8IVX: NRP2

Crystal structure of NRP2 in complex with aNRP2-14 Fab fragment. Determined by X-ray diffraction at 1.9 Å resolution. Released 12 Jul 2023.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,954
Mol. weight: 114.54 kDa
Released: 12 Jul 2023

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

Secondary structure: helices and β-sheets

8IVX contains 24 α-helices and 81 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: 10 helices, 37 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	185-194	10	2
β-strand	212-216	5	1
α-helix	224	1
β-strand	225-229	5	1
α-helix	234-237	4
β-strand	238-240	3	2
β-strand	244-250	7	1
β-strand	260-268	9	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
α-helix	383	1
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	6
α-helix	447-449	3
β-strand	450-452	3	6
α-helix	462-465	4
β-strand	466	1	6
β-strand	474	1	7
β-strand	488-504	17	6
β-strand	506	1	8
β-strand	519	1	8
β-strand	521-529	9	6
β-strand	536-537	2	6
α-helix	538	1
β-strand	539-540	2	9
β-strand	545-546	2	9
β-strand	549-550	2	6
β-strand	559-578	20	6
β-strand	585	1	7
β-strand	586-593	8	6

Chain H: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	18-25	8	10
β-strand	34-40	7	12
β-strand	44-51	8	12
β-strand	57-59	3	12
β-strand	67-72	6	10
α-helix	73-75	3
β-strand	77-82	6	10
α-helix	87-89	3
β-strand	91-98	8	12
β-strand	107-110	4	12
β-strand	114-116	3	12
β-strand	117-118	2	11
α-helix	122-123	2
β-strand	124	1	13
α-helix	125-126	2
β-strand	127-131	5	14
β-strand	142-152	11	14
β-strand	153	1	13
β-strand	158-161	4	15
α-helix	162-164	3
β-strand	166	1	15
β-strand	170-172	3	14
α-helix	173-175	3
β-strand	176-178	3	14
β-strand	181-191	11	14
β-strand	201-206	6	15
α-helix	207-209	3
β-strand	211-216	6	15

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	16
β-strand	10-13	4	17
β-strand	19-25	7	16
β-strand	33-38	6	17
β-strand	45-49	5	17
β-strand	53-54	2	17
α-helix	55	1
β-strand	62-67	6	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	85-90	6	17
α-helix	96	1
β-strand	98-99	2	17
β-strand	103-107	5	17
β-strand	112	1	18
β-strand	115-119	5	19
α-helix	120-122	3
α-helix	123-127	5
β-strand	130-140	11	19
β-strand	141	1	18
β-strand	146-151	6	20
β-strand	154-156	3	20
β-strand	160-164	5	19
α-helix	165-168	4
β-strand	174-183	10	19
α-helix	184-188	5
β-strand	192-198	7	20
β-strand	206-211	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
aNRP2-14	A	protein	583	Homo sapiens	O60462 (AlphaFold model)
Heavy chain of antibody 14V4 Fab fragment	H	protein	231	Homo sapiens
Light chain of antibody 14V4 Fab fragment	L	protein	215	Homo sapiens

Sequence of entity 1 (A), FASTA

>8IVX_1 aNRP2-14 (chains A)
HHHHHHENLYFQDPPCGGRLNSKDAGYITSPGYPQDYPSHQNCEWIVYAPEPNQKIVLNF
NPHFEIEKHDCKYDFIEIRDGDSESADLLGKHCGNIAPPTIISSGSMLYIKFTSDYARQG
AGFSLRYEIFKTGSEDCSKNFTSPNGTIESPGFPEKYPHNLDCTFTILAKPKMEIILQFL
IFDLEHDPLQVGEGDCKYDWLDIWDGIPHVGPLIGKYCGTKTPSELRSSTGILSLTFHTD
MAVAKDGFSARYYLVHQEPLENFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLH
GDDNGWTPNLDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDW
MVYRHGKNHKVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTDA
PCSNMLGMLSGLIADSQISASSTQEYLWSPSAARLVSSRSGWFPRIPQAQPGEEWLQVDL
GTPKTVKGVIIQGARGGDSITAVEARAFVRKFKVSYSLNGKDWEYIQDPRTQQPKLFEGN
MHYDTPDIRRFDPIPAQYVRVYPERWSPAGIGMRLEVLGCDWT

Sequence of entity 2 (H), FASTA

>8IVX_2 Heavy chain of antibody 14V4 Fab fragment (chains H)
QVQLKQSGPGLVQPSQSLSITCTVSGFSLTSYGVHWVRQSPGKGLEWLGLIWSGGSTDYS
PAFISRLSISEDNSKSQVFFKMNSLQADDTAIYFCARNSYSSGYYAMDYWGQGTSVTVSS
AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCGGSHHHHHH

Sequence of entity 3 (L), FASTA

>8IVX_3 Light chain of antibody 14V4 Fab fragment (chains L)
DIVMTQSQKFMSTTVGDRVSITCKASQNVGTAVAWYQQKPGQSPKLLIYSASNRYTGVPD
RFTGSGSGTDFTLTISNMQSEDLADYFCQQYSSYPPYTFGGGTKLEIKRADAAPTVSIFP
PSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTL
TLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

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
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
2QQL 3.1 Å, Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab

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