PDB-8ivw: Crystal structure of NRP2 in complex with aNRP2-10 Fab fragment

ID or keywords:

Entry

Database: PDB / ID: 8ivw

Title

Crystal structure of NRP2 in complex with aNRP2-10 Fab fragment

Components

Heavy chian of antibody 10V8 Fab fragment
Light chain of antibody 10V8 Fab fragment
Neuropilin-2Neuropilin

Keywords

MEMBRANE PROTEIN /

Complex /

Antibody

Function / homology

Function and homology information

vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.205 Å

Authors

Geng, Y. / Zhai, L.

Funding support

1items

Citation

Journal: Sci Transl Med / Year: 2023
Title: Inhibition of VEGF binding to neuropilin-2 enhances chemosensitivity and inhibits metastasis in triple-negative breast cancer.
Authors: Xu, Z. / Goel, H.L. / Burkart, C. / Burman, L. / Chong, Y.E. / Barber, A.G. / Geng, Y. / Zhai, L. / Wang, M. / Kumar, A. / Menefee, A. / Polizzi, C. / Eide, L. / Rauch, K. / Rahman, J. / ...

History

Deposition	Mar 29, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 12, 2023	Provider: repository / Type: Initial release
Revision 1.1	Aug 23, 2023	Group: Data collection Category: chem_comp_atom / chem_comp_bond / pdbx_validate_planes Item: _pdbx_validate_planes.type

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8ivw.cif.gz	695.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8ivw.ent.gz		Display	PDB format
PDBx/mmJSON format	8ivw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iv/8ivw ftp://data.pdbj.org/pub/pdb/validation_reports/iv/8ivw	HTTPS FTP

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Related structure data

Related structure data	8ivxC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #267 - Mar 2022 Vascular Endothelial Growth Factor (VegF similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (3) #141 - Sep 2011 O-GlcNAc Transferase similarity (2)

Deposited unit

A: Neuropilin-2

B: Heavy chian of antibody 10V8 Fab fragment

C: Light chain of antibody 10V8 Fab fragment

D: Neuropilin-2

E: Heavy chian of antibody 10V8 Fab fragment

F: Light chain of antibody 10V8 Fab fragment

G: Neuropilin-2

H: Heavy chian of antibody 10V8 Fab fragment

I: Light chain of antibody 10V8 Fab fragment

J: Neuropilin-2

K: Heavy chian of antibody 10V8 Fab fragment

L: Light chain of antibody 10V8 Fab fragment

456 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Neuropilin-2

B: Heavy chian of antibody 10V8 Fab fragment

C: Light chain of antibody 10V8 Fab fragment

defined by author
Evidence: gel filtration
114 kDa, 3 polymers

2

D: Neuropilin-2

E: Heavy chian of antibody 10V8 Fab fragment

F: Light chain of antibody 10V8 Fab fragment

defined by author
114 kDa, 3 polymers

3

G: Neuropilin-2

H: Heavy chian of antibody 10V8 Fab fragment

I: Light chain of antibody 10V8 Fab fragment

defined by author
114 kDa, 3 polymers

4

J: Neuropilin-2

K: Heavy chian of antibody 10V8 Fab fragment

L: Light chain of antibody 10V8 Fab fragment

defined by author
114 kDa, 3 polymers

Unit cell

Length a, b, c (Å)	70.424, 225.164, 142.996
Angle α, β, γ (deg.)	90.000, 91.300, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: CYS / Beg label comp-ID: CYS / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	TRP	TRP	149 - 594	137 - 582
2	1	1	TRP	TRP	149 - 594	137 - 582
3	2	2	ASP	ASP	149 - 593	137 - 581
4	2	2	ASP	ASP	149 - 593	137 - 581
5	3	3	TRP	TRP	149 - 594	137 - 582
6	3	3	TRP	TRP	149 - 594	137 - 582

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30
16	Local NCS retraints between domains: 31 32
17	Local NCS retraints between domains: 33 34
18	Local NCS retraints between domains: 35 36

#1: Protein	Neuropilin-2 / Neuropilin / Vascular endothelial cell growth factor 165 receptor 2 Mass: 65954.930 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NRP2, VEGF165R2 / Production host: Homo sapiens (human) / References: UniProt: O60462
#2: Antibody	Heavy chian of antibody 10V8 Fab fragment Mass: 24704.592 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody	Light chain of antibody 10V8 Fab fragment Mass: 23440.969 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.47 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 21% PEG1000, 0.1M Sodium citrate tribasic dihydrate pH 5.5, 0.05M Lithium sulfate monohydrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 10, 2021
Radiation	Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 3.2→50 Å / Num. obs: 66035 / % possible obs: 90.9 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / CC_1/2: 0.957 / R_merge(I) obs: 0.274 / R_pim(I) all: 0.116 / R_rim(I) all: 0.298 / Χ²: 0.484 / Net I/σ(I): 4.33
Reflection shell	Resolution: 3.2→3.26 Å / Redundancy: 6.5 % / R_merge(I) obs: 1.247 / Mean I/σ(I) obs: 1 / Num. unique obs: 3201 / CC_1/2: 0.434 / R_pim(I) all: 0.517 / R_rim(I) all: 1.352 / Χ²: 0.452 / % possible all: 89.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.205→49.65 Å / Cor.coef. F_o:F_c: 0.859 / Cor.coef. F_o:F_c free: 0.805 / SU B: 37.687 / SU ML: 0.581 / Cross valid method: FREE R-VALUE / ESU R Free: 0.646
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2941	3309	5 %
R_work	0.2477	62689	-
all	0.25	-	-
obs	-	62689	90.56 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 87.439 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.018 Å²	-0 Å²	-0.975 Å²
2-	-	1.911 Å²	0 Å²
3-	-	-	-0.848 Å²

Refinement step

Cycle: LAST / Resolution: 3.205→49.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26621	0	0	0	26621

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	27322
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	24170
X-RAY DIFFRACTION	r_ext_dist_refined_b	0.049	0.01	1586
X-RAY DIFFRACTION	r_angle_refined_deg	1.313	1.651	37165
X-RAY DIFFRACTION	r_angle_other_deg	0.477	1.561	56578
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.879	5	3387
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.769	5	146
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	24.159	10	4422
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.832	10	1171
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	4078
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	30913
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5447
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	4710
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.222	0.2	23116
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	12565
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	15457
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.233	0.2	398
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.165	0.2	10
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.334	0.2	51
X-RAY DIFFRACTION	r_nbd_other	0.316	0.2	141
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.169	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	6.311	8.8	13629
X-RAY DIFFRACTION	r_mcbond_other	6.31	8.8	13629
X-RAY DIFFRACTION	r_mcangle_it	10.37	13.16	16989
X-RAY DIFFRACTION	r_mcangle_other	10.371	13.161	16990
X-RAY DIFFRACTION	r_scbond_it	5.715	9.213	13693
X-RAY DIFFRACTION	r_scbond_other	5.715	9.213	13694
X-RAY DIFFRACTION	r_scangle_it	9.588	13.678	20176
X-RAY DIFFRACTION	r_scangle_other	9.588	13.678	20177
X-RAY DIFFRACTION	r_lrange_it	18.386	171.465	111150
X-RAY DIFFRACTION	r_lrange_other	18.386	171.465	111151
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.112	0.05	13469
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.123	0.05	12657
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.11	0.05	13733
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.029	0.05	6529
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.02	0.05	6563
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.028	0.05	6523
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.016	0.05	6820
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.009	0.05	6827
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.01	0.05	6812
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.131	0.05	12465
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.103	0.05	13665
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.027	0.05	6604
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.013	0.05	6645
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.017	0.05	6822
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.016	0.05	6823
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.126	0.05	12482
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.026	0.05	6603
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.011	0.05	6815

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.11202	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.11202	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.12312	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.12312	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.11039	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.11039	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.02873	0.05011
4	8	A	X-RAY DIFFRACTION	Local ncs	0.02873	0.05011
5	9	A	X-RAY DIFFRACTION	Local ncs	0.02015	0.05011
5	10	A	X-RAY DIFFRACTION	Local ncs	0.02015	0.05011
6	11	A	X-RAY DIFFRACTION	Local ncs	0.02822	0.05011
6	12	A	X-RAY DIFFRACTION	Local ncs	0.02822	0.05011
7	13	A	X-RAY DIFFRACTION	Local ncs	0.01636	0.05012
7	14	A	X-RAY DIFFRACTION	Local ncs	0.01636	0.05012
8	15	A	X-RAY DIFFRACTION	Local ncs	0.00894	0.05012
8	16	A	X-RAY DIFFRACTION	Local ncs	0.00894	0.05012
9	17	A	X-RAY DIFFRACTION	Local ncs	0.01012	0.05012
9	18	A	X-RAY DIFFRACTION	Local ncs	0.01012	0.05012
10	19	A	X-RAY DIFFRACTION	Local ncs	0.13094	0.05009
10	20	A	X-RAY DIFFRACTION	Local ncs	0.13094	0.05009
11	21	A	X-RAY DIFFRACTION	Local ncs	0.10279	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.10279	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.02712	0.05011
12	24	A	X-RAY DIFFRACTION	Local ncs	0.02712	0.05011
13	25	A	X-RAY DIFFRACTION	Local ncs	0.01258	0.05012
13	26	A	X-RAY DIFFRACTION	Local ncs	0.01258	0.05012
14	27	A	X-RAY DIFFRACTION	Local ncs	0.01666	0.05012
14	28	A	X-RAY DIFFRACTION	Local ncs	0.01666	0.05012
15	29	A	X-RAY DIFFRACTION	Local ncs	0.01576	0.05012
15	30	A	X-RAY DIFFRACTION	Local ncs	0.01576	0.05012
16	31	A	X-RAY DIFFRACTION	Local ncs	0.12642	0.05009
16	32	A	X-RAY DIFFRACTION	Local ncs	0.12642	0.05009
17	33	A	X-RAY DIFFRACTION	Local ncs	0.02585	0.05011
17	34	A	X-RAY DIFFRACTION	Local ncs	0.02585	0.05011
18	35	A	X-RAY DIFFRACTION	Local ncs	0.01071	0.05012
18	36	A	X-RAY DIFFRACTION	Local ncs	0.01071	0.05012

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
3.205-3.288	0.374	216	0.345	4285	0.347	5343	0.88	0.901	84.2411	0.343
3.288-3.378	0.375	243	0.343	4425	0.345	5221	0.899	0.919	89.4082	0.34
3.378-3.475	0.349	235	0.316	4274	0.318	5071	0.912	0.932	88.9174	0.311
3.475-3.581	0.318	260	0.303	4119	0.304	4940	0.932	0.938	88.6437	0.294
3.581-3.698	0.305	229	0.283	4059	0.284	4826	0.934	0.947	88.8521	0.269
3.698-3.827	0.316	190	0.259	3837	0.261	4567	0.933	0.956	88.176	0.239
3.827-3.971	0.3	220	0.259	3734	0.261	4491	0.943	0.957	88.0428	0.234
3.971-4.132	0.305	174	0.25	3637	0.253	4330	0.943	0.96	88.0139	0.224
4.132-4.314	0.268	169	0.222	3471	0.224	4089	0.953	0.968	89.0193	0.197
4.314-4.523	0.266	161	0.193	3392	0.196	3950	0.957	0.976	89.9494	0.168
4.523-4.766	0.241	144	0.185	3239	0.187	3779	0.965	0.979	89.521	0.159
4.766-5.052	0.216	143	0.182	3080	0.183	3558	0.968	0.979	90.5846	0.161
5.052-5.397	0.273	155	0.203	2895	0.206	3348	0.945	0.974	91.0992	0.181
5.397-5.823	0.309	140	0.21	2751	0.215	3115	0.944	0.972	92.809	0.188
5.823-6.37	0.259	133	0.224	2661	0.225	2876	0.956	0.968	97.1488	0.202
6.37-7.107	0.312	113	0.234	2487	0.237	2614	0.939	0.964	99.4644	0.214
7.107-8.179	0.23	124	0.209	2170	0.21	2298	0.966	0.972	99.8259	0.199
8.179-9.95	0.229	129	0.207	1853	0.208	1982	0.967	0.974	100	0.204
9.95-13.797	0.231	82	0.231	1453	0.231	1535	0.973	0.969	100	0.232
13.797-49.65	0.587	49	0.491	867	0.496	923	0.867	0.887	99.2416	0.459

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