3F6K | pdb_00003f6k

Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with neurotensin

PDB DOI: https://doi.org/10.2210/pdb3F6K/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): Yes

Deposited: 2008-11-06 Released: 2008-12-30
Deposition Author(s): Quistgaard, E.M., Madsen, P., Groftehauge, M.K., Nissen, P., Petersen, C.M., Thirup, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.229 (Depositor), 0.272 (DCC)
R-Value Work:
0.204 (Depositor)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 3.2 of the entry. See complete history.

Literature

Ligands bind to Sortilin in the tunnel of a ten-bladed beta-propeller domain.

Quistgaard, E.M., Madsen, P., Groftehauge, M.K., Nissen, P., Petersen, C.M., Thirup, S.S.

(2009) Nat Struct Mol Biol 16: 96-98

PubMed: 19122660 Search on PubMed
DOI: https://doi.org/10.1038/nsmb.1543
Primary Citation Related Structures:
3F6K

PubMed Abstract:
The structure of the Sortilin ectodomain in complex with neurotensin has been determined at 2-A resolution, revealing that the C-terminal part of neurotensin binds in the tunnel of a ten-bladed beta-propeller domain. Binding competition studies suggest that additional binding sites, for example, for the prodomain of nerve growth factor-beta, are present in the tunnel and that competition for binding relates to the restricted space inside the propeller.

Organizational Affiliation

MIND Centre, Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK 8000 Arhus C, Denmark.

Macromolecule Content

Total Structure Weight: 79.7 kDa
Atom Count: 5,600
Modeled Residue Count: 661
Deposited Residue Count: 698
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sortilin	A	685	Homo sapiens	Mutation(s): 1 Gene Names: SORT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99523 (Homo sapiens) Explore Q99523 Go to UniProtKB: Q99523
PHAROS: Q99523 GTEx: ENSG00000134243
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99523
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A	Go to GlyGen: Q99523-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neurotensin	B [auth N]	13	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P30990 (Homo sapiens) Explore P30990 Go to UniProtKB: P30990
PHAROS: P30990 GTEx: ENSG00000133636
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30990
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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	C [auth B]	2		N-Glycosylation	Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 C]	3		N-Glycosylation	Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE 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]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [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]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	B [auth N]	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.229 (Depositor), 0.272 (DCC)
R-Value Work: 0.204 (Depositor)
R-Value Observed: 0.205 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.76	α = 90
b = 74.53	β = 131.87
c = 108.33	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
SHARP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-12-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-12-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 2.0: 2019-12-25
Changes: Database references, Derived calculations, Polymer sequence
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 3.1: 2023-12-27
Changes: Data collection, Database references, Structure summary
Version 3.2: 2024-11-06
Changes: Structure summary