Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19856.10 
• Atom Count: 1363 
• Residue Count: 171 
• Unique protein chains: 1

3LTQ

Structure of Interleukin 1B solved by SAD using an inserted Lanthanide Binding Tag

• DOI: 10.2210/pdb3LTQ/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2010-02-16 Released: 2011-02-16 
• Deposition Author(s): Peisach, E., Allen, K.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.221 
• R-Value Work: 0.192 

Literature

Engineering encodable lanthanide-binding tags into loop regions of proteins.

Barthelmes, K., Reynolds, A.M., Peisach, E., Jonker, H.R., DeNunzio, N.J., Allen, K.N., Imperiali, B., Schwalbe, H.

(2011) J.Am.Chem.Soc. 133: 808-819

• PubMed: 21182275 
• DOI: 10.1021/ja104983t
• Primary Citation of Related Structures:  
  3POK


• PubMed Abstract: 
  

Lanthanide-binding tags (LBTs) are valuable tools for investigation of protein structure, function, and dynamics by NMR spectroscopy, X-ray crystallography, and luminescence studies. We have inserted LBTs into three different loop positions (denoted L, R, and S) of the model protein interleukin-1β (IL1β) and varied the length of the spacer between the LBT and the protein (denoted 1−3). Luminescence studies demonstrate that all nine constructs bind Tb3+ tightly in the low nanomolar range. No significant change in the fusion protein occurs from insertion of the LBT, as shown by two X-ray crystallographic structures of the IL1β-S1 and IL1β-L3 constructs and for the remaining constructs by comparing the 1H−15N heteronuclear single-quantum coherence NMR spectra with that of the wild-type IL1β. Additionally, binding of LBT-loop IL1β proteins to their native binding partner in vitro remains unaltered. X-ray crystallographic phasing was successful using only the signal from the bound lanthanide. Large residual dipolar couplings (RDCs) could be determined by NMR spectroscopy for all LBT-loop constructs and revealed that the LBT-2 series were rigidly incorporated into the interleukin-1β structure. The paramagnetic NMR spectra of loop-LBT mutant IL1β-R2 were assigned and the Δχ tensor components were calculated on the basis of RDCs and pseudocontact shifts. A structural model of the IL1β-R2 construct was calculated using the paramagnetic restraints. The current data provide support that encodable LBTs serve as versatile biophysical tags when inserted into loop regions of proteins of known structure or predicted via homology modeling.

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Related Citations: 

• Double-Lanthanide-Binding Tags for Macromolecular Crystallographic Structure Determination
  Silvaggi, N.R.,Martin, L.J.,Schwalbe, H.,Imperiali, B.,Allen, K.N.
  (2007) J.Am.Chem.Soc. 129: 7114




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Organizational Affiliation: 

Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University of Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Interleukin-1 beta	A	171	Homo sapiens	Mutation(s): 0  Gene Names: IL1B (IL1F2)
Find proteins for P01584 (Homo sapiens) Go to Gene View: IL1B Go to UniProtKB:  P01584

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
TB	A	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.221 
• R-Value Work: 0.192 
• Space Group: P 6₃ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 120.584	α = 90.00
b = 120.584	β = 90.00
c = 74.899	γ = 120.00

Software Package:

Software Name	Purpose
CBASS	data collection
RESOLVE	phasing
DENZO	data reduction
PHENIX	refinement
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-02-16 
• Released Date: 2011-02-16 
• Deposition Author(s): Peisach, E., Allen, K.N.

Revision History 

• Version 1.0: 2011-02-16
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2017-11-01
  Type: Refinement description