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- PDB-6k1h: Structure of membrane protein -

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Basic information

Entry
Database: PDB / ID: 6k1h
TitleStructure of membrane protein
Components
  • PTS mannose transporter subunit IID
  • PTS system mannose-specific EIIC component
KeywordsPROTEIN TRANSPORT / PTS / ManYZ / transporter / Mannose
Function / homology
Function and homology information


mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / glucose import across plasma membrane / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / membrane / plasma membrane
Similarity search - Function
Phosphotransferase system, mannose/fructose/sorbose family, IIC subunit / Phosphotransferase system, mannose/fructose/sorbose family IID component / PTS system sorbose-specific iic component / PTS system mannose/fructose/sorbose family IID component / PTS_EIIC type-4 domain profile. / PTS_EIID domain profile.
Similarity search - Domain/homology
alpha-D-mannopyranose / : / PTS system mannose-specific EIIC component / PTS system mannose-specific EIID component
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsWang, J.W. / Zeng, J.W.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)No. 2016YFA0501103 China
Ministry of Science and Technology (MoST, China)2015CB910104 China
National Natural Science Foundation of China (NSFC)31621092 China
CitationJournal: Cell Res / Year: 2019
Title: Structure of the mannose transporter of the bacterial phosphotransferase system.
Authors: Xueli Liu / Jianwei Zeng / Kai Huang / Jiawei Wang /
History
DepositionMay 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Sep 16, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / entity_poly / entity_src_gen / pdbx_audit_support / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_torsion / refine_ls_restr / software / struct_conf / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.pdbx_synonyms / _entity.pdbx_description ..._chem_comp.pdbx_synonyms / _entity.pdbx_description / _entity_name_com.entity_id / _entity_name_com.name / _entity_poly.pdbx_strand_id / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_assembly_prop.value / _pdbx_validate_peptide_omega.auth_asym_id_1 / _pdbx_validate_peptide_omega.auth_asym_id_2 / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega / _software.version / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Description: Model orientation/position / Provider: author / Type: Coordinate replacement
Revision 2.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
Z: PTS mannose transporter subunit IID
Y: PTS system mannose-specific EIIC component
F: PTS mannose transporter subunit IID
E: PTS system mannose-specific EIIC component
C: PTS mannose transporter subunit IID
B: PTS system mannose-specific EIIC component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,7499
Polymers179,2086
Non-polymers5403
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area36330 Å2
ΔGint-316 kcal/mol
Surface area62340 Å2

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Components

#1: Protein PTS mannose transporter subunit IID


Mass: 30983.373 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: D8B36_09735 / Variant: K-12
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Variant (production host): BL21 / References: UniProt: A0A387CW08, UniProt: P69805*PLUS
#2: Protein PTS system mannose-specific EIIC component / EII-P-Man / EIIC-Man / Mannose permease IIC component


Mass: 28752.783 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: manY, pel, ptsP, b1818, JW1807 / Variant: K-12
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Variant (production host): BL21 / References: UniProt: P69801
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY

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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: ManYZ trimer complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 176 kDa/nm / Experimental value: YES
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain: BL21
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.1_3865: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 309996 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0064000
ELECTRON MICROSCOPYf_angle_d0.8425440
ELECTRON MICROSCOPYf_dihedral_angle_d19.471559
ELECTRON MICROSCOPYf_chiral_restr0.048662
ELECTRON MICROSCOPYf_plane_restr0.006676

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