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- PDB-2qqi: Crystal Structure of the b1b2 Domains from Human Neuropilin-1 -

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Basic information

Entry
Database: PDB / ID: 2qqi
TitleCrystal Structure of the b1b2 Domains from Human Neuropilin-1
ComponentsNeuropilin-1
KeywordsSIGNALING PROTEIN / VEGF receptor / semaphorin receptor / Angiogenesis / Developmental protein / Differentiation / Glycoprotein / Heparan sulfate / Membrane / Neurogenesis / Proteoglycan / Secreted / Transmembrane / HORMONE
Function / homology
Function and homology information


endothelial tip cell fate specification / basal dendrite development / otic placode development / basal dendrite arborization / 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 ...endothelial tip cell fate specification / basal dendrite development / otic placode development / basal dendrite arborization / 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 / sensory neuron axon guidance / facial nerve structural organization / trigeminal nerve structural organization / branchiomotor neuron axon guidance / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / protein localization to early endosome / axon extension involved in axon guidance / VEGF-activated neuropilin signaling pathway / motor neuron migration / renal artery morphogenesis / neurofilament / sympathetic neuron projection extension / Neuropilin interactions with VEGF and VEGFR / regulation of vascular endothelial growth factor receptor signaling pathway / angiogenesis involved in coronary vascular morphogenesis / postsynapse organization / vascular endothelial growth factor binding / sympathetic ganglion development / neural crest cell migration involved in autonomic nervous system development / axonogenesis involved in innervation / vascular endothelial growth factor receptor activity / positive regulation of axon extension involved in axon guidance / CHL1 interactions / endothelial cell chemotaxis / retinal ganglion cell axon guidance / regulation of vesicle-mediated transport / semaphorin receptor complex / substrate-dependent cell migration, cell extension / neuropilin signaling pathway / Signaling by ROBO receptors / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / coronary artery morphogenesis / motor neuron axon guidance / CRMPs in Sema3A signaling / neural crest cell migration / semaphorin receptor activity / cell migration involved in sprouting angiogenesis / commissural neuron axon guidance / outflow tract septum morphogenesis / artery morphogenesis / branching involved in blood vessel morphogenesis / cellular response to hepatocyte growth factor stimulus / sprouting angiogenesis / platelet-derived growth factor receptor signaling pathway / hepatocyte growth factor receptor signaling pathway / positive regulation of filopodium assembly / regulation of Cdc42 protein signal transduction / positive regulation of smooth muscle cell migration / positive regulation of cell migration involved in sprouting angiogenesis / growth factor binding / sorting endosome / positive chemotaxis / cytokine binding / vasculogenesis / cellular response to vascular endothelial growth factor stimulus / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / positive regulation of phosphorylation / positive regulation of focal adhesion assembly / vascular endothelial growth factor receptor signaling pathway / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / coreceptor activity / positive regulation of endothelial cell proliferation / animal organ morphogenesis / positive regulation of endothelial cell migration / axon guidance / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / Signal transduction by L1 / GTPase activator activity / response to wounding / neuron migration / mitochondrial membrane / positive regulation of angiogenesis / cell-cell signaling / heparin binding / negative regulation of neuron apoptotic process / angiogenesis / cytoplasmic vesicle / early endosome / Attachment and Entry / positive regulation of ERK1 and ERK2 cascade / signaling receptor complex / postsynaptic membrane / neuron projection / axon / focal adhesion / symbiont entry into host cell
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 / MAM domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 2. ...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 / 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 / Spermadhesin, CUB domain superfamily / CUB domain profile. / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsAppleton, B.A. / Desmarais, W. / Wiesmann, C.
CitationJournal: Embo J. / Year: 2007
Title: Structural studies of neuropilin/antibody complexes provide insights into semaphorin and VEGF binding
Authors: Appleton, B.A. / Wu, P. / Maloney, J. / Yin, J. / Liang, W.C. / Stawicki, S. / Mortara, K. / Bowman, K.K. / Elliott, J.M. / Desmarais, W. / Bazan, J.F. / Bagri, A. / Tessier-Lavigne, M. / ...Authors: Appleton, B.A. / Wu, P. / Maloney, J. / Yin, J. / Liang, W.C. / Stawicki, S. / Mortara, K. / Bowman, K.K. / Elliott, J.M. / Desmarais, W. / Bazan, J.F. / Bagri, A. / Tessier-Lavigne, M. / Koch, A.W. / Wu, Y. / Watts, R.J. / Wiesmann, C.
History
DepositionJul 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuropilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1712
Polymers36,0791
Non-polymers921
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.920, 66.979, 74.679
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Neuropilin-1 / Vascular endothelial cell growth factor 165 receptor / CD304 antigen


Mass: 36078.930 Da / Num. of mol.: 1 / Fragment: F5/8 type C 1 and C 2 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP1, NRP, VEGF165R / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: O14786
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.2 M Sodium Fluoride, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 30653 / % possible obs: 97.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 26.2 Å2 / Rsym value: 0.05 / Χ2: 1.019 / Net I/σ(I): 26.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 3047 / Rsym value: 0.515 / Χ2: 0.89 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KEX

1kex


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.946 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1526 5 %RANDOM
Rwork0.159 ---
obs0.161 29018 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.584 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å20 Å2
2--0.32 Å20 Å2
3---1.27 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2514 0 6 282 2802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222623
X-RAY DIFFRACTIONr_bond_other_d0.0010.021848
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9513557
X-RAY DIFFRACTIONr_angle_other_deg0.8943.0024492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5535329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85323.833120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12615471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3481519
X-RAY DIFFRACTIONr_chiral_restr0.0960.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022915
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02539
X-RAY DIFFRACTIONr_nbd_refined0.1880.2419
X-RAY DIFFRACTIONr_nbd_other0.2030.21930
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21251
X-RAY DIFFRACTIONr_nbtor_other0.0870.21453
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2206
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.222
X-RAY DIFFRACTIONr_mcbond_it3.3972.52047
X-RAY DIFFRACTIONr_mcbond_other0.7082.5650
X-RAY DIFFRACTIONr_mcangle_it3.90452579
X-RAY DIFFRACTIONr_scbond_it3.5192.51243
X-RAY DIFFRACTIONr_scangle_it4.7115970
LS refinement shellResolution: 1.8→1.837 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.329 82 -
Rwork0.185 1703 -
all-1785 -
obs--98.67 %
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)
12.15430.16060.86140.8145-0.13532.1690.09230.0501-0.08970.0167-0.109-0.19850.07620.19450.0167-0.09470.006-0.0085-0.09370.0391-0.04016.457228.935732.3526
21.4220.11270.67660.5187-0.16571.72290.0650.11770.0044-0.1045-0.07590.020.21210.15980.0109-0.01830.02970.0103-0.0597-0.0225-0.0611-12.954329.80814.7476
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA272 - 4254 - 157
2X-RAY DIFFRACTION2AA426 - 586158 - 318

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