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

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Basic information

Entry
Database: PDB / ID: 2orx
TitleStructural Basis for Ligand Binding and Heparin Mediated Activation of Neuropilin
ComponentsNeuropilin-1Neuropilin 1
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: 2.4 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 1.1Apr 21, 2008Group: 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


Theoretical massNumber of molelcules
Total (without water)35,7261
Polymers35,7261
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.094, 92.221, 120.115
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 / Fragment: F5/8 type C1 and C2 domains, residues 273-586
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 100mM HEPES pH 7.6, 10% PEG 20K, 7% Ethylene glycol, 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 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 9, 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: 2.4→50 Å / Num. obs: 16862

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KEX

1kex


Resolution: 2.4→29.37 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / SU B: 15.425 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25178 823 5 %RANDOM
Rwork0.20138 ---
obs0.20402 15556 94.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.395 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 0 198 2708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222572
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9463478
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3565313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82423.583120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.66115452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3221520
X-RAY DIFFRACTIONr_chiral_restr0.0950.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021958
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.21182
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21716
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2187
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5631.51601
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9222519
X-RAY DIFFRACTIONr_scbond_it1.30231131
X-RAY DIFFRACTIONr_scangle_it1.9564.5959
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 43 -
Rwork0.314 838 -
obs--72.15 %
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)
11.9899-0.51650.38916.8449-3.47656.15860.13810.20640.32030.2498-0.3497-0.4633-0.23290.70710.2116-0.1949-0.10160.0044-0.39280.0999-0.27819.55-4.499-19.522
21.242-0.662-0.00199.298-0.47412.08020.16690.06480.40930.1625-0.3248-0.3871-0.61040.24660.1579-0.0702-0.0830.0232-0.44460.0323-0.27445.932-4.245-16.745
33.0495-0.798-0.02327.51-1.46063.40630.18690.18940.14640.4901-0.12490.3794-0.1979-0.0364-0.0621-0.1798-0.06280.0476-0.4681-0.017-0.34790.415-11.545-15.369
41.9776-0.36680.89542.4139-0.10233.34350.03750.3057-0.2097-0.06170.04060.204-0.04450.2681-0.0781-0.23670.02340.062-0.4102-0.0912-0.266410.859-41.148-17.641
53.2383-1.40771.85293.90180.0172.3861-0.0612-0.1589-0.32020.34340.05260.3917-0.0099-0.07850.0086-0.172-0.01720.1534-0.4002-0.0619-0.20026.676-40.043-9.092
60.62390.223-0.44442.38641.57721.62630.1639-0.1926-0.28460.32240.06740.10240.0217-0.0427-0.2313-0.1263-0.00830.0846-0.3552-0.0289-0.193110.287-40.78-9.698
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA273 - 3241 - 52
2X-RAY DIFFRACTION2AA325 - 35553 - 83
3X-RAY DIFFRACTION3AA356 - 42584 - 153
4X-RAY DIFFRACTION4AA426 - 486154 - 214
5X-RAY DIFFRACTION5AA487 - 553215 - 281
6X-RAY DIFFRACTION6AA554 - 586282 - 314

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