8ZI4 | pdb_00008zi4

Cryo-EM structure of wtEP-trypsinogen

• PDB DOI: https://doi.org/10.2210/pdb8ZI4/pdb
• EM Map EMD-60121: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-05-13 Released: 2025-05-21 
• Deposition Author(s): Song, Q.Y., Ding, Z.Y., Huang, H.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.95 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of trypsinogen-engaged EP at 2.95 angstroms resolution

Song, Q.Y., Ding, Z.Y., Huang, H.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 126.04 kDa 
• Atom Count: 8,818 
• Modeled Residue Count: 1,070 
• Deposited Residue Count: 1,070 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease 1	A [auth C]	232	Homo sapiens	Mutation(s): 0  EC: 3.4.21.4
UniProt & NIH Common Fund Data Resources
Find proteins for P07477 (Homo sapiens) Explore P07477  Go to UniProtKB:  P07477
PHAROS:  P07477 GTEx:  ENSG00000204983

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Enteropeptidase catalytic light chain	B [auth D]	235	Homo sapiens	Mutation(s): 3  Gene Names: TMPRSS15, ENTK, PRSS7 EC: 3.4.21.9
UniProt & NIH Common Fund Data Resources
Find proteins for P98073 (Homo sapiens) Explore P98073  Go to UniProtKB:  P98073
PHAROS:  P98073 GTEx:  ENSG00000154646
Glycosylation
Glycosylation Sites: 5		Go to GlyGen: P98073-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Enteropeptidase non-catalytic heavy chain	C [auth A]	603	Homo sapiens	Mutation(s): 0  Gene Names: TMPRSS15, ENTK, PRSS7 EC: 3.4.21.9
UniProt & NIH Common Fund Data Resources
Find proteins for P98073 (Homo sapiens) Explore P98073  Go to UniProtKB:  P98073
PHAROS:  P98073 GTEx:  ENSG00000154646
Glycosylation
Glycosylation Sites: 11		Go to GlyGen: P98073-1

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B], E, L, M, N, O	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, K	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC GlyCosmos:  G22573RC GlyGen:  G22573RC

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G73474XW GlyCosmos:  G73474XW GlyGen:  G73474XW

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	P [auth D], Q [auth A], R [auth A], S [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: 2.95 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Song, Q.Y., Ding, Z.Y., Huang, H.J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release
  
• Version 1.1: 2025-07-23
  Changes: Data collection