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- PDB-2qqj: Crystal Structure of the b1b2 Domains from Human Neuropilin-2 -

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Basic information

Entry
Database: PDB / ID: 2qqj
TitleCrystal Structure of the b1b2 Domains from Human Neuropilin-2
ComponentsNeuropilin-2
KeywordsSIGNALING PROTEIN / VEGF receptor / semaphorin receptor / Developmental protein / Differentiation / Glycoprotein / Membrane / Neurogenesis / Transmembrane / HORMONE
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 / sympathetic neuron projection extension / NrCAM interactions / Neurophilin interactions with VEGF and VEGFR / neural crest cell migration involved in autonomic nervous system development / sympathetic ganglion development / vascular endothelial growth factor receptor activity / outflow tract septum morphogenesis / nerve development / semaphorin receptor complex / semaphorin receptor activity / regulation of postsynapse organization / negative chemotaxis / cytokine binding / growth factor binding / semaphorin-plexin signaling pathway / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / cellular response to leukemia inhibitory factor / axon guidance / heparin binding / signaling receptor activity / angiogenesis / postsynaptic membrane / cell adhesion / axon / glutamatergic synapse / extracellular region / identical protein binding / membrane / 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 / MAM domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. ...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 / 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 / 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 domain-like / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsAppleton, B.A. / Wiesmann, C.
CitationJournal: Embo J. / Year: 2007
Title: Structural studies of neuropilin/antibody complexes provide insights into semaphorin and VEGF binding
Authors: Appleton, B.A. / Wu, P. / Maloney, J. / Yin, J. / Liang, W.C. / Stawicki, S. / Mortara, K. / Bowman, K.K. / Elliott, J.M. / Desmarais, W. / Bazan, J.F. / Bagri, A. / Tessier-Lavigne, M. / ...Authors: Appleton, B.A. / Wu, P. / Maloney, J. / Yin, J. / Liang, W.C. / Stawicki, S. / Mortara, K. / Bowman, K.K. / Elliott, J.M. / Desmarais, W. / Bazan, J.F. / Bagri, A. / Tessier-Lavigne, M. / Koch, A.W. / Wu, Y. / Watts, R.J. / Wiesmann, C.
History
DepositionJul 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuropilin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7822
Polymers36,6901
Non-polymers921
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.456, 70.501, 121.929
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 36690.297 Da / Num. of mol.: 1 / Fragment: F5/8 type C 1 and C 2 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP2, VEGF165R2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: O60462
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris, 20% PEG 5000 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 23691 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 32.6 Å2 / Rsym value: 0.089 / Χ2: 0.969 / Net I/σ(I): 16.8
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 2349 / Rsym value: 0.53 / Χ2: 0.9 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QQI

2qqi


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.486 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1216 5.1 %RANDOM
Rwork0.172 ---
obs0.176 22404 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.462 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å20 Å20 Å2
2---1.22 Å20 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2503 0 6 239 2748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222579
X-RAY DIFFRACTIONr_bond_other_d0.0010.021789
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9433503
X-RAY DIFFRACTIONr_angle_other_deg0.9353.0024319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3265316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48223.387124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99215425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6081523
X-RAY DIFFRACTIONr_chiral_restr0.0910.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022882
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02539
X-RAY DIFFRACTIONr_nbd_refined0.1810.2374
X-RAY DIFFRACTIONr_nbd_other0.2010.21816
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21157
X-RAY DIFFRACTIONr_nbtor_other0.0840.21360
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2172
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.220
X-RAY DIFFRACTIONr_mcbond_it3.432.52023
X-RAY DIFFRACTIONr_mcbond_other0.722.5638
X-RAY DIFFRACTIONr_mcangle_it4.03352536
X-RAY DIFFRACTIONr_scbond_it3.3582.51205
X-RAY DIFFRACTIONr_scangle_it4.4945965
LS refinement shellResolution: 1.95→1.991 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.278 63 -
Rwork0.196 1296 -
all-1359 -
obs--99.2 %
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)
10.53030.0354-0.01681.4666-0.27761.81630.0394-0.0288-0.0231-0.0206-0.00460.038-0.02690.0574-0.0348-0.0633-0.01710.0095-0.07460.0175-0.07510.9324-8.755847.6435
21.6942-0.6933-0.19772.9144-0.12542.2929-0.08610.01320.11010.33660.0319-0.0969-0.06580.06340.0542-0.0794-0.0641-0.0298-0.05410.0066-0.03592.656523.708545.2506
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA276 - 4286 - 158
2X-RAY DIFFRACTION2AA429 - 595159 - 325

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