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- PDB-5dn2: Human NRP2 b1 domain in complex with the peptide corresponding to... -

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Basic information

Entry
Database: PDB / ID: 5dn2
TitleHuman NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-A
Components
  • Neuropilin-2
  • Vascular endothelial growth factor A
KeywordsSIGNALING PROTEIN / Neuropilin-2 / VEGFA / Angiogenesis / heparin / receptor
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 / basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / VEGF-A complex / Signaling by VEGF ...vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / VEGF-A complex / Signaling by VEGF / cellular stress response to acid chemical / trigeminal nerve structural organization / sensory neuron axon guidance / positive regulation of lymphangiogenesis / facial nerve structural organization / vascular endothelial growth factor receptor 1 binding / negative regulation of adherens junction organization / branchiomotor neuron axon guidance / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / negative regulation of establishment of endothelial barrier / VEGF ligand-receptor interactions / primitive erythrocyte differentiation / positive regulation of mast cell chemotaxis / vascular endothelial growth factor receptor binding / post-embryonic camera-type eye development / lymph vessel morphogenesis / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / negative regulation of blood-brain barrier permeability / axon extension involved in axon guidance / : / VEGF-activated neuropilin signaling pathway / bone trabecula formation / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / sympathetic neuron projection extension / lymphangiogenesis / NrCAM interactions / Neuropilin interactions with VEGF and VEGFR / motor neuron migration / vascular endothelial growth factor receptor-2 signaling pathway / VEGF binds to VEGFR leading to receptor dimerization / neural crest cell migration involved in autonomic nervous system development / sympathetic ganglion development / positive regulation of trophoblast cell migration / lung vasculature development / positive regulation of axon extension involved in axon guidance / regulation of hematopoietic progenitor cell differentiation / vascular endothelial growth factor receptor activity / eye photoreceptor cell development / endothelial cell chemotaxis / positive regulation of protein localization to early endosome / positive regulation of protein autophosphorylation / nerve development / vascular wound healing / positive regulation of epithelial tube formation / neuropilin binding / semaphorin receptor complex / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / camera-type eye morphogenesis / positive regulation of branching involved in ureteric bud morphogenesis / induction of positive chemotaxis / transmembrane receptor protein tyrosine kinase activator activity / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of vascular permeability / semaphorin receptor activity / dopaminergic neuron differentiation / vascular endothelial growth factor receptor 2 binding / tube formation / positive regulation of peptidyl-tyrosine phosphorylation / commissural neuron axon guidance / positive regulation of vascular endothelial growth factor signaling pathway / cell migration involved in sprouting angiogenesis / outflow tract septum morphogenesis / positive regulation of blood vessel branching / surfactant homeostasis / platelet-derived growth factor receptor binding / sprouting angiogenesis / extracellular matrix binding / endothelial cell proliferation / epithelial cell maturation / positive regulation of positive chemotaxis / retinal ganglion cell axon guidance / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of leukocyte migration / regulation of postsynapse organization / positive regulation of endothelial cell chemotaxis / artery morphogenesis / cardiac muscle cell development / positive regulation of cell migration involved in sprouting angiogenesis / vascular endothelial growth factor signaling pathway / positive regulation of DNA biosynthetic process / negative chemotaxis / negative regulation of epithelial to mesenchymal transition / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / growth factor binding / positive chemotaxis / negative regulation of fat cell differentiation / positive regulation of sprouting angiogenesis
Similarity search - Function
Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / : / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain ...Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / : / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / : / Coagulation factors 5/8 type C domain (FA58C) signature 2. / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / Spermadhesin, CUB domain superfamily / CUB domain profile. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Cystine-knot cytokine / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Neuropilin-2 / Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsTsai, Y.C.I. / Frankel, P. / Fotinou, C. / Rana, R. / Zachary, I. / Djordjevic, S.
CitationJournal: Febs J. / Year: 2016
Title: Structural studies of neuropilin-2 reveal a zinc ion binding site remote from the vascular endothelial growth factor binding pocket.
Authors: Tsai, Y.C. / Fotinou, C. / Rana, R. / Yelland, T. / Frankel, P. / Zachary, I. / Djordjevic, S.
History
DepositionSep 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.3Mar 25, 2026Group: Database references / Category: pdbx_database_related

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuropilin-2
B: Neuropilin-2
C: Neuropilin-2
D: Neuropilin-2
F: Vascular endothelial growth factor A
G: Vascular endothelial growth factor A
E: Vascular endothelial growth factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,76310
Polymers81,4957
Non-polymers2683
Water4,846269
1
A: Neuropilin-2
G: Vascular endothelial growth factor A


Theoretical massNumber of molelcules
Total (without water)21,2182
Polymers21,2182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neuropilin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0213
Polymers17,8411
Non-polymers1802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Neuropilin-2
E: Vascular endothelial growth factor A


Theoretical massNumber of molelcules
Total (without water)21,2182
Polymers21,2182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Neuropilin-2
F: Vascular endothelial growth factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3063
Polymers21,2182
Non-polymers881
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.250, 139.520, 106.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 5 / Auth seq-ID: 274 - 429 / Label seq-ID: 1 - 156

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Neuropilin-2 / Vascular endothelial cell growth factor 165 receptor 2


Mass: 17841.074 Da / Num. of mol.: 4
Fragment: Neuropilin-2 domain B1 F5/8 type C 1, UNP residues 275-429
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP2, VEGF165R2 / Plasmid: pET15b-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / Variant (production host): Rosetta-gami 2(DE3)pLysS / References: UniProt: O60462
#2: Protein/peptide Vascular endothelial growth factor A / VEGF-A / Vascular permeability factor / VPF


Mass: 3376.897 Da / Num. of mol.: 3 / Fragment: VEGF-A165-HBD, UNP residues 205-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VEGFA, VEGF / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / Variant (production host): Shuffle / References: UniProt: P15692
#3: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 10% PEG20000, 0.1M Bicine, 2% v/v dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.95→86.5 Å / Num. obs: 59661 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.8
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 4.3 / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QQJ

2qqj


Resolution: 1.95→86.5 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.187 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23368 3006 5 %RANDOM
Rwork0.20425 ---
obs0.20576 56630 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.756 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å20 Å20 Å2
2---1.79 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.95→86.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5160 0 18 269 5447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195359
X-RAY DIFFRACTIONr_bond_other_d0.0020.025049
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9367262
X-RAY DIFFRACTIONr_angle_other_deg0.923311550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2985651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85223.213277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20715922
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5891554
X-RAY DIFFRACTIONr_chiral_restr0.0860.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026159
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021367
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9191.8492571
X-RAY DIFFRACTIONr_mcbond_other0.9121.8482570
X-RAY DIFFRACTIONr_mcangle_it1.5942.7533206
X-RAY DIFFRACTIONr_mcangle_other1.5942.7543207
X-RAY DIFFRACTIONr_scbond_it0.912.0272788
X-RAY DIFFRACTIONr_scbond_other0.9082.0272788
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5492.9814047
X-RAY DIFFRACTIONr_long_range_B_refined4.24514.8715806
X-RAY DIFFRACTIONr_long_range_B_other4.24514.8765807
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A907medium positional0.190.5
B907medium positional0.170.5
C907medium positional0.170.5
D907medium positional0.140.5
A1451loose positional0.55
B1451loose positional0.65
C1451loose positional0.545
D1451loose positional0.535
A907medium thermal2.182
B907medium thermal1.632
C907medium thermal1.372
D907medium thermal2.372
A1451loose thermal2.5410
B1451loose thermal1.8710
C1451loose thermal1.6510
D1451loose thermal2.6410
LS refinement shellResolution: 1.947→1.998 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 199 -
Rwork0.254 4069 -
obs--97.38 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3164-0.38230.39921.155-0.18260.79420.0561-0.026-0.0203-0.1616-0.04680.07220.02550.0752-0.00940.02390.006-0.00210.138-0.00420.0544-10.791343.0668-3.7927
20.2048-0.2311-0.26571.2594-0.01630.6560.0259-0.03380.0142-0.148-0.0647-0.09650.0183-0.07530.03880.02190.00820.0270.13820.00930.06314.351426.6766-3.6816
30.64530.0967-0.02770.1865-0.26070.8729-0.0149-0.0780.017-0.00250.020.02220.02840.0631-0.0050.0756-0.0068-0.01660.0831-0.00130.023630.279455.499-24.0966
40.6538-0.00930.02250.13560.31911.01990.0060.08760.05150.01890.0074-0.00690.0852-0.0242-0.01330.07940.0228-0.00420.08870.01330.010421.097855.451624.2083
500000000000000-00.066000.06600.066000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A274 - 429
2X-RAY DIFFRACTION2B274 - 429
3X-RAY DIFFRACTION3C274 - 429
4X-RAY DIFFRACTION4D274 - 429

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