Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 127.50 kDa 
• Atom Count: 9028 
• Modelled Residue Count: 1016 
• Deposited Residue Count: 1084 
• Unique protein chains: 2

3OJA

Crystal structure of LRIM1/APL1C complex

• DOI: 10.2210/pdb3OJA/pdb

• Classification: PROTEIN BINDING
• Organism(s): Anopheles gambiae
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2010-08-20 Released: 2010-09-22 
• Deposition Author(s): Baxter, R.H.G., Deisenhofer, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.265 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 

Literature

A heterodimeric complex of the LRR proteins LRIM1 and APL1C regulates complement-like immunity in Anopheles gambiae.

Baxter, R.H., Steinert, S., Chelliah, Y., Volohonsky, G., Levashina, E.A., Deisenhofer, J.

(2010) Proc Natl Acad Sci U S A 107: 16817-16822

• PubMed: 20826443 
• DOI: 10.1073/pnas.1010575107
• Primary Citation of Related Structures:  
  3O53, 3O6N, 3OJA


• PubMed Abstract: 
  

The leucine-rich repeat (LRR) proteins LRIM1 and APL1C control the function of the complement-like protein TEP1 in Anopheles mosquitoes. The molecular structure of LRIM1 and APL1C and the basis of their interaction with TEP1 represent a new type of innate immune complex. The LRIM1/APL1C complex specifically binds and solubilizes a cleaved form of TEP1 without an intact thioester bond. The LRIM1 and APL1C LRR domains have a large radius of curvature, glycosylated concave face, and a novel C-terminal capping motif. The LRIM1/APL1C complex is a heterodimer with a single intermolecular disulfide bond. The structure of the LRIM1/APL1C heterodimer reveals an interface between the two LRR domains and an extensive C-terminal coiled-coil domain. We propose that a cleaved form of TEP1 may act as a convertase for activation of other TEP1 molecules and that the LRIM1/APL1C heterodimer regulates formation of this TEP1 convertase.

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Organizational Affiliation: 

Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9050, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich Immune Molecule 1	A	487	Anopheles gambiae	Mutation(s): 0  Gene Names: AGAP006348, LRIM1, 1276956, AgaP_AGAP006348
UniProt
Find proteins for Q7Q5N3 (Anopheles gambiae) Explore Q7Q5N3  Go to UniProtKB:  Q7Q5N3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anopheles Plasmodium-responsive Leucine-rich repeat protein 1	B	597	Anopheles gambiae	Mutation(s): 0  Gene Names: AGAP007033, APL1C

Oligosaccharides

Help

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

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G98400NB GlyCosmos:  G98400NB GlyGen:  G98400NB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	H [auth B], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.265 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.89	α = 90
b = 110.89	β = 90
c = 168.33	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2010-08-20 
• Released Date: 2010-09-22 
Deposition Author(s): Baxter, R.H.G., Deisenhofer, J.

Revision History  

• Version 1.0: 2010-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary