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- PDB-6tkk: Neuropilin 1-b1 domain in a complex with the C-terminal VEGFB186 ... -

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Basic information

Entry
Database: PDB / ID: 6tkk
TitleNeuropilin 1-b1 domain in a complex with the C-terminal VEGFB186 peptide
Components
  • ACE-ARG-PRO-GLN-PRO-ARG
  • Neuropilin-1
KeywordsSIGNALING PROTEIN / VEGF-binding / NRP1 / angiogenesis / immunomodulation
Function / homology
Function and homology information


endothelial tip cell fate specification / basal dendrite development / otic placode development / protein localization to early endosome / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration ...endothelial tip cell fate specification / basal dendrite development / otic placode development / protein localization to early endosome / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / positive regulation of vascular wound healing / trigeminal nerve structural organization / sensory neuron axon guidance / postsynapse organization / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / vascular endothelial growth factor receptor 1 binding / branchiomotor neuron axon guidance / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / negative regulation of axon extension involved in axon guidance / positive regulation of mast cell chemotaxis / axon extension involved in axon guidance / renal artery morphogenesis / VEGF-activated neuropilin signaling pathway / neurofilament / sympathetic neuron projection extension / regulation of vascular endothelial growth factor receptor signaling pathway / Neurophilin interactions with VEGF and VEGFR / vascular endothelial growth factor binding / endothelial cell chemotaxis / VEGF binds to VEGFR leading to receptor dimerization / motor neuron migration / neural crest cell migration involved in autonomic nervous system development / sympathetic ganglion development / positive regulation of axon extension involved in axon guidance / axonogenesis involved in innervation / CHL1 interactions / semaphorin receptor complex / regulation of vesicle-mediated transport / Signaling by ROBO receptors / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / neuropilin signaling pathway / angiogenesis involved in coronary vascular morphogenesis / substrate-dependent cell migration, cell extension / hepatocyte growth factor receptor signaling pathway / coronary artery morphogenesis / induction of positive chemotaxis / CRMPs in Sema3A signaling / semaphorin receptor activity / commissural neuron axon guidance / outflow tract septum morphogenesis / protein O-linked glycosylation / coronary vasculature development / motor neuron axon guidance / regulation of Cdc42 protein signal transduction / cell migration involved in sprouting angiogenesis / axonal fasciculation / positive regulation of vascular endothelial growth factor receptor signaling pathway / neural crest cell migration / sprouting angiogenesis / positive regulation of filopodium assembly / vascular endothelial growth factor signaling pathway / artery morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to hepatocyte growth factor stimulus / retinal ganglion cell axon guidance / branching involved in blood vessel morphogenesis / positive regulation of smooth muscle cell migration / positive chemotaxis / growth factor binding / cytokine binding / chemoattractant activity / sorting endosome / semaphorin-plexin signaling pathway / platelet-derived growth factor receptor signaling pathway / positive regulation of cell division / Sema3A PAK dependent Axon repulsion / cellular response to vascular endothelial growth factor stimulus / positive regulation of focal adhesion assembly / vascular endothelial growth factor receptor signaling pathway / vasculogenesis / positive regulation of phosphorylation / coreceptor activity / cardiac muscle contraction / positive regulation of stress fiber assembly / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / GTPase activator activity / axon guidance / platelet alpha granule lumen / animal organ morphogenesis / Signal transduction by L1 / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway
Similarity search - Function
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 ...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 / MAM domain signature. / 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-1 / Vascular endothelial growth factor B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsEldrid, C. / Yu, L. / Yelland, T. / Fotinou, C. / Djordjevic, S.
CitationJournal: To Be Published
Title: Neuropilin 1-b1 domain in a complex with the C-terminal VEGFB186 peptide
Authors: Eldrid, C. / Yu, L. / Yelland, T. / Fotinou, C. / Djordjevic, S.
History
DepositionNov 28, 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

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Assembly

Deposited unit
A: Neuropilin-1
B: ACE-ARG-PRO-GLN-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7845
Polymers18,5982
Non-polymers1863
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint3 kcal/mol
Surface area8890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.880, 39.980, 97.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 17917.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP1, NRP, VEGF165R / Production host: Escherichia coli (E. coli) / References: UniProt: O14786
#2: Protein/peptide ACE-ARG-PRO-GLN-PRO-ARG


Mass: 680.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49765*PLUS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.04 Å3/Da / Density % sol: 39.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 16 % w/v PEG3350 and 200 mM ammonium chloride

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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: Feb 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.06→48.81 Å / Num. obs: 55937 / % possible obs: 80.2 % / Redundancy: 5.5 % / Biso Wilson estimate: 8.76 Å2 / CC1/2: 0.999 / Net I/σ(I): 29.4
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
1.06-1.096450.5591
4.62-48.819720.9971

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Processing

Software
NameVersionClassification
REFMAC1.14_3260refinement
PHENIX1.14_3260refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RN5

4rn5


Resolution: 1.06→48.805 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 13.7871
RfactorNum. reflection% reflection
Rfree0.1495 2785 4.98 %
Rwork0.1361 --
obs0.1367 55869 80.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 13.29 Å2
Refinement stepCycle: LAST / Resolution: 1.06→48.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1299 0 12 195 1506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01181381
X-RAY DIFFRACTIONf_angle_d1.29941872
X-RAY DIFFRACTIONf_chiral_restr0.1113200
X-RAY DIFFRACTIONf_plane_restr0.01239
X-RAY DIFFRACTIONf_dihedral_angle_d14.6262521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.080.201150.2901263X-RAY DIFFRACTION8.05
1.08-1.10.1395460.1497700X-RAY DIFFRACTION21.79
1.1-1.120.1615400.10341062X-RAY DIFFRACTION32
1.12-1.140.1463600.09521417X-RAY DIFFRACTION42.81
1.14-1.170.11791020.09671823X-RAY DIFFRACTION56.07
1.17-1.190.11611290.09742238X-RAY DIFFRACTION68.89
1.19-1.220.13141380.09872665X-RAY DIFFRACTION81.46
1.22-1.260.13081630.09953068X-RAY DIFFRACTION93.01
1.26-1.290.12261880.10763199X-RAY DIFFRACTION97.78
1.29-1.340.12781830.10543259X-RAY DIFFRACTION99.25
1.34-1.380.12651580.10763285X-RAY DIFFRACTION99.42
1.38-1.440.14051610.10433282X-RAY DIFFRACTION99.45
1.44-1.510.12111740.1083305X-RAY DIFFRACTION99.66
1.51-1.580.13582110.11353221X-RAY DIFFRACTION99.56
1.58-1.680.13111660.11883339X-RAY DIFFRACTION99.55
1.68-1.810.15741970.13353285X-RAY DIFFRACTION99.4
1.81-20.15271610.13883342X-RAY DIFFRACTION99.66
2-2.290.16151550.14293378X-RAY DIFFRACTION99.75
2.29-2.880.16171520.16493409X-RAY DIFFRACTION99.66
2.88-48.8050.16661860.16143544X-RAY DIFFRACTION99.31

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