+Open data
-Basic information
Entry | Database: PDB / ID: 5tsj | |||||||||
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Title | Thermus thermophilus V/A-ATPase bound to VH dAbs | |||||||||
Components |
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Keywords | membrane protein / hydrolase / V/A-ATPase / complex / antibody | |||||||||
Function / homology | Function and homology information proton-transporting V-type ATPase, V0 domain / proton-transporting two-sector ATPase complex, catalytic domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting ATP synthase complex / plant-type vacuole / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / fungal-type vacuole membrane / H+-transporting two-sector ATPase / phagocytic vesicle ...proton-transporting V-type ATPase, V0 domain / proton-transporting two-sector ATPase complex, catalytic domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting ATP synthase complex / plant-type vacuole / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / fungal-type vacuole membrane / H+-transporting two-sector ATPase / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATPase binding / lysosomal membrane / ATP binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Thermus thermophilus (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.7 Å | |||||||||
Authors | Davies, R.B. / Smits, C. / Wong, A.S.W. / Stock, D. / Sandin, S. / Stewart, A.G. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: J Struct Biol / Year: 2017 Title: Cryo-EM analysis of a domain antibody bound rotary ATPase complex. Authors: Roberta B Davies / Callum Smits / Andrew S W Wong / Daniela Stock / Mary Christie / Sara Sandin / Alastair G Stewart / Abstract: The bacterial A/V-type ATPase/synthase rotary motor couples ATP hydrolysis/synthesis with proton translocation across biological membranes. The A/V-type ATPase/synthase from Thermus thermophilus has ...The bacterial A/V-type ATPase/synthase rotary motor couples ATP hydrolysis/synthesis with proton translocation across biological membranes. The A/V-type ATPase/synthase from Thermus thermophilus has been extensively studied both structurally and functionally for many years. Here we provide an 8.7Å resolution cryo-electron microscopy 3D reconstruction of this complex bound to single-domain antibody fragments, small monomeric antibodies containing just the variable heavy domain. Docking of known structures into the density revealed the molecular orientation of the domain antibodies, suggesting that structure determination of co-domain antibody:protein complexes could be a useful avenue for unstable or smaller proteins. Although previous studies suggested that the presence of fluoroaluminate in this complex could change the rotary state of this enzyme, we observed no gross structural rearrangements under these conditions. | |||||||||
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 | 5tsj.cif.gz | 729.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tsj.ent.gz | 449.6 KB | Display | PDB format |
PDBx/mmJSON format | 5tsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tsj_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5tsj_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5tsj_validation.xml.gz | 118.3 KB | Display | |
Data in CIF | 5tsj_validation.cif.gz | 210 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/5tsj ftp://data.pdbj.org/pub/pdb/validation_reports/ts/5tsj | HTTPS FTP |
-Related structure data
Related structure data | 8462MC 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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1 |
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-Components
-V-type ATP synthase ... , 6 types, 11 molecules ABCDEFGHKLM
#1: Protein | Mass: 63628.902 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 References: UniProt: Q56403, H+-transporting two-sector ATPase #2: Protein | Mass: 50850.738 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q72J73, UniProt: Q56404*PLUS #3: Protein | Mass: 20481.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P74901 #5: Protein | | Mass: 23350.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q72J74, UniProt: O87880*PLUS #6: Protein | | Mass: 10824.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P74903 #7: Protein | | Mass: 35968.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P74902 |
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-Protein , 3 types, 15 molecules IJNOPQRSTUVWXYZ
#4: Protein | Mass: 11752.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: H9ZQR3, UniProt: Q5SIT5*PLUS #8: Protein | | Mass: 72272.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: H9ZQR4, UniProt: Q5SIT6*PLUS #9: Protein | Mass: 9841.714 Da / Num. of mol.: 12 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P74900, UniProt: Q5SIT7*PLUS |
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-Antibody , 1 types, 2 molecules 12
#10: Antibody | Mass: 16345.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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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: Thermus thermophilus V/A-ATPase bound to VH dAbs / Type: COMPLEX / Entity ID: #1-#11 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 13.8 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61045 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT |