5ZNN | pdb_00005znn

Crystal structure of ligand-free form of the Vps10 ectodomain of Sortilin

PDB DOI: https://doi.org/10.2210/pdb5ZNN/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Mus musculus
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2018-04-10 Released: 2018-07-18
Deposition Author(s): Yabe-Wada, T., Unno, M.
Funding Organization(s): Japan Society for the Promotion of Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.217 (Depositor), 0.218 (DCC)
R-Value Work:
0.180 (Depositor), 0.181 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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Literature

Crystal structure of the ligand-free form of the Vps10 ectodomain of dimerized Sortilin at acidic pH

Yabe-Wada, T., Matsuba, S., Unno, M., Onai, N.

(2018) FEBS Lett 592: 2647-2657

PubMed: 29972886 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.13181
Primary Citation Related Structures:
5ZNN

PubMed Abstract:
Sortilin is a multifunctional sorting receptor involved in cytokine production in immune cells. To understand the mechanism of Sortilin-mediated cytokine trafficking, we determined the 2.45-Å structure of the dimerized Sortilin ectodomain (sSortilin or the Vps10-domain) crystallized at acidic pH. Substantial conformational changes upon dimerization lead to the intermolecular hydrophobic interaction between the conserved E455 and F137. Analysis of the electrostatic surface and size-exclusion chromatography revealed that sSortilin dimerization occurs due to an increase in hydrophobic interactions at the neutral dimer interface at acidic pH. The N682-attached N-glycan in the vicinity of the dimer interface implies its involvement in the dimerization. The disruption of Sortilin dimerization by mutations impairs efficient interferon-alpha secretion from cells. These results suggest the functional importance of Sortilin dimerization in cytokine trafficking.

Organizational Affiliation

Department of Immunology, Kanazawa Medical University, Uchinada, Japan.

Macromolecule Content

Total Structure Weight: 155.58 kDa
Atom Count: 10,780
Modeled Residue Count: 1,293
Deposited Residue Count: 1,358
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sortilin	A, B	679	Mus musculus	Mutation(s): 0 Gene Names: Sort1
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PHU5 (Mus musculus) Explore Q6PHU5 Go to UniProtKB: Q6PHU5
IMPC: MGI:1338015
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6PHU5
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q6PHU5-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
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	C, E, F, G	3		N-Glycosylation	Interactions Focus chain C Focus chain E Focus chain F Focus chain G Interactions & Density Focus chain C Focus chain E Focus chain F Focus chain G
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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

Small Molecules

Ligands 3 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 B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] MOL2 format, chain S [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] mmCIF format, chain S [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A]	M [auth A], N [auth A], O [auth A], S [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth B] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A], L [auth A], Q [auth B], R [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.217 (Depositor), 0.218 (DCC)
R-Value Work: 0.180 (Depositor), 0.181 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.264	α = 90
b = 138.496	β = 90
c = 146.68	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-07-18

Deposition Author(s):

Yabe-Wada, T.

Unno, M.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	--

Revision History (Full details and data files)

Version 1.0: 2018-07-18
Type: Initial release
Version 1.1: 2018-09-19
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-22
Changes: Data collection, Database references, Refinement description, Structure summary
Version 3.0: 2025-09-17
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary