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- PDB-7jjc: Crystal structure of neuropilin-1 b1 domain in complex with SARS-... -

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Basic information

Entry
Database: PDB / ID: 7jjc
TitleCrystal structure of neuropilin-1 b1 domain in complex with SARS-CoV-2 S1 C-end rule (CendR) peptide
Components
  • Neuropilin-1
  • Spike protein S1
KeywordsSIGNALING PROTEIN / Neuropilin-1 / receptor binding / Coronavirus / SARS-CoV-2 / spike protein
Function / homology
Function and homology information


endothelial tip cell fate specification / basal dendrite development / otic placode development / protein localization to early endosome / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration ...endothelial tip cell fate specification / basal dendrite development / otic placode development / protein localization to early endosome / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / 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 / trigeminal nerve structural organization / sensory neuron axon guidance / postsynapse organization / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / branchiomotor neuron axon guidance / negative regulation of axon extension involved in axon guidance / axon extension involved in axon guidance / renal artery morphogenesis / VEGF-activated neuropilin signaling pathway / neurofilament / sympathetic neuron projection extension / regulation of vascular endothelial growth factor receptor signaling pathway / Neurophilin interactions with VEGF and VEGFR / vascular endothelial growth factor binding / endothelial cell chemotaxis / motor neuron migration / neural crest cell migration involved in autonomic nervous system development / sympathetic ganglion development / positive regulation of axon extension involved in axon guidance / axonogenesis involved in innervation / CHL1 interactions / semaphorin receptor complex / regulation of vesicle-mediated transport / Signaling by ROBO receptors / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / neuropilin signaling pathway / substrate-dependent cell migration, cell extension / hepatocyte growth factor receptor signaling pathway / coronary artery morphogenesis / angiogenesis involved in coronary vascular morphogenesis / CRMPs in Sema3A signaling / semaphorin receptor activity / commissural neuron axon guidance / outflow tract septum morphogenesis / motor neuron axon guidance / regulation of Cdc42 protein signal transduction / axonal fasciculation / cell migration involved in sprouting angiogenesis / neural crest cell migration / sprouting angiogenesis / positive regulation of filopodium assembly / artery morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / cellular response to hepatocyte growth factor stimulus / retinal ganglion cell axon guidance / branching involved in blood vessel morphogenesis / positive regulation of smooth muscle cell migration / positive chemotaxis / growth factor binding / cytokine binding / sorting endosome / semaphorin-plexin signaling pathway / platelet-derived growth factor receptor signaling pathway / Sema3A PAK dependent Axon repulsion / cellular response to vascular endothelial growth factor stimulus / positive regulation of focal adhesion assembly / vascular endothelial growth factor receptor signaling pathway / vasculogenesis / positive regulation of phosphorylation / coreceptor activity / positive regulation of stress fiber assembly / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / GTPase activator activity / axon guidance / animal organ morphogenesis / Signal transduction by L1 / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / mitochondrial membrane / vascular endothelial growth factor receptor activity / response to wounding / neuron migration / positive regulation of angiogenesis / cell-cell signaling / heparin binding / cytoplasmic vesicle / angiogenesis / Maturation of spike protein / viral translation / negative regulation of neuron apoptotic process / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space
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) / : / Coagulation factors 5/8 type C domain (FA58C) signature 2. / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. ...Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / : / Coagulation factors 5/8 type C domain (FA58C) signature 2. / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / 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 / CUB domain profile. / 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 / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Neuropilin-1 / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.36 Å
AuthorsChen, K.-E. / Collins, B.M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP160101743 Australia
CitationJournal: Science / Year: 2020
Title: Neuropilin-1 is a host factor for SARS-CoV-2 infection.
Authors: Daly, J.L. / Simonetti, B. / Klein, K. / Chen, K.E. / Williamson, M.K. / Anton-Plagaro, C. / Shoemark, D.K. / Simon-Gracia, L. / Bauer, M. / Hollandi, R. / Greber, U.F. / Horvath, P. / ...Authors: Daly, J.L. / Simonetti, B. / Klein, K. / Chen, K.E. / Williamson, M.K. / Anton-Plagaro, C. / Shoemark, D.K. / Simon-Gracia, L. / Bauer, M. / Hollandi, R. / Greber, U.F. / Horvath, P. / Sessions, R.B. / Helenius, A. / Hiscox, J.A. / Teesalu, T. / Matthews, D.A. / Davidson, A.D. / Collins, B.M. / Cullen, P.J. / Yamauchi, Y.
History
DepositionJul 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 27, 2021Group: Structure summary / Category: entity / entity_name_com / Item: _entity.pdbx_description / _entity_name_com.name
Revision 1.3Oct 18, 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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuropilin-1
B: Neuropilin-1
C: Neuropilin-1
D: Neuropilin-1
E: Spike protein S1
F: Spike protein S1
G: Spike protein S1
H: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,20115
Polymers78,5008
Non-polymers7017
Water2,306128
1
A: Neuropilin-1
E: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7313
Polymers19,6252
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neuropilin-1
F: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7313
Polymers19,6252
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neuropilin-1
G: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9155
Polymers19,6252
Non-polymers2903
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Neuropilin-1
H: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8234
Polymers19,6252
Non-polymers1982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.930, 89.890, 108.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 18766.152 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP1, NRP, VEGF165R / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-Gami 2 / References: UniProt: O14786
#2: Protein/peptide
Spike protein S1 / S glycoprotein / E2 / Peplomer protein / Spike glycoprotein


Mass: 858.970 Da / Num. of mol.: 4 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M Sodium Citrate pH 5, 20% PEG 6K / PH range: 5 - 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.36→46.39 Å / Num. obs: 36732 / % possible obs: 99.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 50.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.039 / Rrim(I) all: 0.108 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.36-2.457.61.4782783736560.6130.5651.584196.2
8.83-46.397.10.0256798000.9990.0080.02246.799.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.62 Å46.38 Å
Translation6.62 Å46.38 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KEX

1kex


Resolution: 2.36→46.3830147666 Å / SU ML: 0.370203315951 / Cross valid method: FREE R-VALUE / σ(F): 1.35013224637 / Phase error: 28.7832434993
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.24993728705 1852 5.05182760502 %
Rwork0.203249081691 34808 -
obs0.205604973312 36660 99.5546382794 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.6212059302 Å2
Refinement stepCycle: LAST / Resolution: 2.36→46.3830147666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5312 0 46 128 5486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003366356508925532
X-RAY DIFFRACTIONf_angle_d0.709053571237480
X-RAY DIFFRACTIONf_chiral_restr0.0527758095496794
X-RAY DIFFRACTIONf_plane_restr0.00396482820838952
X-RAY DIFFRACTIONf_dihedral_angle_d19.33490174382070
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.42270.3540791947491120.3182414999612541X-RAY DIFFRACTION94.7838513755
2.4227-2.4940.3737091759291160.2958776382352677X-RAY DIFFRACTION99.9642090193
2.494-2.57450.3333325256831390.2888873395072642X-RAY DIFFRACTION99.964054637
2.5745-2.66650.3577019003671500.2684907043832625X-RAY DIFFRACTION99.9279798344
2.6665-2.77330.3377767676751510.2599565297172640X-RAY DIFFRACTION100
2.7733-2.89940.3041086102461430.2619026123712670X-RAY DIFFRACTION99.9644633973
2.8994-3.05230.2913350725871410.2486982308962660X-RAY DIFFRACTION100
3.0523-3.24350.3019130422171550.2295884992082663X-RAY DIFFRACTION99.9645264278
3.2435-3.49380.2711493786011540.2187426630922675X-RAY DIFFRACTION100
3.4938-3.84530.2494421993581330.1946515901212706X-RAY DIFFRACTION99.8944405348
3.8453-4.40130.1913131691731630.1705296356232698X-RAY DIFFRACTION99.965059399
4.4013-5.54370.1978633652871450.1382859193482742X-RAY DIFFRACTION99.9653739612

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