3LTQ

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

PDB DOI: 10.2210/pdb3LTQ/pdb

Classification: CYTOKINE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.221
R-Value Work: 0.192
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: 10.1021/ja104983t
Primary Citation of Related Structures:
3LTQ, 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.

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

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:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 beta	A	171	Homo sapiens	Mutation(s): 0 Gene Names: IL1B, IL1F2
UniProt & NIH Common Fund Data Resources
Find proteins for P01584 (Homo sapiens) Explore P01584 Go to UniProtKB: P01584
PHAROS: P01584
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01584
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TB Query on TB Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction