7Q5D | pdb_00007q5d

Structure of EPCR in a non-canonical conformation

PDB DOI: https://doi.org/10.2210/pdb7Q5D/pdb

Classification: BLOOD CLOTTING
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2021-11-03 Released: 2022-09-14
Deposition Author(s): Lopez-Sagaseta, J., Erausquin, E.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.195 (Depositor), 0.200 (DCC)
R-Value Work:
0.183 (Depositor), 0.186 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural vulnerability in EPCR suggests functional modulation.

Erausquin, E., Rodriguez-Fernandez, A., Rodriguez-Lumbreras, L.A., Fernandez-Recio, J., Dichiara-Rodriguez, M.G., Lopez-Sagaseta, J.

(2024) Sci Rep 14: 2591-2591

PubMed: 38297105 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41598-024-53160-7
Primary Citation Related Structures:
7Q5D

PubMed Abstract:
The endothelial protein C receptor (EPCR) is a fundamental component of the vascular system in mammals due to its contribution in maintaining blood in a non-prothrombotic state, which is crucial for overall life development. It accomplishes this by enhancing the conversion of protein C (PC) into the anticoagulant activated protein C (APC), with this property being dependent on a known EPCR conformation that enables direct interaction with PC/APC. In this study, we report a previously unidentified conformation of EPCR whereby Tyr154, critical for PC/APC binding, shows a striking non-canonical configuration. This unconventional form is incompatible with PC/APC binding, and reveals, for the first time, a region of structural vulnerability and potential modulation in EPCR. The identification of this malleability enhances our understanding of this receptor, prompting inquiries into the interplay between its plasticity and function, as well as its significance within the broader framework of EPCR's biology, which extends to immune conditions.

Organizational Affiliation

Unit of Protein Crystallography and Structural Immunology, Navarrabiomed, 31008, Navarra, Spain.

Macromolecule Content

Total Structure Weight: 24 kDa
Atom Count: 1,575
Modeled Residue Count: 173
Deposited Residue Count: 195
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothelial protein C receptor	A	195	Homo sapiens	Mutation(s): 0 Gene Names: PROCR, EPCR
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNN8 (Homo sapiens) Explore Q9UNN8 Go to UniProtKB: Q9UNN8
PHAROS: Q9UNN8 GTEx: ENSG00000101000
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UNN8
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A	Go to GlyGen: Q9UNN8-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTY Query on PTY Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CYS Query on CYS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CYSTEINE C₃ H₇ N O₂ S XUJNEKJLAYXESH-REOHCLBHSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.195 (Depositor), 0.200 (DCC)
R-Value Work: 0.183 (Depositor), 0.186 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.47	α = 90
b = 70.47	β = 90
c = 96.635	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-09-14

Deposition Author(s):

Lopez-Sagaseta, J.

Erausquin, E.

Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	PGC2018-094894-B-I00
Spanish Ministry of Science, Innovation, and Universities	Spain	RYC-2017-21683

Revision History (Full details and data files)

Version 1.0: 2022-09-14
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary
Version 1.3: 2026-08-12
Changes: Database references