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- PDB-6bpl: E. coli MsbA in complex with LPS and inhibitor G907 -

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Basic information

Entry
Database: PDB / ID: 6bpl
TitleE. coli MsbA in complex with LPS and inhibitor G907
ComponentsLipid A export ATP-binding/permease protein MsbA
KeywordsLIPID TRANSPORT / ABC transporter / inhibitor / LPS / MsbA
Function / homology
Function and homology information


ABC-type lipid A-core oligosaccharide transporter / ATPase-coupled lipid transmembrane transporter activity / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Lipid A export ATP-binding/permease protein msbA family profile. / ABC transporter, lipid A-core flippase, MsbA / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...Lipid A export ATP-binding/permease protein msbA family profile. / ABC transporter, lipid A-core flippase, MsbA / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / 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
1,2-Distearoyl-sn-glycerophosphoethanolamine / Chem-AU7 / LAURIC ACID / DIPHOSPHATE / 3-HYDROXY-TETRADECANOIC ACID / MYRISTIC ACID / 2-amino-2-deoxy-alpha-D-glucopyranose / PHOSPHATE ION / ATP-dependent lipid A-core flippase / ATP-dependent lipid A-core flippase
Similarity search - Component
Biological speciesEscherichia coli O6:H1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.908 Å
AuthorsHo, H. / Koth, C.M. / Payandeh, J.
CitationJournal: Nature / Year: 2018
Title: Structural basis for dual-mode inhibition of the ABC transporter MsbA.
Authors: Ho, H. / Miu, A. / Alexander, M.K. / Garcia, N.K. / Oh, A. / Zilberleyb, I. / Reichelt, M. / Austin, C.D. / Tam, C. / Shriver, S. / Hu, H. / Labadie, S.S. / Liang, J. / Wang, L. / Wang, J. / ...Authors: Ho, H. / Miu, A. / Alexander, M.K. / Garcia, N.K. / Oh, A. / Zilberleyb, I. / Reichelt, M. / Austin, C.D. / Tam, C. / Shriver, S. / Hu, H. / Labadie, S.S. / Liang, J. / Wang, L. / Wang, J. / Lu, Y. / Purkey, H.E. / Quinn, J. / Franke, Y. / Clark, K. / Beresini, M.H. / Tan, M.W. / Sellers, B.D. / Maurer, T. / Koehler, M.F.T. / Wecksler, A.T. / Kiefer, J.R. / Verma, V. / Xu, Y. / Nishiyama, M. / Payandeh, J. / Koth, C.M.
History
DepositionNov 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 12, 2018Group: Data collection / Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene ..._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 / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_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 / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipid A export ATP-binding/permease protein MsbA
B: Lipid A export ATP-binding/permease protein MsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,48320
Polymers128,9732
Non-polymers7,51018
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20900 Å2
ΔGint-50 kcal/mol
Surface area51030 Å2
Unit cell
Length a, b, c (Å)74.747, 91.606, 111.013
Angle α, β, γ (deg.)90.00, 89.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lipid A export ATP-binding/permease protein MsbA


Mass: 64486.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (bacteria)
Strain: CFT073 / ATCC 700928 / UPEC / Gene: msbA, c1054 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: Q8FJB1, UniProt: P60753*PLUS, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

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Sugars , 3 types, 3 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]alpha-D-glucopyranose-(1-3)-[L-glycero- ...alpha-D-glucopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]alpha-D-glucopyranose-(1-3)-[L-glycero-alpha-D-manno-heptopyranose-(1-7)]L-glycero-alpha-D-manno-heptopyranose


Type: oligosaccharide / Mass: 888.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-3[DGlcpa1-6]DGlcpa1-3[LDmanHep1-7]LDmanHep1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a11221h-1a_1-5][a2122h-1a_1-5]/1-2-2-2-1/a3-b1_a7-e1_b3-c1_b6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(3+1)][a-D-Glcp]{[(3+1)][a-D-Glcp]{}[(6+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-[L-glycero-alpha-D-manno-heptopyranose-(1-5)] ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-[L-glycero-alpha-D-manno-heptopyranose-(1-5)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 811.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DKdopa2-4[LDmanHep1-5]DKdopa2-6DGlcpNb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*N][Aad1122h-2a_2-6][a11221h-1a_1-5]/1-2-2-3/a6-b2_b4-c2_b5-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpN]{[(6+2)][a-D-Kdop]{[(4+2)][a-D-Kdop]{}[(5+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#7: Sugar ChemComp-PA1 / 2-amino-2-deoxy-alpha-D-glucopyranose / Glucosamine


Type: D-saccharide, alpha linking / Mass: 179.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13NO5
IdentifierTypeProgram
DGlcpNaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 15 molecules

#4: Chemical
ChemComp-3PE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / 3-SN-PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#5: Chemical ChemComp-AU7 / (2E)-3-{6-[(1S)-1-(2-chloro-6-cyclopropylphenyl)ethoxy]-4-cyclopropylquinolin-3-yl}prop-2-enoic acid


Mass: 433.927 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H24ClNO3
#6: Chemical
ChemComp-FTT / 3-HYDROXY-TETRADECANOIC ACID / 3-HYDROXY-MYRISTIC ACID


Mass: 244.370 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O3
#8: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#9: Chemical ChemComp-DAO / LAURIC ACID / Lauric acid


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#10: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#11: Chemical ChemComp-DPO / DIPHOSPHATE / Pyrophosphate


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 200 mM NaCl, 19% PEG 550 MME, 4% PEG 400, 100 mM HEPES, pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9079→39.9 Å / Num. obs: 29686 / % possible obs: 91.1 % / Redundancy: 4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.97
Reflection shellResolution: 2.9079→3.0017 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.53 / Num. unique obs: 1528 / CC1/2: 0.576 / % possible all: 61

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Processing

Software
NameVersionClassification
PHENIX(dev_2747: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.908→39.9 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.42
RfactorNum. reflection% reflection
Rfree0.2829 1482 4.99 %
Rwork0.2333 --
obs0.2357 29686 89.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.908→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8827 0 353 0 9180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039320
X-RAY DIFFRACTIONf_angle_d0.66612560
X-RAY DIFFRACTIONf_dihedral_angle_d17.6565638
X-RAY DIFFRACTIONf_chiral_restr0.0411507
X-RAY DIFFRACTIONf_plane_restr0.0031544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9079-3.00170.4328900.33771438X-RAY DIFFRACTION51
3.0017-3.1090.34111220.29272233X-RAY DIFFRACTION79
3.109-3.23340.31391300.27072548X-RAY DIFFRACTION90
3.2334-3.38050.32181330.25832658X-RAY DIFFRACTION93
3.3805-3.55860.29951330.25282572X-RAY DIFFRACTION91
3.5586-3.78140.32681450.23222792X-RAY DIFFRACTION98
3.7814-4.07310.2751460.21722811X-RAY DIFFRACTION98
4.0731-4.48250.24571590.19922718X-RAY DIFFRACTION96
4.4825-5.130.22441010.19532836X-RAY DIFFRACTION97
5.13-6.45880.30931610.27282798X-RAY DIFFRACTION98
6.4588-39.91010.26361620.22832800X-RAY DIFFRACTION96

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