6DLD | pdb_00006dld

Crystal structure of IgLON5/NEGR1 heterodimer

PDB DOI: https://doi.org/10.2210/pdb6DLD/pdb

Classification: CELL ADHESION
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2018-06-01 Released: 2019-04-10
Deposition Author(s): Ranaivoson, F.M., Turk, L.S., Ozkan, E., Montelione, G.T., Comoletti, D.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.286 (Depositor), 0.287 (DCC)
R-Value Work:
0.245 (Depositor), 0.249 (DCC)
R-Value Observed:
0.247 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Structure of a heterodimer of neuronal cell surface proteins

Ranaivoson, F.M., Turk, L.S., Ozkan, E., Montelione, G.T., Comoletti, D.

(2019) Structure

Macromolecule Content

Total Structure Weight: 137.95 kDa
Atom Count: 7,856
Modeled Residue Count: 1,056
Deposited Residue Count: 1,214
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IgLON family member 5	A, C	303	Homo sapiens	Mutation(s): 0 Gene Names: IGLON5
UniProt & NIH Common Fund Data Resources
Find proteins for A6NGN9 (Homo sapiens) Explore A6NGN9 Go to UniProtKB: A6NGN9
PHAROS: A6NGN9 GTEx: ENSG00000142549
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6NGN9
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain C	Go to GlyGen: A6NGN9-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuronal growth regulator 1	B, D	304	Homo sapiens	Mutation(s): 0 Gene Names: NEGR1, IGLON4, UNQ2433/PRO4993
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z3B1 (Homo sapiens) Explore Q7Z3B1 Go to UniProtKB: Q7Z3B1
PHAROS: Q7Z3B1 GTEx: ENSG00000172260
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7Z3B1
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B Focus chain D	Go to GlyGen: Q7Z3B1-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
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	E	4		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
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 F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain P [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth B] F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], M [auth C], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth D], S [auth D], T [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.286 (Depositor), 0.287 (DCC)
R-Value Work: 0.245 (Depositor), 0.249 (DCC)
R-Value Observed: 0.247 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.341	α = 90
b = 305.799	β = 100.78
c = 60.029	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-04-10

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1450895

Revision History (Full details and data files)

Version 1.0: 2019-04-10
Type: Initial release
Version 1.1: 2019-11-27
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-11-13
Changes: Structure summary

6DLD | pdb_00006dld

Crystal structure of IgLON5/NEGR1 heterodimer

Literature

Structure of a heterodimer of neuronal cell surface proteins

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2