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- EMDB-43269: Cryo-EM structure of heparosan synthase 2 from Pasteurella multoc... -

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Basic information

Entry
Database: EMDB / ID: EMD-43269
TitleCryo-EM structure of heparosan synthase 2 from Pasteurella multocida with polysaccharide in the GlcNAc-T active site
Map dataPhenix auto-sharpened map, scaled 0.9578358 from original
Sample
  • Organelle or cellular component: pmHS2 with 7-mer polysaccharide
    • Protein or peptide: Heparosan synthase B
  • Ligand: MANGANESE (II) ION
  • Ligand: URIDINE-5'-DIPHOSPHATE
  • Ligand: water
Keywordspolysaccharide synthase / complex / TRANSFERASE
Function / homologyGlycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases / Heparosan synthase B
Function and homology information
Biological speciesPasteurella multocida (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKrahn JM / Pedersen LC / Liu J / Stancanelli E / Borgnia M / Vivarette E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIC ES102645 United States
CitationJournal: Acs Catalysis / Year: 2024
Title: Structural and Functional Analysis of Heparosan Synthase 2 from Pasteurella multocida to Improve the Synthesis of Heparin
Authors: Stancanelli E / Krahn JA / Viverette E / Dutcher R / Pagadala V / Borgnia MJ / Liu J / Pedersen LC
History
DepositionJan 5, 2024-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43269.png

Downloads & links

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Map

FileDownload / File: emd_43269.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhenix auto-sharpened map, scaled 0.9578358 from original
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.28 Å/pix.
x 256 pix.
= 328.576 Å		1.28 Å/pix.
x 256 pix.
= 328.576 Å		1.28 Å/pix.
x 256 pix.
= 328.576 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.9
Minimum - Maximum-29.514887000000002 - 39.405926000000001
Average (Standard dev.)0.000000000009368 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 328.576 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A, scaled 0.9578358 from original

Fileemd_43269_half_map_1.map
AnnotationHalf map A, scaled 0.9578358 from original
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A, scaled 0.9578358 from original

Fileemd_43269_half_map_2.map
AnnotationHalf map A, scaled 0.9578358 from original
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : pmHS2 with 7-mer polysaccharide

EntireName: pmHS2 with 7-mer polysaccharide
Components
  • Organelle or cellular component: pmHS2 with 7-mer polysaccharide
    • Protein or peptide: Heparosan synthase B
  • Ligand: MANGANESE (II) ION
  • Ligand: URIDINE-5'-DIPHOSPHATE
  • Ligand: water

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Supramolecule #1: pmHS2 with 7-mer polysaccharide

SupramoleculeName: pmHS2 with 7-mer polysaccharide / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pasteurella multocida (bacteria)

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Macromolecule #1: Heparosan synthase B

MacromoleculeName: Heparosan synthase B / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Pasteurella multocida (bacteria)
Molecular weightTheoretical: 64.548277 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSAAADKQTT SITDLYNEVA KSDLGLVKET NSANPLVSII MTSHNTAQFI EASINSLLLQ TYKNIEIIIV DDDSSDNTFE IASRIANTT SKVRVFRLNS NLGTYFAKNT GILKSKGDII FFQDSDDVCH HERIERCVNI LLANKETIAV RCAYSRLAPE T QHIIKVNN ...String:
GSAAADKQTT SITDLYNEVA KSDLGLVKET NSANPLVSII MTSHNTAQFI EASINSLLLQ TYKNIEIIIV DDDSSDNTFE IASRIANTT SKVRVFRLNS NLGTYFAKNT GILKSKGDII FFQDSDDVCH HERIERCVNI LLANKETIAV RCAYSRLAPE T QHIIKVNN MDYRLGFITL GMHRKVFQEI GFFNCTTKGS DDEFFHRIAK YYGKEKIKNL LLPLYYNTMR ENSLFTDMVE WI DNHNIIQ KMSDTRQHYA TLFQAMHNET ASHDFKNLFQ FPRIYDALPV PQEMSKLSNP KIPVYINICS IPSRIAQLRR IIG ILKNQC DHFHIYLDGY VEIPDFIKNL GNKATVVHCK DKDNSIRDNG KFILLEELIE KNQDGYYITC DDDIIYPSDY INTM IKKLN EYDDKAVIGL HGILFPSRMT KYFSADRLVY SFYKPLEKDK AVNVLGTGTV SFRVSLFNQF SLSDFTHSGM ADIYF SLLC KKNNILQICI SRPANWLTED NRDSETLYHQ YRDNDEQQTQ LIMENGPWGY SSIYPLVKNH PKFTDLIPCL PFYFL

UniProtKB: Heparosan synthase B

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Macromolecule #3: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #4: URIDINE-5'-DIPHOSPHATE

MacromoleculeName: URIDINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 8 / Formula: UDP
Molecular weightTheoretical: 404.161 Da
Chemical component information

ChemComp-UDP:
URIDINE-5'-DIPHOSPHATE / UDP*YM

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Details: 25 mM Tris pH 7.5, 87.5 mM NaCl, 1 mM MnCl2, 1 mM UDP and 1 mM NS-7mer (GlcA-GlcNS-GlcA-GlcNS-GlcA-GlcNS-GlcA-pNP)
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 4544 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 169 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 104255
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 200 / Avg.num./class: 542 / Software - Name: cryoSPARC (ver. 4.3.1)
FSC plot (resolution estimation)

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