7V63: Dimeric uPAR at low pH

Structure of dimeric uPAR at low pH. Determined by X-ray diffraction at 2.91 Å resolution. Released 22 Dec 2021.

Method: X-ray diffraction
Resolution: 2.91 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,833
Mol. weight: 62.77 kDa
Ligands: NAG
Released: 22 Dec 2021

Explore 7V63 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7V63 contains 9 α-helices and 32 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	1
β-strand	6	1	2
β-strand	13-16	4	1
α-helix	17-18	2
β-strand	23-33	11	2
β-strand	36-46	11	2
β-strand	61-69	9	3
β-strand	155-159	5	3
β-strand	164-172	9	3
β-strand	175	1	3
α-helix	184-186	3
α-helix	188	1
β-strand	189-196	8	4
β-strand	197-199	3	3
β-strand	200	1	5
β-strand	204	1	5
β-strand	211-216	6	4
β-strand	221-226	6	3
β-strand	237-242	6	3
α-helix	244-247	4
β-strand	262-266	5	3
α-helix	274-276	3

Chain B: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	6
β-strand	6	1	2
β-strand	13-16	4	6
β-strand	23-33	11	2
β-strand	36-46	11	2
β-strand	61-69	9	7
β-strand	157-159	3	7
β-strand	164-172	9	7
β-strand	175	1	7
α-helix	184-186	3
α-helix	188	1
β-strand	189-196	8	8
β-strand	197-198	2	7
β-strand	211-216	6	8
β-strand	221-226	6	7
β-strand	237-242	6	7
α-helix	244-247	4
β-strand	262-266	5	7
α-helix	274-276	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Urokinase plasminogen activator surface receptor	A, B	protein	279	Homo sapiens	Q03405 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7V63_1 Urokinase plasminogen activator surface receptor (chains A, B)
RSLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYR
TGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSP
EEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNE
GPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMV
RGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Crystal structure and cellular functions of uPAR dimer. Yu, S., Sui, Y., Wang, J. et al. Nat Commun (2022) 13:1665. DOI 10.1038/s41467-022-29344-y

Other PDB entries of the same protein (UniProt Q03405 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2FD6 1.9 Å, Structure of Human Urokinase Plasminogen Activator in Complex with Urokinase Receptor…
3U74 2.39 Å, Crystal structure of stabilized human uPAR mutant
3BT2 2.5 Å, Structure of urokinase receptor, urokinase and vitronectin complex
1YWH 2.7 Å, crystal structure of urokinase plasminogen activator receptor
2I9B 2.8 Å, Crystal structure of ATF-urokinase receptor complex
3BT1 2.8 Å, Structure of urokinase receptor, urokinase and vitronectin complex
9YC5 2.94 Å, Human uPAR bound to the Fab fragment of targeted cancer therapeutic antibody FL1
7E17 2.96 Å, Structure of dimeric uPAR
4QTI 3.0 Å, Crystal structure of human uPAR in complex with anti-uPAR Fab 8B12
3U73 3.19 Å, Crystal structure of stabilized human uPAR mutant in complex with ATF
4K24 4.5 Å, Structure of anti-uPAR Fab ATN-658 in complex with uPAR
9YC6 4.8 Å, Mutant human uPAR bound to the Fab fragment of the targeted cancer therapeutic antibody…

Browse structure collections

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