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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-2Neuropilin
  • 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 / basophil chemotaxis / trigeminal ganglion development / cellular stress response to acid chemical / 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 / basophil chemotaxis / trigeminal ganglion development / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / branchiomotor neuron axon guidance / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / positive regulation of peptidyl-tyrosine autophosphorylation / negative regulation of adherens junction organization / post-embryonic camera-type eye development / primitive erythrocyte differentiation / positive regulation of protein kinase C signaling / negative regulation of blood-brain barrier permeability / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / axon extension involved in axon guidance / VEGF-activated neuropilin signaling pathway / positive regulation of vascular endothelial growth factor signaling pathway / NrCAM interactions / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / sympathetic neuron projection extension / motor neuron migration / Neurophilin interactions with VEGF and VEGFR / positive regulation of trophoblast cell migration / endothelial cell chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / sympathetic ganglion development / eye photoreceptor cell development / vascular endothelial growth factor receptor-2 signaling pathway / VEGF binds to VEGFR leading to receptor dimerization / regulation of nitric oxide mediated signal transduction / neural crest cell migration involved in autonomic nervous system development / positive regulation of axon extension involved in axon guidance / positive regulation of cell migration by vascular endothelial growth factor signaling pathway / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of protein localization to early endosome / vascular wound healing / vascular endothelial growth factor receptor activity / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / nerve development / semaphorin receptor complex / tube formation / camera-type eye morphogenesis / positive regulation of epithelial tube formation / negative regulation of cell-cell adhesion mediated by cadherin / neuropilin binding / induction of positive chemotaxis / coronary artery morphogenesis / vascular endothelial growth factor receptor 2 binding / outflow tract septum morphogenesis / semaphorin receptor activity / commissural neuron axon guidance / positive regulation of vascular permeability / dopaminergic neuron differentiation / surfactant homeostasis / positive regulation of endothelial cell chemotaxis / platelet-derived growth factor receptor binding / extracellular matrix binding / cell migration involved in sprouting angiogenesis / retinal ganglion cell axon guidance / artery morphogenesis / cardiac muscle cell development / sprouting angiogenesis / positive regulation of positive chemotaxis / regulation of postsynapse organization / Regulation of gene expression by Hypoxia-inducible Factor / vascular endothelial growth factor signaling pathway / positive regulation of leukocyte migration / positive regulation of p38MAPK cascade / positive regulation of DNA biosynthetic process / negative chemotaxis / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / positive regulation of cell migration involved in sprouting angiogenesis / positive chemotaxis / cytokine binding / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of sprouting angiogenesis / outflow tract morphogenesis / activation of protein kinase activity / chemoattractant activity / growth factor binding / positive regulation of focal adhesion assembly / mesoderm development / monocyte differentiation / semaphorin-plexin signaling pathway
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 / Platelet-derived growth factor (PDGF) family signature. ...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) / MAM domain, meprin/A5/mu / MAM domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / MAM domain profile. / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Spermadhesin, CUB domain superfamily / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / Cystine-knot cytokine / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / 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

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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
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 / Neuropilin / 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 / 1,4-Dioxane


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 / Glycerol


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


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

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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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