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- EMDB-61826: Cryo-EM structure of human hyaluronidase PH-20 -

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Basic information

Entry
Database: EMDB / ID: EMD-61826
TitleCryo-EM structure of human hyaluronidase PH-20
Map data
Sample
  • Complex: Complex of human hyaluronidase PH-20 and 79C11Fab
    • Complex: hyaluronidase PH-20
      • Protein or peptide: Hyaluronidase PH-20
    • Complex: 79C11Fab
      • Protein or peptide: Heavy chain of 79C11Fab
      • Protein or peptide: Light chain of 79C11Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordshyaluronidase / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsIm S-B / Jeong T-K / Kim N / Oh B-H
Funding support Korea, Republic Of, 2 items
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, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61826.png

Downloads & links

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Map

FileDownload / File: emd_61826.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 400 pix.
= 265.6 Å		0.66 Å/pix.
x 400 pix.
= 265.6 Å		0.66 Å/pix.
x 400 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.664 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.0531079 - 1.3568425
Average (Standard dev.)-0.00011516294 (±0.021123983)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 265.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61826_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61826_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of human hyaluronidase PH-20 and 79C11Fab

EntireName: Complex of human hyaluronidase PH-20 and 79C11Fab
Components
  • Complex: Complex of human hyaluronidase PH-20 and 79C11Fab
    • Complex: hyaluronidase PH-20
      • Protein or peptide: Hyaluronidase PH-20
    • Complex: 79C11Fab
      • Protein or peptide: Heavy chain of 79C11Fab
      • Protein or peptide: Light chain of 79C11Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of human hyaluronidase PH-20 and 79C11Fab

SupramoleculeName: Complex of human hyaluronidase PH-20 and 79C11Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 90 KDa

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Supramolecule #2: hyaluronidase PH-20

SupramoleculeName: hyaluronidase PH-20 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: 79C11Fab

SupramoleculeName: 79C11Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Hyaluronidase PH-20

MacromoleculeName: Hyaluronidase PH-20 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: hyaluronoglucosaminidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.610211 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: NFRAPPVIPN VPFLWAWNAP SEFCLGKFDE PLDMSLFSFI GSPRINATGQ GVTIFYVDRL GYYPYIDSIT GVTVNGGIPQ KISLQDHLD KAKKDITFYM PVDNLGMAVI DWEEWRPTWA RNWKPKDVYK NRSIELVQQQ NVQLSLTEAT EKAKQEFEKA G KDFLVETI ...String:
NFRAPPVIPN VPFLWAWNAP SEFCLGKFDE PLDMSLFSFI GSPRINATGQ GVTIFYVDRL GYYPYIDSIT GVTVNGGIPQ KISLQDHLD KAKKDITFYM PVDNLGMAVI DWEEWRPTWA RNWKPKDVYK NRSIELVQQQ NVQLSLTEAT EKAKQEFEKA G KDFLVETI KLGKLLRPNH LWGYYLFPDC YNHHYKKPGY NGSCFNVEIK RNDDLSWLWN ESTALYPSIY LNTQQSPVAA TL YVRNRVR EAIRVSKIPD AKSPLPVFAY TRIVFTDQVL KFLSQDELVY TFGETVALGA SGIVIWGTLS IMRSMKSCLL LDN YMETIL NPYIINVTLA AKMCSQVLCQ EQGVCIRKNW NSSDYLHLNP DNFAIQLEKG GKFTVRGKPT LEDLEQFSEK FYCS CYSTL S

UniProtKB: Hyaluronidase PH-20

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Macromolecule #2: Heavy chain of 79C11Fab

MacromoleculeName: Heavy chain of 79C11Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 22.664252 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QSVEESGGRL VTPGGSLTLT CTVSGFSLSS NAISWVRQAP GKGLEYIGII STSGSTYYAN WAKGRFTISK TSTTVDLKMT SLTTEDTAT YFCARDGAYD DFAYYFDLWG QGTLVTVSSG QPKAPSVFPL APCCGDTPSS TVTLGCLVKG YLPEPVTVTW N SGTLTNGV ...String:
QSVEESGGRL VTPGGSLTLT CTVSGFSLSS NAISWVRQAP GKGLEYIGII STSGSTYYAN WAKGRFTISK TSTTVDLKMT SLTTEDTAT YFCARDGAYD DFAYYFDLWG QGTLVTVSSG QPKAPSVFPL APCCGDTPSS TVTLGCLVKG YLPEPVTVTW N SGTLTNGV RTFPSVRQSS GLYSLSSVVS VTSSSQPVTC NVAHPATNTK VDKTVAPS

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Macromolecule #3: Light chain of 79C11Fab

MacromoleculeName: Light chain of 79C11Fab / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 22.270688 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: ALVMTQTPSS VSAAVGGTVT INCQASQNIY SGLAWYQQKL GQPPKLLIYK ASTLASGVPS RFKGSGSGTQ FTLTISGVQC DDAATYYCQ LAYSSTNVDN AFGGGTEVVV KGDPVAPTVL IFPPAADQVA TGTVTIVCVA NKYFPDVTVT WEVDGTTQTT G IENSKTPQ ...String:
ALVMTQTPSS VSAAVGGTVT INCQASQNIY SGLAWYQQKL GQPPKLLIYK ASTLASGVPS RFKGSGSGTQ FTLTISGVQC DDAATYYCQ LAYSSTNVDN AFGGGTEVVV KGDPVAPTVL IFPPAADQVA TGTVTIVCVA NKYFPDVTVT WEVDGTTQTT G IENSKTPQ NSADCTYNLS STLTLTSTQY NSHKEYTCKV TQGTTSVVQS FNRG

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 69.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 278638
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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