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- PDB-4rn5: B1 domain of human Neuropilin-1 with acetate ion in a ligand-bind... -

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Basic information

Entry
Database: PDB / ID: 4rn5
TitleB1 domain of human Neuropilin-1 with acetate ion in a ligand-binding site
ComponentsNeuropilin-1
KeywordsPROTEIN BINDING / VEGF binding
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 / VEGF-activated neuropilin signaling pathway / axon extension involved in axon guidance / motor neuron migration / renal artery morphogenesis / neurofilament / regulation of vascular endothelial growth factor receptor signaling pathway / sympathetic neuron projection extension / Neuropilin interactions with VEGF and VEGFR / 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 / regulation of vesicle-mediated transport / retinal ganglion cell axon guidance / 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 / 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 / platelet-derived growth factor receptor signaling pathway / growth factor binding / sorting endosome / positive chemotaxis / cytokine binding / cellular response to vascular endothelial growth factor stimulus / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / vasculogenesis / positive regulation of phosphorylation / positive regulation of focal adhesion assembly / vascular endothelial growth factor receptor signaling pathway / coreceptor activity / positive regulation of stress fiber assembly / positive regulation of substrate adhesion-dependent cell spreading / 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 / neuron migration / response to wounding / mitochondrial membrane / positive regulation of angiogenesis / cell-cell signaling / heparin binding / angiogenesis / cytoplasmic vesicle / negative regulation of neuron apoptotic process / 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
ACETATE ION / Neuropilin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsAllerston, C.K. / Yelland, T.S. / Jarvis, A. / Jenkins, K. / Winfield, N. / Cheng, L. / Jia, H. / Zachary, I. / Selwood, D.L. / Djordjevic, S.
CitationJournal: To be Published
Title: Conserved water molecules in a ligand-binding site of neuropilin-1
Authors: Allerston, C.K. / Yelland, T.S. / Jarvis, A. / Jenkins, K. / Winfield, N. / Cheng, L. / Jia, H. / Zachary, I. / Selwood, D.L. / Djordjevic, S.
History
DepositionOct 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)18,1995
Polymers17,9171
Non-polymers2824
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.839, 62.839, 87.918
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 / Vascular endothelial cell growth factor 165 receptor


Mass: 17917.291 Da / Num. of mol.: 1 / Fragment: B1 domain (UNP residues 273-427)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP1, NRP, VEGF165R / Production host: Escherichia coli (E. coli) / References: UniProt: O14786
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 100mM MES, 200mM Zinc Acetate, 10% PEG 8000, pH 6.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.73→21.54 Å / Num. all: 16198 / Num. obs: 16198 / % possible obs: 84.87 % / Observed criterion σ(F): 1.34 / Observed criterion σ(I): 1.34
Reflection shellResolution: 1.73→1.84 Å / % possible all: 31

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
d*TREKdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→21.54 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2008 808 4.99 %RANDOM
Rwork0.1763 ---
obs0.1776 16198 84.87 %-
all-16198 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.416 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1475 Å2-0 Å2-0 Å2
2---0.1475 Å20 Å2
3---0.2949 Å2
Refinement stepCycle: LAST / Resolution: 1.73→21.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1261 0 12 159 1432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131301
X-RAY DIFFRACTIONf_angle_d1.3841759
X-RAY DIFFRACTIONf_dihedral_angle_d14.64476
X-RAY DIFFRACTIONf_chiral_restr0.102189
X-RAY DIFFRACTIONf_plane_restr0.007223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.8360.3872460.2993901X-RAY DIFFRACTION31
1.836-1.97760.2541220.18972347X-RAY DIFFRACTION79
1.9776-2.17650.21161710.16662887X-RAY DIFFRACTION98
2.1765-2.4910.21781490.16872998X-RAY DIFFRACTION100
2.491-3.13680.18841750.17743039X-RAY DIFFRACTION100
3.1368-21.54140.17811450.17343218X-RAY DIFFRACTION100

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