OCA Atlas for 3ULV

3ULV

Immune System

date

Nov 11, 2011

title

Structure Of Quaternary Complex Of Human Tlr3ecd With Three (Form2)

authors

J.Luo, G.L.Gilliland, O.Obmolova, T.Malia, A.Teplyakov

compound

source

Molecule: Toll-Like Receptor 3
Chain: A
Fragment: Unp Residues 22-702
Synonym: Tlr3ecd
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tlr3
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_strain: Sf9
Expression_system_vector_type: Baculovirus

Molecule: Fab15 Light Chain
Chain: L
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293
Expression_system_vector: Pcdna 3.1-Based
Other_details: Synthetic Fab Library

Molecule: Fab15 Heavy Chain
Chain: H
Engineered: Yes

Molecule: Fab12 Light Chain
Chain: C
Engineered: Yes

Molecule: Fab12 Heavy Chain
Chain: D
Engineered: Yes

Molecule: Fab1068 Light Chain
Chain: E
Engineered: Yes

Molecule: Fab1068 Heavy Chain
Chain: F
Engineered: Yes

symmetry

Space Group: C 1 2 1

R_factor

0.231

R_Free

0.253

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
363.300	131.660	154.200	90.00	91.35	90.00

method

X-Ray Diffraction

resolution

3.52 Å

ligand

BMA, MAN, NAG, SO4

enzyme

Gene
Ontology

Chain	Function	Process	Component
A

Primary reference

Lateral Clustering of TLR3:dsRNA Signaling Units Revealed by TLR3ecd:3Fabs Quaternary Structure., Luo J, Obmolova G, Malia TJ, Wu SJ, Duffy KE, Marion JD, Bell JK, Ge P, Zhou ZH, Teplyakov A, Zhao Y, Lamb RJ, Jordan JL, San Mateo LR, Sweet RW, Gilliland GL, J Mol Biol. 2012 May 9. PMID:22579623

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (322 Kb) [Save to disk]

Biological Unit Coordinates (3ulv.pdb1.gz) 315 Kb

LPC: Ligand-Protein Contacts for 3ULV

CSU: Contacts of Structural Units for 3ULV

Structure Factors (448 Kb)

Retrieve 3ULV in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 3ULV from S2C, [Save to disk]

Re-refined 3ulv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3ULV in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 3ULV

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 3ULV, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ulv_C] [3ulv_A] [3ulv_H] [3ulv] [3ulv_D] [3ulv_F] [3ulv_L] [3ulv_E]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Domains found in 3ULV: [IG_like] [IGv] [LRR] [LRRCT] [LRRNT] [LRR_TYP ] by SMART

Other resources with information on 3ULV

Community annotation for 3ULV at PDBWiki (http://pdbwiki.org)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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