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- PDB-8pfe: Crystal Structure of an Hexavariant of the b1 Domain of Human Neu... -

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Basic information

Entry
Database: PDB / ID: 8pfe
TitleCrystal Structure of an Hexavariant of the b1 Domain of Human Neuropilin-1 in Complex with the KDKPPR Peptide
Components
  • LYS-ASP-LYS-PRO-PRO-ARG
  • Neuropilin-1Neuropilin 1
KeywordsPROTEIN BINDING / NEUROPILIN-1 / HUMAN / BLOOD COAGULATION FACTORS / CELL ADHESION / BINDING SITES
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-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
ACETATE ION / Neuropilin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsJelsch, C. / Favier, F. / Didierjean, C.
Funding support France, 1items
OrganizationGrant numberCountry
Not funded France
Citation
Journal: Molecules / Year: 2023
Title: New Crystal Form of Human Neuropilin-1 b1 Fragment with Six Electrostatic Mutations Complexed with KDKPPR Peptide Ligand.
Authors: Goudiaby, I. / Malliavin, T.E. / Mocchetti, E. / Mathiot, S. / Acherar, S. / Frochot, C. / Barberi-Heyob, M. / Guillot, B. / Favier, F. / Didierjean, C. / Jelsch, C.
#1: Journal: Bioorg Med Chem / Year: 2016
Title: Carbohydrate-based peptidomimetics targeting neuropilin-1: Synthesis, molecular docking study and in vitro biological activities.
Authors: Richard, M. / Chateau, A. / Jelsch, C. / Didierjean, C. / Manival, X. / Charron, C. / Maigret, B. / Barberi-Heyob, M. / Chapleur, Y. / Boura, C. / Pellegrini-Moise, N.
History
DepositionJun 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.entity_id_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuropilin-1
B: LYS-ASP-LYS-PRO-PRO-ARG
C: Neuropilin-1
D: LYS-ASP-LYS-PRO-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1355
Polymers42,0764
Non-polymers591
Water6,792377
1
A: Neuropilin-1
B: LYS-ASP-LYS-PRO-PRO-ARG
hetero molecules


  • defined by author
  • Evidence: homology
  • 21.1 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)21,0973
Polymers21,0382
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Neuropilin-1
D: LYS-ASP-LYS-PRO-PRO-ARG


  • defined by author
  • 21 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)21,0382
Polymers21,0382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.773, 59.773, 174.604
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 20295.021 Da / Num. of mol.: 2 / Mutation: E277K, E285K, D289K, E367K, K373E, K397E
Source method: isolated from a genetically manipulated source
Details: fragment : hexavariant of the neuropilin-1 b1 domain
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP1, NRP, VEGF165R / Production host: Escherichia coli (E. coli) / References: UniProt: O14786
#2: Protein/peptide LYS-ASP-LYS-PRO-PRO-ARG


Mass: 742.886 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.3 ul protein + 0.3 ul crystallization solution (0.2 M ammonium citrate, 0.1 M bis-tris pH 5.5 and 25% w/v PEG 3350, from JCSGplus); soaked in their mother liquor supplemented with 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.979511 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979511 Å / Relative weight: 1
ReflectionResolution: 1.35→44.53 Å / Num. obs: 80230 / % possible obs: 99.7 % / Redundancy: 8.7 % / Biso Wilson estimate: 21.14 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.011 / Rrim(I) all: 0.033 / Χ2: 1.01 / Net I/σ(I): 28.7
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3895 / CC1/2: 0.685 / Rpim(I) all: 0.369 / Rrim(I) all: 0.779 / Χ2: 0.88 / % possible all: 95.7

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (21-NOV-2022)refinement
XDSVERSION Feb 5, 2021 BUILT=20210323data reduction
Aimlessversion 0.7.4 : 13/12/18data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→19.57 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.963 / SU R Cruickshank DPI: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.059 / SU Rfree Blow DPI: 0.058 / SU Rfree Cruickshank DPI: 0.055
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 3976 4.96 %RANDOM
Rwork0.1942 ---
obs0.1949 80230 99.6 %-
Displacement parametersBiso mean: 25.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.6334 Å20 Å20 Å2
2---0.6334 Å20 Å2
3---1.2668 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.35→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 4 377 2910
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125313HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.159650HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1590SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes808HARMONIC5
X-RAY DIFFRACTIONt_it2675HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.42
X-RAY DIFFRACTIONt_other_torsion15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion357SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5057SEMIHARMONIC4
LS refinement shellResolution: 1.35→1.36 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.276 -4.8 %
Rwork0.2826 1528 -
all0.2823 1605 -
obs--93.81 %

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