4QTI: Human uPAR

Crystal structure of human uPAR in complex with anti-uPAR Fab 8B12. Determined by X-ray diffraction at 3.0 Å resolution. Released 25 Feb 2015.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 5,290
Mol. weight: 79.18 kDa
Released: 25 Feb 2015

Explore 4QTI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4QTI contains 19 α-helices and 68 β-strands across 3 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 H: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	32-39	8	2
β-strand	45-52	8	2
β-strand	57-60	4	2
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-100	9	2
α-helix	105-107	3
β-strand	108-112	5	2
β-strand	116-120	5	2
β-strand	126	1	3
β-strand	129-133	5	4
β-strand	144-154	11	4
β-strand	155	1	3
β-strand	160-163	4	5
α-helix	164-166	3
β-strand	173-174	2	4
α-helix	175-177	3
β-strand	178-180	3	4
β-strand	183-193	11	4
β-strand	203-208	6	5
α-helix	209-211	3
β-strand	213-218	6	5

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	33-38	6	7
β-strand	44-49	6	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	85-90	6	7
β-strand	93	1	8
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-106	5	7
β-strand	111	1	9
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153	1	11
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-186	4
β-strand	191-197	7	11
β-strand	205	1	11
β-strand	209-210	2	11

Chain U: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	12
β-strand	12-16	5	12
α-helix	17-18	2
β-strand	23-33	11	12
β-strand	38-46	9	12
β-strand	53-59	7	12
β-strand	62-68	7	12
β-strand	70-71	2	12
β-strand	90	1	8
β-strand	93-97	5	13
β-strand	98-99	2	12
α-helix	100-102	3
β-strand	111-115	5	13
β-strand	121-128	8	12
β-strand	143-149	7	12
β-strand	157-160	4	12
β-strand	165-171	7	12
β-strand	189-196	8	14
β-strand	197-199	3	12
β-strand	200	1	15
β-strand	204	1	15
β-strand	211-216	6	14
β-strand	219	1	14
β-strand	221-228	8	12
β-strand	235-242	8	12
α-helix	249-255	7
β-strand	262-266	5	12
α-helix	274-276	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
anti-uPAR antibody, heavy chain	H	protein	224	Mus musculus
anti-uPAR antibody, light chain	L	protein	214	Mus musculus
Urokinase plasminogen activator surface receptor	U	protein	283	Homo sapiens	Q03405 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>4QTI_1 anti-uPAR antibody, heavy chain (chains H)
QVQLQQSGAELMKPGASVKLSCKAAGYTFTAYWIEWIRQRPGHGLEWIGEILPGSSSTNC
NEMFKGKATFTADTSSNSAYMQLSSLTTEDSAIYYCTRDFSGDRSNLYFDVWGTGTTVTV
SSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQ
SDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 2 (L), FASTA

>4QTI_2 anti-uPAR antibody, light chain (chains L)
DIQMTQSPSSLSASLGERVSLTCRASQDIGSSLNWLQQEPDGTIKRLIYATSSLDSGVPK
RFSGSRSGSDYSLTISRLESEDFVDYYCLQYATSPYTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (U), FASTA

>4QTI_3 Urokinase plasminogen activator surface receptor (chains U)
LRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYRTG
LKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEE
QCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGP
ILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRG
CATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDVQYRSG

Primary citation

Stabilizing a flexible interdomain hinge region harboring the SMB binding site drives uPAR into its closed conformation. Zhao, B., Gandhi, S., Yuan, C. et al. J Mol Biol (2015) 427:1389-1403. DOI 10.1016/j.jmb.2015.01.022 · PubMed

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
7V63 2.91 Å, Structure of dimeric uPAR at low pH
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
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

About this viewer

MolViewer shows 4QTI directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.