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- PDB-9jub: Cryo-EM structure of human hyaluronidase PH-20 -

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Basic information

Entry
Database: PDB / ID: 9jub
TitleCryo-EM structure of human hyaluronidase PH-20
Components
  • Heavy chain of 79C11Fab
  • Hyaluronidase PH-20
  • Light chain of 79C11Fab
KeywordsHYDROLASE/IMMUNE SYSTEM / hyaluronidase / endoglycosidase hydrolase / fab complex / HYDROLASE / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


hyaluronoglucosaminidase / Interaction With Cumulus Cells And The Zona Pellucida / fusion of sperm to egg plasma membrane involved in single fertilization / hyalurononglucosaminidase activity / hyaluronan catabolic process / binding of sperm to zona pellucida / side of membrane / acrosomal vesicle / carbohydrate metabolic process / cell adhesion / plasma membrane
Similarity search - Function
Hyaluronidase PH20/Hyaluronidase-5 / Hyaluronidase / Hyaluronidase / Aldolase-type TIM barrel / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsIm, S.-B. / Jeong, T.-K. / Kim, N. / Oh, B.-H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Other government2023R1A2C3007329 Korea, Republic Of
Other governmentNRF-2021M3A9G8025599 Korea, Republic Of
CitationJournal: Proteins / Year: 2025
Title: Cryo-EM Structure of Human Hyaluronidase PH-20.
Authors: Seong-Bin Im / Hyung Nam Song / Tae-Kyeong Jeong / Nayun Kim / Kyuwan Kim / Soon-Jae Park / Byung-Ha Oh /
Abstract: PH-20 is a specific type of hyaluronidase that plays a critical role in the fertilization process by facilitating the initial binding of sperm to the glycoprotein layer surrounding the oocyte and ...PH-20 is a specific type of hyaluronidase that plays a critical role in the fertilization process by facilitating the initial binding of sperm to the glycoprotein layer surrounding the oocyte and subsequently breaking down hyaluronic acid polymers in the cumulus cell layer. PH-20 contains an epidermal growth factor (EGF)-like domain, which may be involved in the recognition of the glycoprotein layer in addition to the catalytic domain. Herein, we report the structure of human PH-20 determined by cryogenic electron microscopy. Comparative analyses of the PH-20 structure with two other available hyaluronidase structures reveal a general similarity in the central catalytic domains, including the conservation of catalytically essential residues at the equivalent spatial positions. However, unique difference is found in the EGF-like domain, characterized by a longer sequence that is likely to form a flexibly anchored β-hairpin containing a disulfide bond.
History
DepositionOct 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update
Revision 1.2Jan 15, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.3Apr 16, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hyaluronidase PH-20
B: Heavy chain of 79C11Fab
C: Light chain of 79C11Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6337
Polymers91,5453
Non-polymers1,0884
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Hyaluronidase PH-20 / Hyal-PH20 / Hyaluronoglucosaminidase PH-20 / Sperm adhesion molecule 1 / Sperm surface protein PH-20


Mass: 46610.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPAM1, HYAL3, PH20 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P38567, hyaluronoglucosaminidase
#2: Protein Heavy chain of 79C11Fab


Mass: 22664.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Light chain of 79C11Fab


Mass: 22270.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Cricetulus griseus (Chinese hamster)
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#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.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
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
Has ligand of interestN
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

Component
IDNameTypeEntity IDParent-IDSource
1Complex of human hyaluronidase PH-20 and 79C11FabCOMPLEX#1-#30RECOMBINANT
2hyaluronidase PH-20COMPLEX#11RECOMBINANT
379C11FabCOMPLEX#2-#31RECOMBINANT
Molecular weightValue: 0.09 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Oryctolagus cuniculus (rabbit)9986
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2300 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 69 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (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: 278638 / Symmetry type: POINT

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