3CIY
Mouse Toll-like receptor 3 ectodomain complexed with double-stranded RNA
- PDB DOI: https://doi.org/10.2210/pdb3CIY/pdb
- NAKB: 3CIY
- Classification: IMMUNE SYSTEM/RNA
- Organism(s): Mus musculus
- Expression System: Trichoplusia ni
- Mutation(s): No 
- Deposited: 2008-03-12 Released: 2008-05-06 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.41 Å
- R-Value Free: 0.333 
- R-Value Work: 0.288 
- R-Value Observed: 0.288 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Toll-like receptor 3 | C [auth A], D [auth B] | 697 | Mus musculus | Mutation(s): 0  Gene Names: Tlr3 | |
UniProt | |||||
Find proteins for Q99MB1 (Mus musculus) Explore Q99MB1  Go to UniProtKB:  Q99MB1 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q99MB1 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Length | Organism | Image | |
46-MER | A [auth C] | 46 | N/A | ||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
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Molecule | Chains | Length | Organism | Image | |
46-MER | B [auth D] | 46 | N/A | ||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 4 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E, H, L, O | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G07375KG GlyCosmos:  G07375KG GlyGen:  G07375KG |
Entity ID: 5 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | F | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO |
Entity ID: 6 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | G | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB |
Entity ID: 7 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | I | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G21381MC GlyCosmos:  G21381MC GlyGen:  G21381MC |
Entity ID: 8 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | J, Q | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G35926TG GlyCosmos:  G35926TG GlyGen:  G35926TG |
Entity ID: 9 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | K, R | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 10 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | M | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 11 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | N | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G28454KX GlyCosmos:  G28454KX GlyGen:  G28454KX |
Entity ID: 12 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | P | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G34198FQ GlyCosmos:  G34198FQ GlyGen:  G34198FQ |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | S [auth A], T [auth A], U [auth B], V [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: 3.41 Å
- R-Value Free: 0.333 
- R-Value Work: 0.288 
- R-Value Observed: 0.288 
- Space Group: C 2 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 117.846 | α = 90 |
b = 225.877 | β = 90 |
c = 259.53 | γ = 90 |
Software Name | Purpose |
---|---|
CNS | refinement |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2008-05-06  Deposition Author(s): Liu, L., Botos, I., Wang, Y., Leonard, J.N., Shiloach, J., Segal, D.M., Davies, D.R.
Revision History (Full details and data files)
- Version 1.0: 2008-05-06
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary