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- PDB-6tdb: Neuropilin2-b1 domain in a complex with the C-terminal VEGFB167 p... -

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Basic information

Entry
Database: PDB / ID: 6tdb
TitleNeuropilin2-b1 domain in a complex with the C-terminal VEGFB167 peptide
Components
  • C-terminal VEGFB167 peptide
  • Neuropilin-2
KeywordsSIGNALING PROTEIN / VEGF-binding / NRP2 / angiogenesis / immunomodulation
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 ...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 / branchiomotor neuron axon guidance / axon extension involved in axon guidance / sympathetic neuron projection extension / NrCAM interactions / Neurophilin interactions with VEGF and VEGFR / neural crest cell migration involved in autonomic nervous system development / sympathetic ganglion development / vascular endothelial growth factor receptor activity / outflow tract septum morphogenesis / nerve development / semaphorin receptor complex / semaphorin receptor activity / regulation of postsynapse organization / negative chemotaxis / cytokine binding / growth factor binding / semaphorin-plexin signaling pathway / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / cellular response to leukemia inhibitory factor / axon guidance / heparin binding / signaling receptor activity / angiogenesis / postsynaptic membrane / cell adhesion / axon / glutamatergic synapse / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / : / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. ...Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / : / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 2. / 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 / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
ACETYL GROUP / Neuropilin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsEldrid, C. / Yu, L. / Yelland, T. / Fotinou, C. / Djordjevic, S.
Citation
Journal: To Be Published
Title: NRP2-b1 domain in a complex with the C-terminal VEGFB167 peptide
Authors: Eldrid, C. / Yu, L. / Yelland, T. / Fotinou, C. / Djordjevic, S.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionNov 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuropilin-2
B: Neuropilin-2
C: Neuropilin-2
D: Neuropilin-2
F: C-terminal VEGFB167 peptide
J: C-terminal VEGFB167 peptide
K: C-terminal VEGFB167 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,90011
Polymers75,6707
Non-polymers2304
Water4,990277
1
A: Neuropilin-2
F: C-terminal VEGFB167 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2074
Polymers19,1012
Non-polymers1062
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neuropilin-2
F: C-terminal VEGFB167 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2074
Polymers19,1012
Non-polymers1062
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neuropilin-2
J: C-terminal VEGFB167 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1633
Polymers19,1012
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Neuropilin-2
K: C-terminal VEGFB167 peptide


Theoretical massNumber of molelcules
Total (without water)19,1012
Polymers19,1012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.359, 140.122, 74.357
Angle α, β, γ (deg.)90.000, 132.972, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11D-555-

HOH

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Components

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


Mass: 18368.584 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The first N terminal residue in chains B, C and D, the four C terminal residues in chain A, B and C, and the two C terminal residues in chain D, were not seen in an electron density map.
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP2, VEGF165R2 / Production host: Escherichia coli (E. coli) / References: UniProt: O60462
#2: Protein/peptide C-terminal VEGFB167 peptide


Mass: 731.934 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: The electron density for this peptide only allows for modelling of two C terminal residues.
Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: N2b1-apo 0.05 M KCl, 0.01 M MgCl2 and 15 % (w/v) PEG600 N2b1/VEGFB167 0.1 M HEPES pH 7.5, 10 % (w/v) PEG4000, 20 % (w/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.977 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: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.45→70.06 Å / Num. obs: 29170 / % possible obs: 98.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 47.64 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
2.45-2.5842780.7381
7.75-70.069280.9971

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Processing

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

4rn5


Resolution: 2.45→70.06 Å / SU ML: 0.3616 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.2635
RfactorNum. reflection% reflection
Rfree0.2497 1428 4.9 %
Rwork0.1827 --
obs0.1859 29159 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.42 Å2
Refinement stepCycle: LAST / Resolution: 2.45→70.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5126 0 12 277 5415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00395291
X-RAY DIFFRACTIONf_angle_d0.69087170
X-RAY DIFFRACTIONf_chiral_restr0.0465767
X-RAY DIFFRACTIONf_plane_restr0.003938
X-RAY DIFFRACTIONf_dihedral_angle_d21.0231948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.540.31431660.25322756X-RAY DIFFRACTION99.52
2.54-2.640.33551770.25372747X-RAY DIFFRACTION99.8
2.64-2.760.34231390.24142794X-RAY DIFFRACTION99.39
2.76-2.910.29981410.22922767X-RAY DIFFRACTION99.22
2.91-3.090.29361390.20532787X-RAY DIFFRACTION99.46
3.09-3.330.28291280.1882793X-RAY DIFFRACTION99.59
3.33-3.660.27691200.17532815X-RAY DIFFRACTION98.89
3.66-4.190.2011480.16462746X-RAY DIFFRACTION98
4.19-5.280.21061240.14332780X-RAY DIFFRACTION97.88
5.28-70.060.21511460.18022746X-RAY DIFFRACTION96.63

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