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Yorodumi- PDB-8qqj: CryoEM structure of the type IV pilin PilA5 from Thermus thermophilus -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qqj | ||||||
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Title | CryoEM structure of the type IV pilin PilA5 from Thermus thermophilus | ||||||
Components | Type IV narrow pilus major component PilA5 | ||||||
Keywords | PROTEIN FIBRIL / Type IV pilin glycosylation / twitching motility | ||||||
Function / homology | : / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / cell outer membrane / periplasmic space / plasma membrane / Type IV narrow pilus major component PilA5 Function and homology information | ||||||
Biological species | Thermus thermophilus HB27 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.63 Å | ||||||
Authors | Gold, V.A.M. / Neuhaus, A. / Gaines, M. / Isupov, M. / McLaren, M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: CryoEM structure of the type IV pilin PilA4 from Thermus thermophilus Authors: Gold, V.A.M. / Neuhaus, A. / Gaines, M. / Isupov, M. / McLaren, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qqj.cif.gz | 638.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qqj.ent.gz | 548.4 KB | Display | PDB format |
PDBx/mmJSON format | 8qqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qqj_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 8qqj_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 8qqj_validation.xml.gz | 88.3 KB | Display | |
Data in CIF | 8qqj_validation.cif.gz | 145.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/8qqj ftp://data.pdbj.org/pub/pdb/validation_reports/qq/8qqj | HTTPS FTP |
-Related structure data
Related structure data | 18593MC 8qqdC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 11441.797 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72GL2 #2: Polysaccharide | 7-Acetamido-5-acetimidoyl-3,5,7,9-tetradeoxy-L-glycero-L-manno-nonulosonic aci-(1-4)-alpha-D- ...7-Acetamido-5-acetimidoyl-3,5,7,9-tetradeoxy-L-glycero-L-manno-nonulosonic aci-(1-4)-alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose Type: oligosaccharide / Mass: 901.864 Da / Num. of mol.: 31 / Source method: obtained synthetically #3: Chemical | ChemComp-MG / Has ligand of interest | Y | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Thermus thermophilus wide pilus / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Source (natural) | Organism: Thermus thermophilus HB27 (bacteria) |
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: 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 / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 47.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2455 |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 84 ° / Axial rise/subunit: 11.25 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2763060 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 475441 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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