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5BSC|pdb_00005bsc
Crystal structure of K66A mutant of human macrophage migration inhibitory factor
- PDB DOI: https://doi.org/10.2210/pdb5BSC/pdb
- Classification: ISOMERASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2015-06-01 Released: 2015-09-30
- Deposition Author(s): Pantouris, G.,Lolis, E.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.89 Å
- R-Value Free: 0.218 (Depositor), 0.220 (DCC)
- R-Value Work: 0.198 (Depositor), 0.210 (DCC)
- R-Value Observed: 0.199 (Depositor)
Starting Model:experimental
View more details
wwPDB Validation 3D Report Full Report
Download MendeleyAn Analysis of MIF Structural Features that Control Functional Activation of CD74.
Pantouris, G., Syed, M.A., Fan, C., Rajasekaran, D., Cho, T.Y., Rosenberg, E.M., Bucala, R., Bhandari, V., Lolis, E.J.(2015) Chem Biol 22: 1197-1205
- PubMed: 26364929 Search on PubMedSearch on PubMed Central
- DOI: https://doi.org/10.1016/j.chembiol.2015.08.006
- Primary Citation of Related Structures:
4P01,4P0H,4PKZ,4PLU,4TRF,4TRU,4XX7,4XX8,5BS9,5BSC,5BSI - PubMed Abstract:
For more than 15 years, the tautomerase active site of macrophage migration inhibitory factor (MIF) and its catalytic residue Pro1 have been being targeted for the development of therapeutics that block activation of its cell surface receptor, CD74. Neither the biological role of the MIF catalytic site nor the mechanistic details of CD74 activation are well understood. The inherently unstable structure of CD74 remains the biggest obstacle in structural studies with MIF for understanding the basis of CD74 activation. Using a novel approach, we elucidate the mechanistic details that control activation of CD74 by MIF surface residues and identify structural parameters of inhibitors that reduce CD74 biological activation. We also find that N-terminal mutants located deep in the catalytic site affect surface residues immediately outside the catalytic site, which are responsible for reduction of CD74 activation.
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06510, USA.
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06510, USA.
- Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06510, USA.
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06510, USA. Electronic address: elias.lolis@yale.edu.
Organizational Affiliation:
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (IPA)
Global Symmetry: Cyclic - C3 (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3
Find Similar Assemblies
Biological assembly 1 assigned by authors and generated by PISA (software)
Macromolecule Content
- Total Structure Weight: 37.07 kDa
- Atom Count: 2,828
- Modeled Residue Count: 342
- Deposited Residue Count: 342
- Unique protein chains: 1
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Macrophage migration inhibitory factor | 114 | Homo sapiens | Mutation(s): 1 Gene Names: MIF, GLIF, MMIF EC: 5.3.2.1 (PDB Primary Data), 5.3.3.12 (PDB Primary Data) |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P14174 (Homo sapiens) Explore P14174 Go to UniProtKB: P14174 | |||||
PHAROS: P14174 GTEx: ENSG00000240972 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P14174 | ||||
Sequence AnnotationsExpand | |||||
| |||||
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| IPA Query on IPA Download Ideal Coordinates CCD File | D [auth A], E [auth B], F [auth C] | ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N |  | ||
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.89 Å
- R-Value Free: 0.218 (Depositor), 0.220 (DCC)
- R-Value Work: 0.198 (Depositor), 0.210 (DCC)
- R-Value Observed: 0.199 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 67.275 | α = 90 |
| b = 67.771 | β = 90 |
| c = 87.535 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| PHASER | phasing |
Deposition Data
- Released Date: 2015-09-30 Deposition Author(s): Pantouris, G.,Lolis, E.
Revision History (Full details and data files)
- Version 1.0: 2015-09-30
Type: Initial release - Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
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