9JUB

Cryo-EM structure of human hyaluronidase PH-20

• PDB DOI: https://doi.org/10.2210/pdb9JUB/pdb
• EM Map EMD-61826: EMDB EMDataResource

• Classification: HYDROLASE/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Oryctolagus cuniculus
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2024-10-07 Released: 2024-10-30 
• Deposition Author(s): Im, S.-B., Jeong, T.-K., Kim, N., Oh, B.-H.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of human hyaluronidase PH-20

Im, S.-B., Jeong, T.-K., Kim, N., Oh, B.-H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 92.63 kDa 
• Atom Count: 6,479 
• Modelled Residue Count: 829 
• Deposited Residue Count: 834 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hyaluronidase PH-20	A	406	Homo sapiens	Mutation(s): 0  Gene Names: SPAM1, HYAL3, PH20 EC: 3.2.1.35
UniProt & NIH Common Fund Data Resources
Find proteins for P38567 (Homo sapiens) Explore P38567  Go to UniProtKB:  P38567
GTEx:  ENSG00000106304
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P38567-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of 79C11Fab	B	216	Oryctolagus cuniculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of 79C11Fab	C	212	Oryctolagus cuniculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-30 
Deposition Author(s): Im, S.-B., Jeong, T.-K., Kim, N., Oh, B.-H.

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Funding Organization	Location	Grant Number
Other government	Korea, Republic Of	2023R1A2C3007329
Other government	Korea, Republic Of	NRF-2021M3A9G8025599

Revision History  

• Version 1.0: 2024-10-30
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection