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- PDB-4deq: Structure of the Neuropilin-1/VEGF-A complex -

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Basic information

Entry
Database: PDB / ID: 4deq
TitleStructure of the Neuropilin-1/VEGF-A complex
ComponentsNeuropilin-1, Vascular endothelial growth factor A
KeywordsPROTEIN BINDING/CYTOKINE / Coagulation factor domain / heparin binding domain / Angiogenesis / PROTEIN BINDING-CYTOKINE complex
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 / Signaling by VEGF / vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance ...endothelial tip cell fate specification / basal dendrite development / otic placode development / basal dendrite arborization / retina vasculature morphogenesis in camera-type eye / Signaling by VEGF / vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / basophil chemotaxis / lymph vessel morphogenesis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / trigeminal ganglion development / sensory neuron axon guidance / cellular stress response to acid chemical / : / facial nerve structural organization / trigeminal nerve structural organization / VEGF ligand-receptor interactions / vascular endothelial growth factor receptor 1 binding / negative regulation of adherens junction organization / branchiomotor neuron axon guidance / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / protein localization to early endosome / post-embryonic camera-type eye development / primitive erythrocyte differentiation / positive regulation of mast cell chemotaxis / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / negative regulation of blood-brain barrier permeability / axon extension involved in axon guidance / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / VEGF-activated neuropilin signaling pathway / motor neuron migration / eye photoreceptor cell development / renal artery morphogenesis / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / mammary gland alveolus development / 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 / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor binding / vascular endothelial growth factor receptor-2 signaling pathway / sympathetic ganglion development / neural crest cell migration involved in autonomic nervous system development / axonogenesis involved in innervation / vascular endothelial growth factor receptor activity / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of axon extension involved in axon guidance / CHL1 interactions / camera-type eye morphogenesis / endothelial cell chemotaxis / positive regulation of protein localization to early endosome / positive regulation of trophoblast cell migration / surfactant homeostasis / retinal ganglion cell axon guidance / regulation of vesicle-mediated transport / induction of positive chemotaxis / vascular wound healing / positive regulation of protein autophosphorylation / dopaminergic neuron differentiation / positive regulation of epithelial tube formation / semaphorin receptor complex / substrate-dependent cell migration, cell extension / neuropilin signaling pathway / neuropilin binding / Signaling by ROBO receptors / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of branching involved in ureteric bud morphogenesis / tube formation / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of leukocyte migration / motor neuron axon guidance / CRMPs in Sema3A signaling / neural crest cell migration / semaphorin receptor activity / cell migration involved in sprouting angiogenesis / vascular endothelial growth factor receptor 2 binding / positive regulation of vascular permeability / commissural neuron axon guidance / outflow tract septum morphogenesis / artery morphogenesis / cardiac muscle cell development / branching involved in blood vessel morphogenesis / positive regulation of vascular endothelial growth factor signaling pathway / cellular response to hepatocyte growth factor stimulus / positive regulation of blood vessel branching / sprouting angiogenesis / platelet-derived growth factor receptor signaling pathway / platelet-derived growth factor receptor binding / hepatocyte growth factor receptor signaling pathway
Similarity search - Function
Vascular Endothelial Growth Factor-165, Heparin-binding Domain / Vascular endothelial growth factor, heparin-binding domain / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / Vascular endothelial growth factor A, long form-like domain / : ...Vascular Endothelial Growth Factor-165, Heparin-binding Domain / Vascular endothelial growth factor, heparin-binding domain / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / Vascular endothelial growth factor A, long form-like domain / : / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / 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 / Cystine-knot cytokine / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Ribbon / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Neuropilin-1 / Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.649 Å
AuthorsVander Kooi, C.W.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Basis for Selective Vascular Endothelial Growth Factor-A (VEGF-A) Binding to Neuropilin-1.
Authors: Parker, M.W. / Xu, P. / Li, X. / Vander Kooi, C.W.
History
DepositionJan 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Jul 18, 2012Group: Database references
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 13, 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 1.5Nov 27, 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, Vascular endothelial growth factor A
B: Neuropilin-1, Vascular endothelial growth factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4173
Polymers49,3222
Non-polymers951
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Neuropilin-1, Vascular endothelial growth factor A


Theoretical massNumber of molelcules
Total (without water)24,6611
Polymers24,6611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Neuropilin-1, Vascular endothelial growth factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7562
Polymers24,6611
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.978, 114.978, 50.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Neuropilin-1, Vascular endothelial growth factor A / Vascular endothelial cell growth factor 165 receptor / VEGF-A / Vascular permeability factor / VPF


Mass: 24660.928 Da / Num. of mol.: 2
Fragment: Neuropilin b1 domain/VEGF-A Heparin Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP1, NRP, VEGF165R, VEGF, VEGFA / Production host: Escherichia coli (E. coli) / References: UniProt: O14786, UniProt: P15692
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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

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Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.5M Na/K phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 21, 2011
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.649→20 Å / Num. all: 19687 / Num. obs: 18014 / % possible obs: 91.5 % / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QQI

2qqi


Resolution: 2.649→19.9 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 26.465 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.594 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26698 916 5.1 %RANDOM
Rwork0.20881 ---
all0.21155 19687 --
obs0.21155 17074 91.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.228 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0 Å2
2--0.11 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.649→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 5 16 3445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.023510
X-RAY DIFFRACTIONr_bond_other_d0.0010.022501
X-RAY DIFFRACTIONr_angle_refined_deg1.0111.9534747
X-RAY DIFFRACTIONr_angle_other_deg0.7243.0066043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9065430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43123.522159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14415628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1111530
X-RAY DIFFRACTIONr_chiral_restr0.0570.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213876
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02722
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.649→2.716 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.498 43 -
Rwork0.436 667 -
obs--51.41 %
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)
14.5847-1.44751.15564.57330.59752.0082-0.08850.16380.5113-0.123-0.1152-0.2578-0.1718-0.01630.20370.1784-0.0433-0.01430.16040.01410.06576.853521.4271-7.9612
26.3675-1.72810.16284.29490.78062.7831-0.1463-0.12690.08110.16560.1371-0.47940.00080.22260.00910.1120.0602-0.04580.0578-0.02780.075229.33144.24086.9105
315.3787.72114.49143.98712.40552.4969-0.36020.8682-0.6862-0.33280.4676-0.4582-0.04870.1717-0.10750.37760.07220.16920.4395-0.05540.415839.245820.4311-5.9145
42.528-3.15914.25884.3236-5.17877.4026-0.07280.0040.2370.2239-0.0937-0.3527-0.1410.00640.16650.32410.05930.02310.28750.06120.34065.288162.5084-11.9045
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 155
2X-RAY DIFFRACTION2B0 - 155
3X-RAY DIFFRACTION3A156 - 214
4X-RAY DIFFRACTION4B156 - 214

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