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- PDB-4qds: Physical basis for Nrp2 ligand binding -

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Basic information

Entry
Database: PDB / ID: 4qds
TitlePhysical basis for Nrp2 ligand binding
ComponentsNeuropilin-2Neuropilin
KeywordsCELL ADHESION / coagulation factor domain / discoidin domain / receptor / VEGF-C / secreted
Function / homology
Function and homology information


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 ...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 / branchiomotor neuron axon guidance / axon extension involved in axon guidance / NrCAM interactions / sympathetic neuron projection extension / Neurophilin interactions with VEGF and VEGFR / sympathetic ganglion development / neural crest cell migration involved in autonomic nervous system development / vascular endothelial growth factor receptor activity / nerve development / semaphorin receptor complex / outflow tract septum morphogenesis / semaphorin receptor activity / regulation of postsynapse organization / negative chemotaxis / cytokine binding / growth factor binding / semaphorin-plexin signaling pathway / positive regulation of endothelial cell proliferation / cellular response to leukemia inhibitory factor / positive regulation of endothelial cell migration / axon guidance / signaling receptor activity / heparin binding / postsynaptic membrane / angiogenesis / cell adhesion / axon / glutamatergic synapse / extracellular region / membrane / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / 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. ...Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / 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
ACETATE ION / Neuropilin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsParker, M.W. / Vander Kooi, C.W.
CitationJournal: Structure / Year: 2015
Title: Structural Basis for VEGF-C Binding to Neuropilin-2 and Sequestration by a Soluble Splice Form.
Authors: Parker, M.W. / Linkugel, A.D. / Goel, H.L. / Wu, T. / Mercurio, A.M. / Vander Kooi, C.W.
History
DepositionMay 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Sep 20, 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_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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: Neuropilin-2
B: Neuropilin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0184
Polymers41,8672
Non-polymers1512
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-23 kcal/mol
Surface area17090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.359, 91.386, 67.326
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Neuropilin-2 / Neuropilin / Vascular endothelial cell growth factor 165 receptor 2


Mass: 20933.463 Da / Num. of mol.: 2
Fragment: Proteolytic fragment of s9Nrp2 coagulation factor domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP2, VEGF165R2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami 2(DE3) / References: UniProt: O60462
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 105 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 10% PEG 1000, 10% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 17377 / Num. obs: 16303 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Rmerge(I) obs: 0.099
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 3.2 / % possible all: 79.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2QQJ

2qqj


Resolution: 2.4→19.72 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.914 / SU B: 17.29 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.476 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26388 821 5 %RANDOM
Rwork0.21037 ---
obs0.21301 15439 93.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.497 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å20 Å2
2--0.33 Å2-0 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 0 10 105 2955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022914
X-RAY DIFFRACTIONr_angle_refined_deg1.0391.9363950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2995361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9823.972141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24315490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9331522
X-RAY DIFFRACTIONr_chiral_restr0.0660.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212226
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 48 -
Rwork0.253 849 -
obs--77.93 %
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)
11.0316-0.5037-0.2083.0581.31952.3749-0.0415-0.07230.02370.14610.00320.0030.041-0.06930.03840.4723-0.04780.01660.1417-0.00880.013515.254-24.165-5.564
21.02090.43670.24363.97581.2541.98580.02440.0718-0.0850.1388-0.04910.00570.0007-0.09680.02480.35620.0269-0.02680.1231-0.00940.021115.561-59.746-28.081
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A272 - 453
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION1A601 - 646
4X-RAY DIFFRACTION2B275 - 453
5X-RAY DIFFRACTION2B501
6X-RAY DIFFRACTION2B601 - 659

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