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Yorodumi- PDB-6wu0: CryoEM structure of Burkholderia pseudomallei hopanoid biosynthes... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wu0 | ||||||
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Title | CryoEM structure of Burkholderia pseudomallei hopanoid biosynthesis-associated RND transporter HpnN | ||||||
Components | Hopanoid biosynthesis associated RND transporter like protein HpnN | ||||||
Keywords | PROTEIN TRANSPORT / CryoEM structure / hopanoid transporter HpnN | ||||||
Function / homology | Hopanoid biosynthesis associated RND transporter-like protein HpnN / Membrane transport protein MMPL domain / MMPL family / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / membrane => GO:0016020 / plasma membrane / Hopanoid biosynthesis associated RND transporter like protein HpnN Function and homology information | ||||||
Biological species | Burkholderia pseudomallei MSHR346 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.59 Å | ||||||
Authors | Lyu, M. / Yu, E.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Methods / Year: 2021 Title: A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins. Authors: Chih-Chia Su / Meinan Lyu / Christopher E Morgan / Jani Reddy Bolla / Carol V Robinson / Edward W Yu / Abstract: Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein ...Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein samples hampers the progress of their structural determination. Here, we develop a bottom-up iterative method, Build and Retrieve (BaR), that enables the identification and determination of cryo-EM structures of a variety of inner and outer membrane proteins, including membrane protein complexes of different sizes and dimensions, from a heterogeneous, impure protein sample. We also use the BaR methodology to elucidate structural information from Escherichia coli K12 crude membrane and raw lysate. The findings demonstrate that it is possible to solve high-resolution structures of a number of relatively small (<100 kDa) and less abundant (<10%) unidentified membrane proteins within a single, heterogeneous sample. Importantly, these results highlight the potential of cryo-EM for systems structural proteomics. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6wu0.cif.gz | 148.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wu0.ent.gz | 116.5 KB | Display | PDB format |
PDBx/mmJSON format | 6wu0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wu0_validation.pdf.gz | 722.1 KB | Display | wwPDB validaton report |
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Full document | 6wu0_full_validation.pdf.gz | 732.1 KB | Display | |
Data in XML | 6wu0_validation.xml.gz | 26.9 KB | Display | |
Data in CIF | 6wu0_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/6wu0 ftp://data.pdbj.org/pub/pdb/validation_reports/wu/6wu0 | HTTPS FTP |
-Related structure data
Related structure data | 21901MC 6wtiC 6wtzC 6wu6C 7jz2C 7jz3C 7jz6C 7jzhC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 92600.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei MSHR346 (bacteria) Gene: hpnN, GBP346_B2639 / Production host: Escherichia coli (E. coli) / References: UniProt: C4I4K0 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: hopanoid transporter HpnN / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia Coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15_3459: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63910 / Symmetry type: POINT | ||||||||||||||||||||||||
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