RCSB PDB - 1YWH: crystal structure of urokinase plasminogen activator receptor (original) (raw)
crystal structure of urokinase plasminogen activator receptor
This is version 2.1 of the entry. See complete history.
Crystal structure of the human urokinase plasminogen activator receptor bound to an antagonist peptide
[Llinas, P.](/search?q=citation.rcsb%5Fauthors:Llinas, P.), [Le Du, M.H.](/search?q=citation.rcsb%5Fauthors:Le Du, M.H.), [Gardsvoll, H.](/search?q=citation.rcsb%5Fauthors:Gardsvoll, H.), [Dano, K.](/search?q=citation.rcsb%5Fauthors:Dano, K.), [Ploug, M.](/search?q=citation.rcsb%5Fauthors:Ploug, M.), [Gilquin, B.](/search?q=citation.rcsb%5Fauthors:Gilquin, B.), [Stura, E.A.](/search?q=citation.rcsb%5Fauthors:Stura, E.A.), [Menez, A.](/search?q=citation.rcsb%5Fauthors:Menez, A.)
(2005) EMBO J 24: 1655-1663
PubMed Abstract:
We report the crystal structure of a soluble form of human urokinase-type plasminogen activator receptor (uPAR/CD87), which is expressed at the invasive areas of the tumor-stromal microenvironment in many human cancers. The structure was solved at 2.7 A in association with a competitive peptide inhibitor of the urokinase-type plasminogen activator (uPA)-uPAR interaction. uPAR is composed of three consecutive three-finger domains organized in an almost circular manner, which generates both a deep internal cavity where the peptide binds in a helical conformation, and a large external surface. This knowledge combined with the discovery of a convergent binding motif shared by the antagonist peptide and uPA allowed us to build a model of the human uPA-uPAR complex. This model reveals that the receptor-binding module of uPA engages the uPAR central cavity, thus leaving the external receptor surface accessible for other protein interactions (vitronectin and integrins). By this unique structural assembly, uPAR can orchestrate the fine interplay with the partners that are required to guide uPA-focalized proteolysis on the cell surface and control cell adhesion and migration.
Organizational Affiliation:
CEA, Département d'Ingénierie et d'Etudes des Protéines, CE Saclay, Gif sur Yvette, France.
Macromolecule Content
- Total Structure Weight: 304.71 kDa
- Atom Count: 18,552
- Modelled Residue Count: 2,193
- Deposited Residue Count: 2,608
- Unique protein chains: 2
Find similar proteins by:
(by identity cutoff) | 3D Structure
| Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Urokinase plasminogen activator surface receptor | A, C, E, G, IA, C, E, G, I, K, M, O | 313 | [Homo sapiens](/search?q=rcsb%5Fentity%5Fsource%5Forganism.taxonomy%5Flineage.name:Homo sapiens) | Mutation(s): 0 Gene Names: PLAUR, MO3, UPAR |  |
| UniProt & NIH Common Fund Data Resources | |||||
| Find proteins for [Q03405](/search?q=rcsb%5Fpolymer%5Fentity%5Fcontainer%5Fidentifiers.reference%5Fsequence%5Fidentifiers.database%5Faccession:Q03405 AND rcsb%5Fpolymer%5Fentity%5Fcontainer%5Fidentifiers.reference%5Fsequence%5Fidentifiers.database%5Fname:UniProt) _(Homo sapiens)_Explore Q03405 Go to UniProtKB: Q03405 | |||||
| PHAROS: Q03405GTEx: ENSG00000011422 | |||||
| Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q03405 | ||||
| Glycosylation | |||||
| Glycosylation Sites: 3 | Glycosylation | Go to GlyGen: Q03405-1 | |||
| Sequence AnnotationsExpand | |||||
| Reference Sequence |
Find similar proteins by: Sequence | 3D Structure
| Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| antagonist peptide | B, D, F, H, JB, D, F, H, J, L, N, P | 13 | N/A | Mutation(s): 0 |  |
| Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| Sequence AnnotationsExpand | |||||
| Reference Sequence |
| Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | BA [auth b],Q,S,T | 3 |  |
N-Glycosylation | Interactions Interactions & Density |
| Glycosylation Resources | |||||
| GlyTouCan: G21290RBGlyCosmos: G21290RBGlyGen: G21290RB |
| Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | AA [auth a],DA [auth d],GA [auth g],R,U,AA [auth a],DA [auth d],GA [auth g],R,U,V,X,Y | 2 |  |
N-Glycosylation | Interactions Interactions & Density |
| Glycosylation Resources | |||||
| GlyTouCan: G86851RCGlyCosmos: G86851RCGlyGen: G86851RC |
| Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | FA [auth f],W | 2 |  |
N-Glycosylation | Interactions Interactions & Density |
| Glycosylation Resources | |||||
| GlyTouCan: G42666HTGlyCosmos: G42666HTGlyGen: G42666HT |
| Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-3)-[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 | CA [auth c],EA [auth e],HA [auth h],Z | 5 |  |
N-Glycosylation | Interactions Interactions & Density |
| Glycosylation Resources | |||||
| GlyTouCan: G22768VOGlyCosmos: G22768VOGlyGen: G22768VO |
| Ligands 2 Unique | ||||
|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions |
| NAGQuery on NAGDownload Ideal Coordinates CCD File | BB [auth I]FB [auth K]GB [auth K]IA [auth A]JA [auth A]BB [auth I],FB [auth K],GB [auth K],IA [auth A],JA [auth A],JB [auth M],MB [auth O],NA [auth C],OA [auth C],SA [auth E],WA [auth G] | 2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O6OVRNDRQMDRJTHS-FMDGEEDCSA-N |  |
Interactions Interactions & Density |
| SO4Query on SO4Download Ideal Coordinates CCD File | AB [auth G]CB [auth I]DB [auth I]EB [auth I]HB [auth K]AB [auth G],CB [auth I],DB [auth I],EB [auth I],HB [auth K],IB [auth K],KA [auth A],KB [auth M],LA [auth A],LB [auth M],MA [auth A],NB [auth O],PA [auth C],QA [auth C],RA [auth C],TA [auth E],UA [auth E],VA [auth E],XA [auth G],YA [auth G],ZA [auth G] | SULFATE IONO4 SQAOWNCQODCNURD-UHFFFAOYSA-L |  |
Interactions Interactions & Density |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| ALCQuery on ALC | B, D, F, H, JB, D, F, H, J, L, N, P | L-PEPTIDE LINKING | C9 H17 N O2 |  |
ALA |
Experimental Data & Validation
Experimental Data
- Space Group: [P 1 21 1](/search?q=symmetry.space%5Fgroup%5Fname%5FH%5FM:P 1 21 1)
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 106.928 | α = 90 |
| b = 136.831 | β = 97.27 |
| c = 140.536 | γ = 90 |
Software Package:
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
Deposition Data
- Released Date: 2005-05-10 Deposition Author(s): [Llinas, P.](/search?q=audit%5Fauthor.name:Llinas, P.), [Le Du, M.H.](/search?q=audit%5Fauthor.name:Le Du, M.H.), [Gardsvoll, H.](/search?q=audit%5Fauthor.name:Gardsvoll, H.), [Dano, K.](/search?q=audit%5Fauthor.name:Dano, K.), [Ploug, M.](/search?q=audit%5Fauthor.name:Ploug, M.), [Gilquin, B.](/search?q=audit%5Fauthor.name:Gilquin, B.), [Stura, E.A.](/search?q=audit%5Fauthor.name:Stura, E.A.), [Menez, A.](/search?q=audit%5Fauthor.name:Menez, A.)
Revision History (Full details and data files)
- Version 1.0: 2005-05-10
Type: Initial release - Version 1.1: 2007-10-16
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance - Version 1.3: 2018-01-31
Changes: Experimental preparation - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2024-10-30
Changes: Data collection, Database references, Structure summary