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- PDB-6tjt: Neuropilin2-b1 domain in a complex with the C-terminal VEGFC peptide -

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Basic information

Entry
Database: PDB / ID: 6tjt
TitleNeuropilin2-b1 domain in a complex with the C-terminal VEGFC peptide
Components
  • Neuropilin-2
  • VEGFC C terminal peptide
KeywordsSIGNALING PROTEIN / VEGF-binding / NRP2 / angiogenesis / immunomodulation
Function / homology
Function and homology information


vascular endothelial growth factor receptor 3 binding / substrate-dependent cell migration / 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 ...vascular endothelial growth factor receptor 3 binding / substrate-dependent cell migration / 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 / positive regulation of lymphangiogenesis / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / branchiomotor neuron axon guidance / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / axon extension involved in axon guidance / morphogenesis of embryonic epithelium / sympathetic neuron projection extension / NrCAM interactions / regulation of vascular endothelial growth factor receptor signaling pathway / Neurophilin interactions with VEGF and VEGFR / positive regulation of mesenchymal stem cell proliferation / VEGF binds to VEGFR leading to receptor dimerization / neural crest cell migration involved in autonomic nervous system development / sympathetic ganglion development / vascular endothelial growth factor receptor activity / nerve development / semaphorin receptor complex / induction of positive chemotaxis / semaphorin receptor activity / outflow tract septum morphogenesis / sprouting angiogenesis / regulation of postsynapse organization / vascular endothelial growth factor signaling pathway / negative chemotaxis / growth factor binding / positive regulation of neuroblast proliferation / chemoattractant activity / cytokine binding / semaphorin-plexin signaling pathway / positive regulation of cell division / positive regulation of glial cell proliferation / positive regulation of blood vessel endothelial cell migration / vascular endothelial growth factor receptor signaling pathway / negative regulation of osteoblast differentiation / glial cell proliferation / negative regulation of blood pressure / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / axon guidance / platelet alpha granule lumen / cellular response to leukemia inhibitory factor / animal organ morphogenesis / positive regulation of epithelial cell proliferation / positive regulation of protein secretion / growth factor activity / positive regulation of angiogenesis / Platelet degranulation / signaling receptor activity / heparin binding / angiogenesis / postsynaptic membrane / response to hypoxia / cell adhesion / response to xenobiotic stimulus / axon / positive regulation of cell population proliferation / glutamatergic synapse / signal transduction / extracellular space / extracellular region / metal ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
CXCXC repeat / CXCXC repeat / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / : / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. ...CXCXC repeat / CXCXC repeat / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / : / 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 / CUB domain profile. / Spermadhesin, CUB domain superfamily / 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-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Neuropilin-2 / Vascular endothelial growth factor C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsEldrid, C. / Yu, L. / Yelland, T. / Fotinou, C. / Djordjevic, S.
CitationJournal: To Be Published
Title: NRP2-b1 domain in a complex with the C-terminal VEGFC peptide
Authors: Eldrid, C. / Yu, L. / Yelland, T. / Fotinou, C. / Djordjevic, S.
History
DepositionNov 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
D: VEGFC C terminal peptide
F: VEGFC C terminal peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,84313
Polymers38,0814
Non-polymers7639
Water5,531307
1
A: Neuropilin-2
D: VEGFC C terminal peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2955
Polymers19,0402
Non-polymers2543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neuropilin-2
F: VEGFC C terminal peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5498
Polymers19,0402
Non-polymers5086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.240, 76.544, 63.357
Angle α, β, γ (deg.)90.000, 96.059, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 18368.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first N-terminal residue and the last two C-terminal residues from the protein construct were not observed in the electron density maps.
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP2, VEGF165R2 / Production host: Escherichia coli (E. coli) / References: UniProt: O60462
#2: Protein/peptide VEGFC C terminal peptide


Mass: 671.834 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The electron density for the acetylated N-terminal Ser and the two Ile residues did not allow for the modeling of these residues.
Source: (synth.) Homo sapiens (human) / References: UniProt: P49767*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M NaOAc, 0.1 M HEPES pH 7.5, 12 % (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.31→63 Å / Num. obs: 86786 / % possible obs: 98.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 13.52 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
1.31-1.38124380.9051
4.13-6327580.9961

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RN5

4rn5


Resolution: 1.31→48.64 Å / SU ML: 0.1122 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.0195
RfactorNum. reflection% reflection
Rfree0.179 4267 4.92 %
Rwork0.1533 --
obs0.1545 86693 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.74 Å2
Refinement stepCycle: LAST / Resolution: 1.31→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2586 0 42 307 2935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842691
X-RAY DIFFRACTIONf_angle_d1.09483648
X-RAY DIFFRACTIONf_chiral_restr0.102391
X-RAY DIFFRACTIONf_plane_restr0.0056470
X-RAY DIFFRACTIONf_dihedral_angle_d9.7011557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.320.33531530.30012535X-RAY DIFFRACTION90.72
1.32-1.340.28881400.28362675X-RAY DIFFRACTION97.47
1.34-1.350.29081230.25372735X-RAY DIFFRACTION98.96
1.35-1.370.29961460.24072791X-RAY DIFFRACTION99.39
1.37-1.390.23011410.21732694X-RAY DIFFRACTION99.54
1.39-1.410.24171530.19742844X-RAY DIFFRACTION99.8
1.41-1.430.22671450.18312716X-RAY DIFFRACTION99.86
1.43-1.450.2131250.16892789X-RAY DIFFRACTION99.83
1.45-1.470.19081650.1612795X-RAY DIFFRACTION99.9
1.47-1.50.18671580.14722706X-RAY DIFFRACTION99.93
1.5-1.520.18251300.13962787X-RAY DIFFRACTION99.9
1.52-1.550.16941320.13162776X-RAY DIFFRACTION99.55
1.55-1.580.16161410.12592781X-RAY DIFFRACTION99.76
1.58-1.610.17371560.13642743X-RAY DIFFRACTION99.59
1.61-1.650.16721350.12622795X-RAY DIFFRACTION99.76
1.65-1.680.16251330.1272773X-RAY DIFFRACTION99.86
1.68-1.730.16881330.12862772X-RAY DIFFRACTION99.66
1.73-1.770.14531410.12622752X-RAY DIFFRACTION99.66
1.77-1.820.16451480.1272801X-RAY DIFFRACTION99.7
1.82-1.880.16211410.13042738X-RAY DIFFRACTION99.41
1.88-1.950.17921490.13552774X-RAY DIFFRACTION99.46
1.95-2.030.16311360.13592758X-RAY DIFFRACTION99.25
2.03-2.120.16171580.13832789X-RAY DIFFRACTION99.33
2.12-2.230.14921500.13932710X-RAY DIFFRACTION98.89
2.23-2.370.18411320.14392775X-RAY DIFFRACTION98.34
2.37-2.560.1951510.15642714X-RAY DIFFRACTION97.98
2.56-2.810.18861400.16412732X-RAY DIFFRACTION97.79
2.81-3.220.17021360.16162728X-RAY DIFFRACTION97.32
3.22-4.060.1721340.15312693X-RAY DIFFRACTION95.86
4.06-48.640.16621420.15252755X-RAY DIFFRACTION96.21

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