3ULU

Structure of quaternary complex of human TLR3ecd with three Fabs (Form1)

PDB DOI: https://doi.org/10.2210/pdb3ULU/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda, Homo sapiens
Mutation(s): No

Deposited: 2011-11-11 Released: 2012-05-23
Deposition Author(s): Luo, J., Gilliland, G.L., Obmolova, O., Malia, T., Teplyakov, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.52 Å
R-Value Free: 0.309
R-Value Work: 0.268
R-Value Observed: 0.270

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Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 225.96 kDa
Atom Count: 15,521
Modelled Residue Count: 1,964
Deposited Residue Count: 2,010
Unique protein chains: 7

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 3	A	694	Homo sapiens	Mutation(s): 0 Gene Names: TLR3
UniProt & NIH Common Fund Data Resources
Find proteins for O15455 (Homo sapiens) Explore O15455 Go to UniProtKB: O15455
PHAROS: O15455 GTEx: ENSG00000164342
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15455
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab15 light chain	B [auth L]	214	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab15 heavy chain	C [auth H]	225	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab12 light chain	D [auth C]	213	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab12 heavy chain	E [auth D]	226	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab1068 light chain	F [auth E]	215	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab1068 heavy chain	G [auth F]	223	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

Oligosaccharides

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Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth B], I [auth G], J [auth I], K [auth J]	2		N-Glycosylation	Interactions Focus chain H [auth B] Focus chain I [auth G] Focus chain J [auth I] Focus chain K [auth J] Interactions & Density Focus chain H [auth B] Focus chain I [auth G] Focus chain J [auth I] Focus chain K [auth J]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L [auth K]	4		N-Glycosylation	Interactions Focus chain L [auth K] Interactions & Density Focus chain L [auth K]
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

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	Interactions Focus chain M Interactions & Density Focus chain M
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A]	N [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain N [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain N [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A]	O [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.52 Å
R-Value Free: 0.309
R-Value Work: 0.268
R-Value Observed: 0.270
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 214.9	α = 90
b = 142.08	β = 103.17
c = 125.04	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-05-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-05-23
Type: Initial release
Version 1.1: 2012-05-30
Changes: Database references
Version 1.2: 2012-07-25
Changes: Database references
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: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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Help and Resources

3ULU

Structure of quaternary complex of human TLR3ecd with three Fabs (Form1)

Entity ID: 1

UniProt & NIH Common Fund Data Resources

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Sequence Annotations

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Entity ID: 2

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Entity ID: 3

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Entity ID: 4

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Entity ID: 5

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Entity ID: 6

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Entity ID: 7

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Entity ID: 8

Glycosylation Resources

Entity ID: 9

Glycosylation Resources

Entity ID: 10

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)