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- EMDB-40591: Xenopus laevis hyaluronan synthase 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-40591
TitleXenopus laevis hyaluronan synthase 1
Map dataXenopus laevis hyaluronan synthase 1
Sample
  • Complex: Xenopus laevis hyaluronan synthase 1 in complex with a Fab molecule
    • Protein or peptide: Hyaluronan synthase 1
    • Protein or peptide: Fab15 heavy chain
    • Protein or peptide: Fab15 light chain
Keywordshyaluronic 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGorniak I / Zimmer J
Funding support United States, Germany, 3 items
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 ZS / Erramilli SK / Gawda T / Kossiakoff AA / Zimmer J
History
DepositionApr 26, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40591.png

Downloads & links

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Map

FileDownload / File: emd_40591.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationXenopus laevis hyaluronan synthase 1
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.238
Minimum - Maximum-1.9089223 - 2.9916883
Average (Standard dev.)-0.00042717895 (±0.038553465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_40591_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_40591_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Xenopus laevis hyaluronan synthase 1 in complex with a Fab molecule

EntireName: Xenopus laevis hyaluronan synthase 1 in complex with a Fab molecule
Components
  • Complex: Xenopus laevis hyaluronan synthase 1 in complex with a Fab molecule
    • Protein or peptide: Hyaluronan synthase 1
    • Protein or peptide: Fab15 heavy chain
    • Protein or peptide: Fab15 light chain

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Supramolecule #1: Xenopus laevis hyaluronan synthase 1 in complex with a Fab molecule

SupramoleculeName: Xenopus laevis hyaluronan synthase 1 in complex with a Fab molecule
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 118 KDa

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Macromolecule #1: Hyaluronan synthase 1

MacromoleculeName: Hyaluronan synthase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: hyaluronan synthase
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 70.385047 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHH HHHMKEKAAE TMEIPEGIPK DLEPKHPTLW RIIYYSFGVV LLATITAAYV AEFQVLKHEA ILFSLGLYGL AMLLHLMMQ SLFAFLEIRR VNKSELPCSF KKTVALTIAG YQENPEYLIK CLESCKYVKY PKDKLKIILV IDGNTEDDAY M MEMFKDVF ...String:
MHHHHHHHHH HHHMKEKAAE TMEIPEGIPK DLEPKHPTLW RIIYYSFGVV LLATITAAYV AEFQVLKHEA ILFSLGLYGL AMLLHLMMQ SLFAFLEIRR VNKSELPCSF KKTVALTIAG YQENPEYLIK CLESCKYVKY PKDKLKIILV IDGNTEDDAY M MEMFKDVF HGEDVGTYVW KGNYHTVKKP EETNKGSCPE VSKPLNEDEG INMVEELVRN KRCVCIMQQW GGKREVMYTA FQ AIGTSVD YVQVCDSDTK LDELATVEMV KVLESNDMYG AVGGDVRILN PYDSFISFMS SLRYWMAFNV ERACQSYFDC VSC ISGPLG MYRNNILQVF LEAWYRQKFL GTYCTLGDDR HLTNRVLSMG YRTKYTHKSR AFSETPSLYL RWLNQQTRWT KSYF REWLY NAQWWHKHHI WMTYESVVSF IFPFFITATV IRLIYAGTIW NVVWLLLCIQ IMSLFKSIYA CWLRGNFIML LMSLY SMLY MTGLLPSKYF ALLTLNKTGW GTSGRKKIVG NYMPILPLSI WAAVLCGGVG YSIYMDCQND WSTPEKQKEM YHLLYG CVG YVMYWVIMAV MYWVWVKRCC RKRSQTVTLV HDIPDMCV

UniProtKB: Hyaluronan synthase 1

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Macromolecule #2: Fab15 heavy chain

MacromoleculeName: Fab15 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.674379 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSSYYIHWV RQAPGKGLEW VASISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSGYYWGPY FGGFDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSSYYIHWV RQAPGKGLEW VASISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSGYYWGPY FGGFDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPKS CDKTHT

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Macromolecule #3: Fab15 light chain

MacromoleculeName: Fab15 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.258783 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSSSLITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSSSLITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration8 mg/mL
BufferpH: 7.8
Component:
ConcentrationNameFormula
20.0 mMtris(hydroxymethyl)aminomethane
150.0 mMsodium chlorideNaClSodium chloride
0.01 %glyco-diosgeninGDN
GridModel: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
Details: Glow discharged in the presence of 1 drop of amylamine
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 20.0 µm / Nominal defocus min: 10.0 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6543217
Startup modelType of model: INSILICO MODEL
In silico model: Alphafold2 prediction of Xenopus laevis hyaluronan synthase 1
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 305106

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8smm:
Xenopus laevis hyaluronan synthase 1

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