6ONB

Crystal Structure of the ZIG-8-RIG-5 IG1-IG1 heterodimer, monoclinic form

• PDB DOI: https://doi.org/10.2210/pdb6ONB/pdb

• Classification: CELL ADHESION
• Organism(s): Caenorhabditis elegans
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2019-04-20 Released: 2019-05-15 
• Deposition Author(s): Cheng, S., Kurleto, J.D., Ozkan, E.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.207 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, surface plasmon resonance

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 56.21 kDa 
• Atom Count: 4,033 
• Modelled Residue Count: 449 
• Deposited Residue Count: 486 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zwei Ig domain protein zig-8	A, C	125	Caenorhabditis elegans	Mutation(s): 0  Gene Names: zig-8, Y39E4B.8
UniProt
Find proteins for G5ED00 (Caenorhabditis elegans) Explore G5ED00  Go to UniProtKB:  G5ED00

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NeuRonal IgCAM-5	B, D	118	Caenorhabditis elegans	Mutation(s): 0  Gene Names: rig-5, C36F7.4, CELE_C36F7.4
UniProt
Find proteins for C6KRM7 (Caenorhabditis elegans) Explore C6KRM7  Go to UniProtKB:  C6KRM7

Oligosaccharides

Help

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	F [auth A], G [auth B], H [auth B], I [auth B], K [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.207 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.15785/SBGRID/689

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.46	α = 90
b = 79.103	β = 94.22
c = 89.977	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing
Coot	model building
XDS	data scaling

Structure Validation

Currently 6ONB does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Cheng, S., Kurleto, J.D., Ozkan, E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS097161

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2019-05-29
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  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, Refinement description, Structure summary