3ZYJ | pdb_00003zyj

NetrinG1 in complex with NGL1

PDB DOI: https://doi.org/10.2210/pdb3ZYJ/pdb

Classification: CELL ADHESION
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2011-08-23 Released: 2011-10-05
Deposition Author(s): Seiradake, E., Coles, C.H., Perestenko, P.V., Harlos, K., McIlhinney, R.A.J., Aricescu, A.R., Jones, E.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free:
0.268 (Depositor), 0.303 (DCC)
R-Value Work:
0.256 (Depositor), 0.287 (DCC)
R-Value Observed:
0.257 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural Basis for Cell Surface Patterning Through Netring-Ngl Interactions.

Seiradake, E., Coles, C.H., Perestenko, P.V., Harlos, K., Mcilhinney, R.A.J., Aricescu, A.R., Jones, E.Y.

(2011) EMBO J 30: 4479

PubMed: 21946559 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/emboj.2011.346
Primary Citation Related Structures:
3ZYG, 3ZYI, 3ZYJ, 3ZYN, 3ZYO

PubMed Abstract:
Brain wiring depends on cells making highly localized and selective connections through surface protein-protein interactions, including those between NetrinGs and NetrinG ligands (NGLs). The NetrinGs are members of the structurally uncharacterized netrin family. We present a comprehensive crystallographic analysis comprising NetrinG1-NGL1 and NetrinG2-NGL2 complexes, unliganded NetrinG2 and NGL3. Cognate NetrinG-NGL interactions depend on three specificity-conferring NetrinG loops, clasped tightly by matching NGL surfaces. We engineered these NGL surfaces to implant custom-made affinities for NetrinG1 and NetrinG2. In a cellular patterning assay, we demonstrate that NetrinG-binding selectivity can direct the sorting of a mixed population of NGLs into discrete cell surface subdomains. These results provide a molecular model for selectivity-based patterning in a neuronal recognition system, dysregulation of which is associated with severe neuropsychological disorders.

Organizational Affiliation

Division of Structural Biology, CR-UK Receptor Structure Research Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.

Macromolecule Content

Total Structure Weight: 197.41 kDa
Atom Count: 11,388
Modeled Residue Count: 1,444
Deposited Residue Count: 1,732
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LEUCINE-RICH REPEAT-CONTAINING PROTEIN 4C	A, C	440	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCJ2 (Homo sapiens) Explore Q9HCJ2 Go to UniProtKB: Q9HCJ2
PHAROS: Q9HCJ2 GTEx: ENSG00000148948
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HCJ2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NETRIN-G1	B, D	426	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2I2 (Homo sapiens) Explore Q9Y2I2 Go to UniProtKB: Q9Y2I2
PHAROS: Q9Y2I2 GTEx: ENSG00000162631
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y2I2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain M [auth D] SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain G [auth B] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B]	E [auth A] F [auth B] G [auth B] H [auth B] J [auth C] E [auth A], F [auth B], G [auth B], H [auth B], J [auth C], K [auth D], L [auth D], M [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain O [auth D] MOL2 format, chain O [auth D] mmCIF format, chain O [auth D]	O [auth D]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain O [auth D] Interactions & Density Focus chain O [auth D]
BMA Query on BMA Download:Ideal Coordinates CCD File SDF format, chain N [auth D] MOL2 format, chain N [auth D] mmCIF format, chain N [auth D]	N [auth D]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain N [auth D] Interactions & Density Focus chain N [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain I [auth B] MOL2 format, chain P [auth D] MOL2 format, chain I [auth B] mmCIF format, chain P [auth D] mmCIF format, chain I [auth B]	I [auth B], P [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain P [auth D] Interactions & Density Focus chain I [auth B] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.268 (Depositor), 0.303 (DCC)
R-Value Work: 0.256 (Depositor), 0.287 (DCC)
R-Value Observed: 0.257 (Depositor)

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.42	α = 90
b = 204.43	β = 90
c = 288.07	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-10-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-10-05
Type: Initial release
Version 1.1: 2011-10-26
Changes: Database references
Version 1.2: 2011-11-16
Changes: Database references
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary