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- PDB-8snd: Chlorella virus Hyaluronan Synthase bound to GlcNAc primer and UD... -

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Basic information

Entry
Database: PDB / ID: 8snd
TitleChlorella virus Hyaluronan Synthase bound to GlcNAc primer and UDP-GlcA
Components
  • Hyaluronan synthase
  • Nanobody 872
  • Nanobody 881
KeywordsTRANSFERASE / hyaluronic acid / hyaluronan / HA / HAS / glycosyltransferase / GT / membrane protein / nanobody / n-acetylglucosamine / glucuronic acid
Function / homology
Function and homology information


hyaluronan synthase activity / extracellular matrix assembly / hyaluronan biosynthetic process / : / membrane
Similarity search - Function
Glycosyltransferase like family 2 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / : / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / CHOLESTEROL HEMISUCCINATE / Hyaluronan synthase
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus CZ-2
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsStephens, Z. / Zimmer, J.
Funding support United States, 2items
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
CitationJournal: To Be Published
Title: Molecular insights into hyaluronan synthesis, secretion, and length control
Authors: Gorniak, I. / Stephens, Z. / Erramilli, S.K. / Gawda, T. / Kossiakoff, A.A. / Zimmer, J.
History
DepositionApr 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: 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: Hyaluronan synthase
B: Nanobody 872
C: Nanobody 881
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0749
Polymers95,9283
Non-polymers2,1466
Water1448
1


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

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Components

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Antibody , 2 types, 2 molecules BC

#2: Antibody Nanobody 872


Mass: 14783.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli K-12 (bacteria)
#3: Antibody Nanobody 881


Mass: 15255.735 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli K-12 (bacteria)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Hyaluronan synthase


Mass: 65889.078 Da / Num. of mol.: 1 / Mutation: D302N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium bursaria Chlorella virus CZ-2
Gene: CZ-2_118R / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M1H2Q1
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 13 molecules

#4: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C41H82NO8P / Comment: phospholipid*YM
#6: Chemical ChemComp-UGA / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-GLUCURONIC ACID


Mass: 580.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N2O18P2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4
#8: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

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: Ternary complex of Chlorella virus hyaluronan synthase bound to nanobodies 872 and 881
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 97.14 kDa/nm / Experimental value: NO
Source (natural)Organism: Paramecium bursaria Chlorella virus 1
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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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 FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176543 / Symmetry type: POINT

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