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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 8ZI4

This is version 1.1 of the entry. See complete history.

Literature

Structure of trypsinogen-engaged EP at 2.95 angstroms resolution

Song, Q.Y., Ding, Z.Y., Huang, H.J.

To be published.

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

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07477
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P98073
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain B [auth D]	Go to GlyGen: P98073-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P98073
Glycosylation
Glycosylation Sites: 11	Glycosylation Focus chain C [auth A]	Go to GlyGen: P98073-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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, D [auth B], E, L, M, N, O	3		N-Glycosylation	Interactions Focus chain D [auth B] Focus chain E Focus chain L Focus chain M Focus chain N Focus chain O Interactions & Density Focus chain D [auth B] Focus chain E Focus chain L Focus chain M Focus chain N Focus chain O
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain H Focus chain K Interactions & Density Focus chain H Focus chain K
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G73474XW GlyCosmos: G73474XW GlyGen: G73474XW

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A]	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		Interactions Focus chain P [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain P [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]

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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.