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- PDB-1kex: Crystal Structure of the b1 Domain of Human Neuropilin-1 -

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Basic information

Entry
Database: PDB / ID: 1kex
TitleCrystal Structure of the b1 Domain of Human Neuropilin-1
ComponentsNeuropilin-1Neuropilin 1
KeywordsPROTEIN BINDING / beta barrel / jelly-roll
Function / homology
Function and homology information


positive regulation of cytokine activity / endothelial tip cell fate specification / 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 ...positive regulation of cytokine activity / endothelial tip cell fate specification / 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 / axon extension involved in axon guidance / VEGF-activated neuropilin signaling pathway / negative regulation of axon extension involved in axon guidance / sympathetic neuron projection extension / motor neuron migration / Neurophilin interactions with VEGF and VEGFR / 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 / CHL1 interactions / vascular endothelial growth factor receptor activity / substrate-dependent cell migration, cell extension / semaphorin receptor complex / regulation of vesicle-mediated transport / Signaling by ROBO receptors / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / angiogenesis involved in coronary vascular morphogenesis / 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 / CRMPs in Sema3A signaling / 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 / cytokine binding / positive regulation of smooth muscle cell migration / growth factor binding / sorting endosome / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / platelet-derived growth factor receptor signaling pathway / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / vascular endothelial growth factor receptor signaling pathway / coreceptor activity / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / positive regulation of endothelial cell proliferation / GTPase activator activity / positive regulation of endothelial cell migration / Signal transduction by L1 / integrin-mediated signaling pathway / axon guidance / mitochondrial membrane / negative regulation of extrinsic apoptotic signaling pathway / animal organ morphogenesis / neuron migration / response to wounding / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell signaling / heparin binding / cytoplasmic vesicle / postsynaptic membrane / angiogenesis / negative regulation of neuron apoptotic process / Attachment and Entry / positive regulation of ERK1 and ERK2 cascade / receptor complex / early endosome
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLee, C.C. / Kreusch, A. / McMullan, D. / Ng, K. / Spraggon, G.
CitationJournal: Structure / Year: 2003
Title: Crystal Structure of the Human Neuropilin-1 b1 Domain
Authors: Lee, C.C. / Kreusch, A. / McMullan, D. / Ng, K. / Spraggon, G.
History
DepositionNov 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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)17,5911
Polymers17,5911
Non-polymers00
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.827, 62.827, 88.375
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Neuropilin-1 / Neuropilin 1


Mass: 17590.896 Da / Num. of mol.: 1 / Fragment: b1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: nrp1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O14786
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, MES, zinc acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 %PEG80001reservoir
2100 mMMES1reservoirpH6.0
3200 mM1reservoirZn(OAc)2
420 mMTris1droppH7.9
550 mM1dropNaCl
60.25 mMTCEP1drop
710 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 14523 / Num. obs: 12290 / % possible obs: 97.3 % / Rsym value: 0.042 / Net I/σ(I): 32.1
Reflection shellResolution: 1.9→2.03 Å / Rsym value: 0.105 / % possible all: 90.5
Reflection
*PLUS
Num. measured all: 370706 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
% possible obs: 90.5 % / Rmerge(I) obs: 0.105

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CZT

1czt


Resolution: 1.9→500 Å /
RfactorNum. reflection
Rfree0.266 -
Rwork0.189 -
obs-12290
Refinement stepCycle: LAST / Resolution: 1.9→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 0 0 201 1440
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONc_angle_deg1.984
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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