[English] 日本語
Yorodumi
- PDB-7ui7: CryoEM structure of LARGE1 from C2 reconstruction -

+
Open data


ID or keywords:

Loading...

-
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 / xylosyltransferase activity / principal sensory nucleus of trigeminal nerve development / connective tissue development / Transferases; Glycosyltransferases / walking behavior / glycosphingolipid biosynthetic process / O-linked glycosylation / skeletal muscle organ development ...post-embryonic hindlimb morphogenesis / Defective LARGE causes MDDGA6 and MDDGB6 / xylosyltransferase activity / principal sensory nucleus of trigeminal nerve development / connective tissue development / Transferases; Glycosyltransferases / walking behavior / glycosphingolipid biosynthetic process / O-linked glycosylation / skeletal muscle organ development / glucuronosyltransferase activity / UDP-xylosyltransferase activity / localization of cell / protein O-linked mannosylation / glycoprotein biosynthetic process / N-acetylglucosamine metabolic process / reactive gliosis / neuromuscular process controlling posture / acetylglucosaminyltransferase activity / retina layer formation / water transport / plasma membrane organization / retina vasculature development in camera-type eye / skeletal muscle fiber differentiation / basement membrane organization / nerve development / hexosyltransferase activity / neuromuscular synaptic transmission / dentate gyrus development / skeletal muscle tissue regeneration / protein O-linked glycosylation / astrocyte differentiation / synaptic assembly at neuromuscular junction / protein targeting to membrane / acetylcholine receptor signaling pathway / cardiac muscle cell development / Transferases; Glycosyltransferases; Hexosyltransferases / muscle cell cellular homeostasis / protein glycosylation / blood vessel development / glycosyltransferase activity / macrophage differentiation / Transferases; Glycosyltransferases; Pentosyltransferases / response to light stimulus / behavioral fear response / striated muscle contraction / response to mechanical stimulus / skeletal muscle fiber development / potassium ion transmembrane transport / cytoskeleton organization / myelination / post-translational protein modification / protein localization to plasma membrane / determination of adult lifespan / intracellular protein transport / sensory perception of sound / neuromuscular junction / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more