7RJ9: Vitronectin

Crystal structure of the Vitronectin hemopexin-like domain binding Calcium. Determined by X-ray diffraction at 1.7 Å resolution. Released 27 Jul 2022.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,567
Mol. weight: 47.17 kDa
Ligands: CA
Released: 27 Jul 2022

Explore 7RJ9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7RJ9 contains 17 α-helices and 42 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: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	159-161	3
β-strand	163-164	2	1
α-helix	165-167	3
β-strand	168	1	2
β-strand	171	1	2
β-strand	172-176	5	1
β-strand	179-183	5	1
β-strand	194-195	2	1
α-helix	196-199	4
β-strand	208-211	4	3
β-strand	219-223	5	3
β-strand	226-231	6	3
β-strand	234-235	2	3
α-helix	236	1
β-strand	241-242	2	3
α-helix	250-251	2
β-strand	256-260	5	4
β-strand	270-275	6	4
β-strand	278-283	6	4
β-strand	333-334	2	4
α-helix	335-338	4
β-strand	340	1	5
β-strand	348-351	4	6
β-strand	435-440	6	6
β-strand	443-448	6	6
β-strand	453	1	5
β-strand	454	1	6
α-helix	460	1
β-strand	463-464	2	6
α-helix	465-468	4

Chain B: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	159-161	3
β-strand	163-166	4	7
β-strand	172-176	5	7
β-strand	179-183	5	7
β-strand	194-195	2	7
α-helix	196-199	4
β-strand	208-211	4	8
β-strand	219-223	5	8
β-strand	226-231	6	8
β-strand	234-235	2	8
α-helix	236	1
β-strand	241-242	2	8
α-helix	250-251	2
β-strand	256-260	5	9
α-helix	261-263	3
β-strand	270-275	6	9
β-strand	278-283	6	9
α-helix	331-332	2
β-strand	333-334	2	9
α-helix	335-338	4
β-strand	340	1	10
β-strand	348-351	4	11
β-strand	435-440	6	11
β-strand	443-448	6	11
β-strand	453	1	10
β-strand	454	1	11
α-helix	460	1
β-strand	463-464	2	11
α-helix	465-469	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitronectin	A, B	protein	204	Homo sapiens	P04004 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7RJ9_1 Vitronectin (chains A, B)
MELCSGKPFDAFTDLKNGSLFAFRGQYSYELDEKAVRPGYPKLIRDVWGIEGPIDAAFTR
INSQGKTYLFKGSQYWRFEDGVLDPDYPRNISDGFDGIPDNVDAALALPAHSYSGRERVY
FFKGKQYWEYQFQRTSAGTRQPQFISRDWHGVPGQVDAAMAGRISVFFFSGDKYYRVNLR
TRRVDTVDPPYPRSIAQYWLGCPA

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

Water and common crystallization additives (SO4, NA, CL) are not listed.

Primary citation

Crystal structure of the Vitronectin hemopexin-like domain binding Calcium. Aleshin, A.E., Marassi, F.M. To be published.

Other PDB entries of the same protein (UniProt P04004 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6O5E 1.9 Å, Crystal structure of the Vitronectin hemopexin-like domain
1OC0 2.28 Å, plasminogen activator inhibitor-1 complex with somatomedin B domain of vitronectin
3BT2 2.5 Å, Structure of urokinase receptor, urokinase and vitronectin complex
3BT1 2.8 Å, Structure of urokinase receptor, urokinase and vitronectin complex
4K24 4.5 Å, Structure of anti-uPAR Fab ATN-658 in complex with uPAR
1S4G Somatomedin-B Domain of human plasma vitronectin.
1SSU Structural and biochemical evidence for disulfide bond heterogeneity in active forms of…
2JQ8 Solution structure of the Somatomedin B domain from vitronectin produced in Pichia…

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