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- PDB-7ui7: CryoEM structure of LARGE1 from C2 reconstruction -

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Basic information

Entry
Database: PDB / ID: 7ui7
TitleCryoEM structure of LARGE1 from C2 reconstruction
ComponentsXylosyl- and glucuronyltransferase LARGE1
KeywordsTRANSFERASE / Glycosyltransferase / Metalloenzyme
Function / homology
Function and homology information


post-embryonic hindlimb morphogenesis / Defective LARGE causes MDDGA6 and MDDGB6 / principal sensory nucleus of trigeminal nerve development / xylosyltransferase activity / walking behavior / connective tissue development / Transferases; Glycosyltransferases / glycosphingolipid biosynthetic process / O-linked glycosylation / skeletal muscle organ development ...post-embryonic hindlimb morphogenesis / Defective LARGE causes MDDGA6 and MDDGB6 / principal sensory nucleus of trigeminal nerve development / xylosyltransferase activity / walking behavior / connective tissue development / Transferases; Glycosyltransferases / glycosphingolipid biosynthetic process / O-linked glycosylation / skeletal muscle organ development / glucuronosyltransferase activity / UDP-xylosyltransferase activity / synaptic assembly at neuromuscular junction / localization of cell / protein O-linked glycosylation via mannose / reactive gliosis / N-acetylglucosamine metabolic process / glycoprotein biosynthetic process / neuromuscular process controlling posture / acetylglucosaminyltransferase activity / water transport / plasma membrane organization / retina layer formation / retina vasculature development in camera-type eye / skeletal muscle fiber differentiation / nerve development / basement membrane organization / hexosyltransferase activity / neuromuscular synaptic transmission / dentate gyrus development / skeletal muscle tissue regeneration / protein O-linked glycosylation / astrocyte differentiation / cardiac muscle cell development / acetylcholine receptor signaling pathway / protein targeting to membrane / Transferases; Glycosyltransferases; Hexosyltransferases / muscle cell cellular homeostasis / : / blood vessel development / glycosyltransferase activity / response to light stimulus / macrophage differentiation / Transferases; Glycosyltransferases; Pentosyltransferases / response to mechanical stimulus / behavioral fear response / striated muscle contraction / skeletal muscle fiber development / myelination / cytoskeleton organization / potassium ion transmembrane transport / post-translational protein modification / determination of adult lifespan / protein localization to plasma membrane / neuromuscular junction / intracellular protein transport / sensory perception of sound / bone development / multicellular organism growth / memory / long-term synaptic potentiation / neuron migration / manganese ion binding / protein-containing complex assembly / gene expression / Golgi membrane / Golgi apparatus / protein-containing complex / plasma membrane
Similarity search - Function
: / Glycosyl-transferase for dystroglycan / Glycosyl transferase, family 8 / Glycosyl transferase family 8 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
: / Xylosyl- and glucuronyltransferase LARGE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSchnicker, N.J. / Joseph, S. / Campbell, K.P.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)U54NS053672 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
CitationJournal: To Be Published
Title: CryoEM structure of LARGE1 from C2 reconstruction
Authors: Campbell, K.P.
History
DepositionMar 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xylosyl- and glucuronyltransferase LARGE1
B: Xylosyl- and glucuronyltransferase LARGE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,8326
Polymers179,6122
Non-polymers2204
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, light scattering
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Xylosyl- and glucuronyltransferase LARGE1 / Acetylglucosaminyltransferase-like 1A / Glycosyltransferase-like protein / LARGE xylosyl- and ...Acetylglucosaminyltransferase-like 1A / Glycosyltransferase-like protein / LARGE xylosyl- and glucuronyltransferase 1


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 / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: LARGE1 / Type: COMPLEX / Details: No transmembrane region / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.211 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 6.6
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 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 holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.664 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3.33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 1742250
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107895 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Details: Used initial model from Alphafold2
RefinementHighest resolution: 3.4 Å / Cross valid method: NONE
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003710490
ELECTRON MICROSCOPYf_angle_d0.577614222
ELECTRON MICROSCOPYf_chiral_restr0.0411530
ELECTRON MICROSCOPYf_plane_restr0.0041798
ELECTRON MICROSCOPYf_dihedral_angle_d4.89881366

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