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- PDB-2orz: Structural Basis for Ligand Binding and Heparin Mediated Activati... -

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Basic information

Entry
Database: PDB / ID: 2orz
TitleStructural Basis for Ligand Binding and Heparin Mediated Activation of Neuropilin
Components
  • Neuropilin-1Neuropilin 1
  • Tuftsin
KeywordsSIGNALING PROTEIN / MEMBRANE PROTEIN / Neuropilin / VEGF / Tuftsin
Function / homology
Function and homology information


Neurophilin interactions with VEGF and VEGFR / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / trigeminal nerve morphogenesis / regulation of axon extension involved in axon guidance / basal dendrite development / protein localization to early endosome / otic placode development / neurofilament ...Neurophilin interactions with VEGF and VEGFR / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / trigeminal nerve morphogenesis / regulation of axon extension involved in axon guidance / basal dendrite development / protein localization to early endosome / otic placode development / neurofilament / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / regulation of vascular endothelial growth factor receptor signaling pathway / 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 / postsynapse organization / branchiomotor neuron axon guidance / renal artery morphogenesis / Signal transduction by L1 / axon extension involved in axon guidance / VEGF-activated neuropilin signaling pathway / negative regulation of axon extension involved in axon guidance / retina vasculature development in camera-type eye / blood vessel endothelial cell migration / sympathetic neuron projection extension / motor neuron migration / endothelial cell chemotaxis / vascular endothelial growth factor binding / sympathetic ganglion development / axonogenesis involved in innervation / neural crest cell migration involved in autonomic nervous system development / positive regulation of axon extension involved in axon guidance / negative regulation of axon extension / vascular endothelial growth factor receptor activity / substrate-dependent cell migration, cell extension / angiogenesis involved in coronary vascular morphogenesis / sympathetic nervous system development / hepatocyte growth factor receptor signaling pathway / neuropilin signaling pathway / coronary artery morphogenesis / outflow tract septum morphogenesis / regulation of Cdc42 protein signal transduction / semaphorin receptor activity / commissural neuron axon guidance / axon extension / motor neuron axon guidance / cell migration involved in sprouting angiogenesis / retinal ganglion cell axon guidance / artery morphogenesis / axonal fasciculation / sprouting angiogenesis / neural crest cell migration / positive regulation of filopodium assembly / branching involved in blood vessel morphogenesis / cellular response to hepatocyte growth factor stimulus / positive regulation of cell migration involved in sprouting angiogenesis / positive chemotaxis / dendrite development / growth factor binding / sorting endosome / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / platelet-derived growth factor receptor signaling pathway / neuron development / endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / vascular endothelial growth factor receptor signaling pathway / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phosphorylation / positive regulation of stress fiber assembly / GTPase activator activity / positive regulation of endothelial cell migration / integrin-mediated signaling pathway / axon guidance / mitochondrial membrane / negative regulation of extrinsic apoptotic signaling pathway / neuron migration / response to wounding / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / heparin binding / nervous system development / heart development / growth cone / postsynaptic membrane / angiogenesis / negative regulation of neuron apoptotic process / positive regulation of ERK1 and ERK2 cascade / early endosome / neuron projection
Similarity search - Function
Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / MAM domain signature. / 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 ...Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / MAM domain signature. / 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. / 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
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsVander Kooi, C.W. / Jusino, M.A. / Perman, B. / Neau, D.B. / Bellamy, H.D. / Leahy, D.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for ligand and heparin binding to neuropilin B domains.
Authors: Vander Kooi, C.W. / Jusino, M.A. / Perman, B. / Neau, D.B. / Bellamy, H.D. / Leahy, D.J.
History
DepositionFeb 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuropilin-1
B: Tuftsin


Theoretical massNumber of molelcules
Total (without water)36,2282
Polymers36,2282
Non-polymers00
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.951, 64.653, 102.308
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 35725.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nrp1 / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami-2 / References: UniProt: Q9QWJ9
#2: Protein/peptide Tuftsin /


Mass: 502.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Tuftsin purchased from Bachem
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M magnesium chloride, 0.1 M sodium cacodylate, 15% PEG 4K, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.38
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 13, 2006
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 18747

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2ORX

2orx


Resolution: 2.15→28.34 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.908 / SU B: 11.698 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25675 955 5.1 %RANDOM
Rwork0.20377 ---
obs0.20641 17892 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.505 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.15→28.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 0 261 2789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222604
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.9513523
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6545318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51623.388121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60415463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6541522
X-RAY DIFFRACTIONr_chiral_restr0.0840.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021985
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.21120
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21741
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2231
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4511.51624
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74722552
X-RAY DIFFRACTIONr_scbond_it1.07831142
X-RAY DIFFRACTIONr_scangle_it1.7574.5969
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 58 -
Rwork0.295 1229 -
obs--93.67 %
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)
18.1557-3.36991.16745.42-1.35986.34180.62990.1424-1.168-0.5603-0.23710.52560.6373-0.2002-0.3928-0.0431-0.0408-0.1025-0.24480.0053-0.0812-7.012-4.988-21.154
24.3237-1.27722.81312.4442-1.08065.8690.133-0.0994-0.1096-0.2373-0.01630.2673-0.1049-0.5288-0.1166-0.08840.03920.0056-0.1481-0.0036-0.184-7.1213.297-20.347
33.5235-1.48632.00641.7532-1.41334.9271-0.10190.08730.3290.0337-0.0583-0.1421-0.34240.1080.1602-0.04310.0151-0.0031-0.18140.0198-0.175-0.267.145-19.128
43.3454-0.37263.78094.96962.460114.68530.26080.3407-0.1985-0.14930.020.01050.83120.3606-0.2808-0.17770.0139-0.0924-0.1639-0.0131-0.095716.912-11.635-1.098
53.9646-1.40480.87423.4567-0.81953.0959-0.1287-0.24290.34660.14510.0351-0.033-0.2312-0.23960.0936-0.0727-0.0072-0.0307-0.1463-0.0242-0.183115.842-2.6925.636
66.95156.9786-2.658627.9762-8.72699.15760.3113-0.0420.0829-0.4453-1.1815-1.6993-0.44051.32140.8702-0.16940.0183-0.0334-0.08120.0497-0.023434.068-3.8051.652
73.0655-0.94870.73341.6455-0.55672.57780.01070.08750.3119-0.0671-0.1548-0.2777-0.0824-0.01050.1441-0.0732-0.0098-0.0032-0.15760.0121-0.114319.293-2.598-0.116
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA274 - 3072 - 35
2X-RAY DIFFRACTION2AA308 - 36836 - 96
3X-RAY DIFFRACTION3AA369 - 42397 - 151
4X-RAY DIFFRACTION4AA424 - 457152 - 185
5X-RAY DIFFRACTION5AA458 - 520186 - 248
6X-RAY DIFFRACTION6AA521 - 537249 - 265
7X-RAY DIFFRACTION7AA538 - 586266 - 314

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