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- PDB-8smm: Xenopus laevis hyaluronan synthase 1 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8smm
TitleXenopus laevis hyaluronan synthase 1
Components
  • Fab15 heavy chain
  • Fab15 light chain
  • Hyaluronan synthase 1
KeywordsTransferase/Immune System / hyaluronic acid / hyaluronan / HA / HAS / glycosyltransferase / GT / membrane protein / Fab / Transferase-Immune System complex
Function / homologyhyaluronan synthase / Chitin synthase / hyaluronan synthase activity / extracellular matrix assembly / hyaluronan biosynthetic process / extracellular polysaccharide biosynthetic process / Nucleotide-diphospho-sugar transferases / membrane / Hyaluronan synthase 1
Function and homology information
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGorniak, I. / Zimmer, J.
Funding support United States, Germany, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM144130 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM117372 United States
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: To Be Published
Title: Atomistic insights into hyaluronan synthesis, secretion, and length control
Authors: Gorniak, I. / Stephens, Z.S. / Erramilli, S.K. / Gawda, T. / Kossiakoff, A.A. / Zimmer, J.
History
DepositionApr 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hyaluronan synthase 1
H: Fab15 heavy chain
L: Fab15 light chain


Theoretical massNumber of molelcules
Total (without water)118,3183
Polymers118,3183
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Hyaluronan synthase 1 / / DG42 protein / Hyaluronate synthase 1 / Hyaluronic acid synthase 1 / HA synthase 1 / xHAS1


Mass: 70385.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: has1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P13563, hyaluronan synthase
#2: Antibody Fab15 heavy chain


Mass: 24674.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Antibody Fab15 light chain


Mass: 23258.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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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: Xenopus laevis hyaluronan synthase 1 in complex with a Fab molecule
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.118 MDa / Experimental value: NO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMtris(hydroxymethyl)aminomethane1
2150 mMsodium chlorideNaClSodium chloride1
30.01 %glyco-diosgeninGDN1
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Glow discharged in the presence of 1 drop of amylamine
Grid material: COPPER / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 20000 nm / Nominal defocus min: 10000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 6543217
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 305106 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026156
ELECTRON MICROSCOPYf_angle_d0.4468350
ELECTRON MICROSCOPYf_dihedral_angle_d2.982825
ELECTRON MICROSCOPYf_chiral_restr0.038907
ELECTRON MICROSCOPYf_plane_restr0.0041022

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