedded LolCDE in the nucleotide-free and nucleotide-bound states at 3.8-Å and 3.5-Å resolution, respectively. The structural analyses, together with biochemical and mutagenesis studies, uncover how LolCDE recognizes its substrate by interacting with the lipid and N-terminal peptide moieties of the lipoprotein, and identify the amide-linked acyl chain as the key element for LolCDE interaction. Upon nucleotide binding, the transmembrane helices and the periplasmic domains of LolCDE undergo large-scale, asymmetric movements, resulting in extrusion of the captured lipoprotein. Comparison of LolCDE and MacB reveals the conserved mechanism of type VII ABC transporters and emphasizes the unique properties of LolCDE as a molecule extruder of triacylated lipoproteins.
History
DepositionApr 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 2.0Feb 16, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / em_entity_assembly / em_imaging / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_entity_src_syn / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _em_entity_assembly.source / _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _entity.formula_weight / _entity.src_method / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.type / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sense / _struct_sheet_order.sheet_id
Description: Ligand geometry / Details: The ligand structure has been corrected. / Provider: author / Type: Coordinate replacement
Revision 3.0Apr 17, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / em_entity_assembly / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_validate_torsion / struct_asym / struct_conn / struct_ref / struct_ref_seq
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _em_entity_assembly.entity_id_list / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_gene_src_gene / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 3.1Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Lipoprotein-releasing system transmembrane protein LolC
B: Lipoprotein-releasing system transmembrane protein LolE
D: Lipoprotein-releasing system ATP-binding protein LolD
C: Lipoprotein-releasing system ATP-binding protein LolD
E: Triacyl-lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,6407
Polymers134,8705
Non-polymers7692
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Lipoprotein-releasing system transmembrane protein ... , 2 types, 2 molecules AB

#1: Protein Lipoprotein-releasing system transmembrane protein LolC


Mass: 42530.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lolC, ycfU, b1116, JW5161 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADC3
#2: Protein Lipoprotein-releasing system transmembrane protein LolE


Mass: 44200.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lolE, ycfW, b1118, JW1104 / Production host: Escherichia coli (E. coli) / References: UniProt: P75958

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Protein / Polypeptide(D) , 2 types, 3 molecules DCE

#3: Protein Lipoprotein-releasing system ATP-binding protein LolD


Mass: 23823.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lolD, ycfV, b1117, JW5162 / Production host: Escherichia coli (E. coli)
References: UniProt: P75957, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
#4: Polypeptide(D) Triacyl-lipoprotein


Mass: 492.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-F15 / PENTADECANOIC ACID


Mass: 242.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ZM5 / (2R)-2-(tridecanoyloxy)propyl hexadecanoate / (3-oxidanyl-2-tridecanoyloxy-propyl) hexadecanoate


Mass: 526.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H62O5 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Lipo-releasing system transmembrane protein lolC (E.C.3.6.3.-), Lipoprotein-releasing system transmembrane protein (E.C.3.6.3.-), Lipoprotein-releasing system ATP-binding protein LolD (E.C.7.6. ...Name: Lipo-releasing system transmembrane protein lolC (E.C.3.6.3.-), Lipoprotein-releasing system transmembrane protein (E.C.3.6.3.-), Lipoprotein-releasing system ATP-binding protein LolD (E.C.7.6.2.-), Triacyl-lipoprotein
Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightValue: 130 kDa/nm / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 1.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 46.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
10RELION3initial Euler assignment
11RELION3final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104875 / Symmetry type: POINT

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