8IVW: NRP2

Crystal structure of NRP2 in complex with aNRP2-10 Fab fragment. Determined by X-ray diffraction at 3.21 Å resolution. Released 12 Jul 2023.

Method: X-ray diffraction
Resolution: 3.21 Å
Organism: Homo sapiens
Chains: 12
Atoms: 26,621
Mol. weight: 456.4 kDa
Released: 12 Jul 2023

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

Secondary structure: helices and β-sheets

8IVW contains 91 α-helices and 313 β-strands across 12 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, 43 β-strands

Element	Residues	Length	Sheet
β-strand	151-153	3	1
β-strand	157-161	5	2
α-helix	168-170	3
β-strand	174-180	7	1
β-strand	185-195	11	2
β-strand	212-216	5	1
α-helix	224	1
β-strand	225-229	5	1
α-helix	233-237	5
β-strand	238-240	3	2
β-strand	244-250	7	1
β-strand	259-268	10	2
β-strand	279-280	2	3
α-helix	290-292	3
β-strand	293-295	3	3
α-helix	306-308	3
β-strand	310	1	3
β-strand	318	1	4
β-strand	329-345	17	3
β-strand	347-348	2	5
β-strand	355-356	2	5
β-strand	357-366	10	3
β-strand	373-374	2	3
β-strand	376	1	6
β-strand	381	1	6
β-strand	384-385	2	3
β-strand	394-415	22	3
β-strand	420	1	4
β-strand	421-427	7	3
α-helix	429-431	3
β-strand	436-437	2	7
α-helix	447-449	3
β-strand	450-452	3	8
α-helix	462-464	3
β-strand	466	1	7
β-strand	474	1	9
α-helix	481-482	2
β-strand	488-491	4	8
β-strand	497-504	8	7
β-strand	506	1	10
β-strand	519	1	10
β-strand	521-529	9	8
β-strand	536-537	2	8
β-strand	539	1	11
β-strand	546	1	11
β-strand	549-550	2	8
β-strand	559-567	9	7
β-strand	570-578	9	8
β-strand	579	1	12
β-strand	582	1	12
β-strand	585	1	9
β-strand	586-592	7	7

Chains B, E, H and K: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	13
α-helix	7-9	3
β-strand	10-12	3	14
β-strand	18-25	8	13
β-strand	33-39	7	14
β-strand	46-52	7	14
β-strand	59-60	2	14
α-helix	62-64	3
β-strand	68-73	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-98	7	14
β-strand	110-111	2	14
β-strand	115-119	5	14
β-strand	125	1	15
β-strand	128-132	5	16
β-strand	143-153	11	16
β-strand	154	1	15
β-strand	159-161	3	17
β-strand	171-173	3	16
α-helix	174-176	3
β-strand	177-179	3	16
β-strand	183-193	11	16
α-helix	195-199	5
β-strand	203-208	6	17
α-helix	209-211	3
β-strand	213-218	6	17

Chains C, F, I and L: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	18
β-strand	8-14	7	19
β-strand	19-29	11	18
α-helix	30	1
α-helix	31-33	3
β-strand	34-39	6	19
β-strand	46-49	4	19
β-strand	56	1	19
β-strand	63-76	14	18
α-helix	81-83	3
β-strand	86-91	6	19
α-helix	97	1
β-strand	98-99	2	19
β-strand	103-108	6	19
β-strand	116-119	4	20
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	20
β-strand	146-151	6	21
β-strand	154-155	2	21
β-strand	160-164	5	20
α-helix	165-168	4
β-strand	174-183	10	20
α-helix	184-189	6
β-strand	192-198	7	21
β-strand	206-211	6	21

Chain D: 9 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	151-153	3	22
β-strand	157-161	5	23
α-helix	168-170	3
β-strand	174-180	7	22
β-strand	187-195	9	23
β-strand	212-216	5	22
α-helix	224	1
β-strand	225-229	5	22
α-helix	233-237	5
β-strand	238-240	3	23
β-strand	244-250	7	22
β-strand	259-265	7	23
β-strand	279-280	2	24
α-helix	290-292	3
β-strand	293-295	3	24
α-helix	306-308	3
β-strand	310	1	24
β-strand	318	1	25
β-strand	329-345	17	24
β-strand	347-348	2	26
β-strand	355-356	2	26
β-strand	357-366	10	24
β-strand	373-374	2	24
β-strand	376-377	2	27
β-strand	380-381	2	27
α-helix	382	1
β-strand	384-385	2	24
β-strand	394-415	22	24
β-strand	420	1	25
β-strand	421-427	7	24
α-helix	429-431	3
β-strand	436-437	2	28
β-strand	450-452	3	28
α-helix	462-465	4
β-strand	466	1	28
β-strand	474	1	29
α-helix	481-482	2
β-strand	488-504	17	28
β-strand	521-529	9	28
β-strand	536-537	2	28
β-strand	539	1	30
β-strand	546	1	30
β-strand	549-550	2	28
β-strand	559-578	20	28
β-strand	579	1	31
β-strand	582	1	31
β-strand	585	1	29
β-strand	586-592	7	28

Chain G: 9 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	151-152	2	41
β-strand	157-161	5	42
α-helix	168-170	3
β-strand	174-178	5	41
β-strand	190-195	6	42
β-strand	212-216	5	41
α-helix	224	1
β-strand	225-229	5	41
α-helix	234-237	4
β-strand	246-250	5	41
β-strand	259-265	7	42
β-strand	279-280	2	43
α-helix	290-292	3
β-strand	293-295	3	43
α-helix	306-308	3
β-strand	310	1	43
β-strand	318	1	44
β-strand	329-345	17	43
β-strand	347-348	2	45
β-strand	355-356	2	45
β-strand	357-366	10	43
β-strand	373-374	2	43
β-strand	376-377	2	46
β-strand	380-381	2	46
α-helix	382	1
β-strand	384-385	2	43
β-strand	394-415	22	43
β-strand	420	1	44
β-strand	421-427	7	43
α-helix	429-431	3
β-strand	436-437	2	47
α-helix	447-449	3
β-strand	451-452	2	48
β-strand	466	1	47
α-helix	481-482	2
β-strand	488-491	4	48
β-strand	498-504	7	47
β-strand	521-529	9	48
β-strand	535-537	3	48
β-strand	539	1	49
β-strand	546	1	49
β-strand	549-550	2	48
β-strand	559-566	8	47
β-strand	570-578	9	48
β-strand	579	1	50
β-strand	582	1	50
β-strand	586-591	6	47

Chain J: 8 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	151-153	3	59
β-strand	157-161	5	60
α-helix	168-170	3
β-strand	174-180	7	59
β-strand	185-195	11	60
β-strand	212-216	5	59
α-helix	224	1
β-strand	225-229	5	59
α-helix	233-237	5
β-strand	238-240	3	60
β-strand	244-250	7	59
β-strand	259-268	10	60
β-strand	279-280	2	61
α-helix	290-292	3
β-strand	293-295	3	61
α-helix	306-308	3
β-strand	310	1	61
β-strand	318	1	62
β-strand	329-345	17	61
β-strand	347-348	2	63
β-strand	355-356	2	63
β-strand	357-366	10	61
β-strand	373-374	2	61
β-strand	376-377	2	64
β-strand	380-381	2	64
α-helix	382	1
β-strand	384-385	2	61
β-strand	394-415	22	61
β-strand	420	1	62
β-strand	421-427	7	61
α-helix	429-431	3
β-strand	436-437	2	65
β-strand	451-452	2	65
α-helix	462-464	3
β-strand	466	1	65
β-strand	474	1	66
β-strand	488-504	17	65
β-strand	521-529	9	65
β-strand	536-537	2	65
β-strand	550	1	65
β-strand	559-578	20	65
β-strand	579	1	67
β-strand	582	1	67
β-strand	585	1	66
β-strand	586-592	7	65

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuropilin-2	A, D, G, J	protein	583	Homo sapiens	O60462 (AlphaFold model)
Heavy chian of antibody 10V8 Fab fragment	B, E, H, K	protein	228	Homo sapiens
Light chain of antibody 10V8 Fab fragment	C, F, I, L	protein	215	Homo sapiens

Sequence of entity 1 (A, D, G, J), FASTA

>8IVW_1 Neuropilin-2 (chains A, D, G, J)
HHHHHHENLYFQDPPCGGRLNSKDAGYITSPGYPQDYPSHQNCEWIVYAPEPNQKIVLNF
NPHFEIEKHDCKYDFIEIRDGDSESADLLGKHCGNIAPPTIISSGSMLYIKFTSDYARQG
AGFSLRYEIFKTGSEDCSKNFTSPNGTIESPGFPEKYPHNLDCTFTILAKPKMEIILQFL
IFDLEHDPLQVGEGDCKYDWLDIWDGIPHVGPLIGKYCGTKTPSELRSSTGILSLTFHTD
MAVAKDGFSARYYLVHQEPLENFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLH
GDDNGWTPNLDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDW
MVYRHGKNHKVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTDA
PCSNMLGMLSGLIADSQISASSTQEYLWSPSAARLVSSRSGWFPRIPQAQPGEEWLQVDL
GTPKTVKGVIIQGARGGDSITAVEARAFVRKFKVSYSLNGKDWEYIQDPRTQQPKLFEGN
MHYDTPDIRRFDPIPAQYVRVYPERWSPAGIGMRLEVLGCDWT

Sequence of entity 2 (B, E, H, K), FASTA

>8IVW_2 Heavy chian of antibody 10V8 Fab fragment (chains B, E, H, K)
EVQLVQSGAEVKKPGATVKISCKVSGFNIKDYYIHWVQQAPGKGLEWMGRIDVEDDETKY
APKFQGRVTITADTSTDTAYMELSSLRSEDTAVYYCATPIYGSREAWFAYWGQGTLVTVS
SASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVGGSHHHHHH

Sequence of entity 3 (C, F, I, L), FASTA

>8IVW_3 Light chain of antibody 10V8 Fab fragment (chains C, F, I, L)
DIQMTQSPSSLSASVGDRVTITCTASSSVSSSYLHWYQQKPGKAPKLLIYRTSNLASGVP
SRFSGSGSGTDFTLTISSLQPEDFATYYCHQYYRSPPTFGGGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Inhibition of VEGF binding to neuropilin-2 enhances chemosensitivity and inhibits metastasis in triple-negative breast cancer. Xu, Z., Goel, H.L., Burkart, C. et al. Sci Transl Med (2023) 15:eadf1128-eadf1128. DOI 10.1126/scitranslmed.adf1128 · PubMed

Other PDB entries of the same protein (UniProt O60462 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TJT 1.31 Å, Neuropilin2-b1 domain in a complex with the C-terminal VEGFC peptide
5DQ0 1.8 Å, Structure of human neuropilin-2 b1 domain with novel and unique zinc binding site
8IVX 1.9 Å, Crystal structure of NRP2 in complex with aNRP2-14 Fab fragment
2QQJ 1.95 Å, Crystal Structure of the b1b2 Domains from Human Neuropilin-2
4QDQ 1.95 Å, Physical basis for Nrp2 ligand binding
5DN2 1.95 Å, Human NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-A
2QQO 2.3 Å, Crystal Structure of the a2b1b2 Domains from Human Neuropilin-2
4QDR 2.4 Å, Physical basis for Nrp2 ligand binding
4QDS 2.4 Å, Physical basis for Nrp2 ligand binding
6GH8 2.44 Å, Crystal structure of GP1 domain of Lujo virus in complex with the first CUB domain of…
6TDB 2.45 Å, Neuropilin2-b1 domain in a complex with the C-terminal VEGFB167 peptide
2QQK 2.75 Å, Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab

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