+Open data
-Basic information
Entry | Database: PDB / ID: 7ui7 | ||||||||||||
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Title | CryoEM structure of LARGE1 from C2 reconstruction | ||||||||||||
Components | Xylosyl- and glucuronyltransferase LARGE1 | ||||||||||||
Keywords | TRANSFERASE / Glycosyltransferase / Metalloenzyme | ||||||||||||
Function / homology | Function and homology information post-embryonic hindlimb morphogenesis / Defective LARGE causes MDDGA6 and MDDGB6 / xylosyltransferase activity / walking behavior / Transferases; Glycosyltransferases / glycosphingolipid biosynthetic process / principal sensory nucleus of trigeminal nerve development / striated muscle cell development / connective tissue development / skeletal muscle organ development ...post-embryonic hindlimb morphogenesis / Defective LARGE causes MDDGA6 and MDDGB6 / xylosyltransferase activity / walking behavior / Transferases; Glycosyltransferases / glycosphingolipid biosynthetic process / principal sensory nucleus of trigeminal nerve development / striated muscle cell development / connective tissue development / skeletal muscle organ development / O-linked glycosylation / glucuronosyltransferase activity / UDP-xylosyltransferase activity / localization of cell / protein O-linked mannosylation / reactive gliosis / glycoprotein biosynthetic process / N-acetylglucosamine metabolic process / neuromuscular process controlling posture / retina layer formation / acetylglucosaminyltransferase activity / water transport / plasma membrane organization / retina vasculature development in camera-type eye / basement membrane organization / neuromuscular synaptic transmission / skeletal muscle fiber differentiation / skeletal muscle tissue regeneration / nerve development / hexosyltransferase activity / dentate gyrus development / protein O-linked glycosylation / astrocyte differentiation / synaptic assembly at neuromuscular junction / cardiac muscle cell development / acetylcholine receptor signaling pathway / protein targeting to membrane / Transferases; Glycosyltransferases; Hexosyltransferases / muscle cell cellular homeostasis / glycosyltransferase activity / blood vessel development / protein glycosylation / macrophage differentiation / Transferases; Glycosyltransferases; Pentosyltransferases / response to light stimulus / behavioral fear response / skeletal muscle fiber development / striated muscle contraction / response to mechanical stimulus / cytoskeleton organization / potassium ion transmembrane transport / myelination / bone development / post-translational protein modification / protein localization to plasma membrane / determination of adult lifespan / intracellular protein transport / long-term synaptic potentiation / sensory perception of sound / neuron migration / neuromuscular junction / multicellular organism growth / memory / manganese ion binding / gene expression / protein-containing complex assembly / Golgi membrane / Golgi apparatus / protein-containing complex / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
Authors | Schnicker, N.J. / Joseph, S. / Campbell, K.P. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: CryoEM structure of LARGE1 from C2 reconstruction Authors: Campbell, K.P. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ui7.cif.gz | 479.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ui7.ent.gz | 399.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ui7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ui7_validation.pdf.gz | 984 KB | Display | wwPDB validaton report |
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Full document | 7ui7_full_validation.pdf.gz | 1004.6 KB | Display | |
Data in XML | 7ui7_validation.xml.gz | 52 KB | Display | |
Data in CIF | 7ui7_validation.cif.gz | 75.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/7ui7 ftp://data.pdbj.org/pub/pdb/validation_reports/ui/7ui7 | HTTPS FTP |
-Related structure data
Related structure data | 26541MC 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: 89806.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LARGE1, KIAA0609, LARGE / Production host: Homo sapiens (human) References: UniProt: O95461, Transferases; Glycosyltransferases, Transferases; Glycosyltransferases; Pentosyltransferases, Transferases; Glycosyltransferases; Hexosyltransferases #2: Chemical | ChemComp-MN / Has ligand of interest | Y | |
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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: LARGE1 / Type: COMPLEX / Details: No transmembrane region / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.211 MDa / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 6.6 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.664 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1742250 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107895 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL / Details: Used initial model from Alphafold2 | ||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.4 Å / Cross valid method: NONE | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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