8VGP: Angiopoietin-2

CryoEM structure of Angiopoietin-2 in complex with engineered conformationally rigid Fab 5A12.6DS. Determined by electron microscopy at 2.7 Å resolution. Released 30 Oct 2024.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,046
Mol. weight: 75.03 kDa
Ligands: CA
Released: 30 Oct 2024

Explore 8VGP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VGP contains 29 α-helices and 61 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 A: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	284-289	6
β-strand	296-301	6	1
β-strand	308-314	7	1
α-helix	317-319	3
β-strand	322-328	7	1
α-helix	339-344	6
β-strand	346-347	2	1
β-strand	353-354	2	1
α-helix	357-364	8
β-strand	369-376	8	1
β-strand	382-392	11	1
α-helix	395-397	3
β-strand	401-404	4	1
β-strand	407-408	2	1
α-helix	420-423	4
β-strand	424	1	2
α-helix	437-440	4
β-strand	445	1	2
β-strand	453-454	2	3
β-strand	458	1	4
β-strand	471	1	4
β-strand	473-474	2	3
α-helix	475-478	4
α-helix	482-484	3
β-strand	486-493	8	1

Chain H: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	5
β-strand	11-12	2	6
β-strand	18-25	8	5
α-helix	29-31	3
β-strand	33-39	7	7
β-strand	45-52	8	7
β-strand	56-59	4	7
β-strand	64	1	8
β-strand	67	1	8
β-strand	68-72	5	5
α-helix	73-75	3
β-strand	77-82	6	5
α-helix	84-86	3
β-strand	88-96	9	7
β-strand	100B-103	5	7
β-strand	107-109	3	7
β-strand	110-111	2	6
α-helix	117-123	3
β-strand	124-131	8	9
β-strand	139-149	11	9
β-strand	155-159	5	10
α-helix	160-162	3
β-strand	164	1	10
β-strand	168-170	3	9
α-helix	171-173	3
β-strand	174-175	2	9
β-strand	181-190	10	9
α-helix	191-193	3
β-strand	194	1	11
β-strand	197	1	11
β-strand	200-205	6	10
α-helix	206-208	3
β-strand	210-215	6	10

Chain L: 12 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	12
β-strand	10-14	5	13
β-strand	19-28	11	12
α-helix	30-32	3
β-strand	33-38	6	13
β-strand	45-49	5	13
β-strand	53-54	2	13
α-helix	55	1
β-strand	62-75	14	12
α-helix	80-82	3
β-strand	85-90	6	13
α-helix	97	1
β-strand	98	1	13
α-helix	99	1
β-strand	102-107	6	13
β-strand	111	1	14
α-helix	112-113	2
β-strand	114-118	5	15
α-helix	119-121	3
α-helix	122-125	4
α-helix	126-128	3
β-strand	129-139	11	15
β-strand	140	1	14
β-strand	145-150	6	16
β-strand	153-154	2	16
α-helix	155	1
β-strand	159-163	5	15
α-helix	165-167	3
β-strand	173-182	10	15
α-helix	183-186	4
β-strand	191-197	7	16
β-strand	205-210	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Angiopoietin-2	A	protein	232	Homo sapiens	O15123 (AlphaFold model)
Fab 5A12.6DS heavy chain	H	protein	236	Homo sapiens
Fab 5A12.6DS light chain	L	protein	215	Homo sapiens

Sequence of entity 1 (A), FASTA

>8VGP_1 Angiopoietin-2 (chains A)
AGSEQISFRDCAEVFKSGHTTNGIYTLTFPNSTEEIKAYCDMEAGGGGWTIIQRREDGSV
DFQRTWKEYKVGFGNPSGEYWLGNEFVSQLTNQQRYVLKIHLKDWEGNEAYSLYEHFYLS
SEELNYRIHLKGLTGTAGKISSISQPGNDFSTKDGDNDKCICKCSQMLTGGWWFDACGPS
NLNGMYYPQRQNTNKFNGIKWYYWKGSGYSLKATTMMIRPADFGNSHHHHHH

Sequence of entity 2 (H), FASTA

>8VGP_2 Fab 5A12.6DS heavy chain (chains H)
EVQLVESGGGCVQPGGSLRLSCAASGFTISDYWIHWVRQAPGKGLEWVAGITPAGGYTYY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFVFFLPYAMDYWGQGTCVTVSS
ASTKGPSVCPLAPSSKSTSGGTACLGCLVKDYFCECPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTHHHHHHP

Sequence of entity 3 (L), FASTA

>8VGP_3 Fab 5A12.6DS light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQFLSSFGVAWYQQKCGKAPKLLIYGASSLYSGVP
SRFSGSGSGTDFTLTISSLQCEDFATYYCQQGLLSPLTFGQGTKVEIKRTVAAPSVCIFP
PSDECLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTCQDSKDCTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Primary citation

Disulfi de constrained Fabs overcome target size limitation for high-resolution single-particle cryo-EM. Kung, J.E., Johnson, M.C., Jao, C.C. et al. bioRxiv (2024). DOI 10.1101/2024.05.10.593593 · PubMed

Other PDB entries of the same protein (UniProt O15123 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4JZC 1.9 Å, Angiopoietin-2 fibrinogen domain TAG mutant
1Z3U 2.25 Å, Structure of the Angiopoietin-2 Recptor Binding Domain and Identification of Surfaces…
4ZFG 2.27 Å, Dual-specificity Fab 5A12 in complex with Angiopoietin 2
1Z3S 2.35 Å, Angiopoietin-2 Receptor Binding Domain
9HMI 2.87 Å, Crystal structure of the Calf domains of Integrin Alpha5 in complex with angiopoietin2…
2GY7 3.7 Å, Angiopoietin-2/Tie2 Complex Crystal Structure

Browse structure collections

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