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- PDB-2qql: Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocki... -

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Basic information

Entry
Database: PDB / ID: 2qql
TitleNeuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab
Components
  • Antibody Heavy Chain
  • Antibody Light Chain
  • Neuropilin-2
KeywordsSIGNALING PROTEIN / VEGF receptor / semaphorin receptor / Phage-Derived Antibody / 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 / nerve development / semaphorin receptor complex / semaphorin receptor activity / outflow tract septum morphogenesis / regulation of postsynapse organization / negative chemotaxis / growth factor binding / cytokine binding / semaphorin-plexin signaling pathway / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / axon guidance / cellular response to leukemia inhibitory factor / signaling receptor activity / heparin binding / angiogenesis / postsynaptic membrane / cell adhesion / axon / glutamatergic synapse / extracellular region / metal ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spermadhesin, CUB domain / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / 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. ...Spermadhesin, CUB domain / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / 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 domain-like / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 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
H: Antibody Heavy Chain
L: Antibody Light Chain


Theoretical massNumber of molelcules
Total (without water)113,5763
Polymers113,5763
Non-polymers00
Water00
1
A: Neuropilin-2
H: Antibody Heavy Chain
L: Antibody Light Chain

A: Neuropilin-2
H: Antibody Heavy Chain
L: Antibody Light Chain


Theoretical massNumber of molelcules
Total (without water)227,1526
Polymers227,1526
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area14540 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.406, 121.406, 202.717
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 65385.332 Da / Num. of mol.: 1 / Fragment: CUB 1, CUB2, F5/8 type C 1, and C2 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP2, VEGF165R2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O60462
#2: Antibody Antibody Heavy Chain


Mass: 24847.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Antibody Light Chain


Mass: 23342.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
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: 3.8 Å3/Da / Density % sol: 67.61 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 1000, 10% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 31929 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 102 Å2 / Rsym value: 0.061 / Χ2: 1.044 / Net I/σ(I): 18.3
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 3101 / Rsym value: 0.515 / Χ2: 0.995 / % possible all: 98.9

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Processing

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

2qqk


Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 37.339 / SU ML: 0.295 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1610 5.1 %RANDOM
Rwork0.188 ---
obs0.19 30265 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.086 Å2
Baniso -1Baniso -2Baniso -3
1--2.13 Å2-1.07 Å20 Å2
2---2.13 Å20 Å2
3---3.2 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7740 0 0 0 7740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227954
X-RAY DIFFRACTIONr_bond_other_d0.0010.025414
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.94810818
X-RAY DIFFRACTIONr_angle_other_deg0.8283.00313140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3165983
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68223.835352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.277151270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3061544
X-RAY DIFFRACTIONr_chiral_restr0.0730.21164
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028876
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021631
X-RAY DIFFRACTIONr_nbd_refined0.2050.21594
X-RAY DIFFRACTIONr_nbd_other0.1910.25462
X-RAY DIFFRACTIONr_nbtor_refined0.1880.23742
X-RAY DIFFRACTIONr_nbtor_other0.0870.24454
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2160
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.22
X-RAY DIFFRACTIONr_mcbond_it2.7542.56292
X-RAY DIFFRACTIONr_mcbond_other0.4522.51999
X-RAY DIFFRACTIONr_mcangle_it3.8557966
X-RAY DIFFRACTIONr_scbond_it2.2122.53634
X-RAY DIFFRACTIONr_scangle_it3.3652852
LS refinement shellResolution: 3.1→3.164 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.328 94 -
Rwork0.267 1709 -
all-1803 -
obs--98.42 %
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)
15.48562.4527-1.34193.2562-0.00374.32180.6606-0.43011.26210.8843-0.43430.8907-0.5291-0.1925-0.22620.0426-0.09380.5535-0.5616-0.0835-0.078140.9844-66.6712-21.7118
22.9563-1.7107-1.44277.1993.67157.5997-0.04480.37360.0224-0.1765-0.1357-0.58080.11110.31660.1805-0.2707-0.33380.2144-0.2152-0.0256-0.217470.2656-49.9567-19.1061
34.92720.2815-1.06896.9575-0.95274.7733-0.05491.03910.7366-0.4171-0.03880.1308-0.2721-0.23780.0937-0.2564-0.3213-0.0288-0.08490.1-0.449159.0804-22.5032-21.9708
48.64450.7939-1.76054.9990.06415.5272-0.3989-0.0218-0.11580.5461-0.06660.620.5485-0.180.4655-0.0835-0.28030.2763-0.5732-0.1714-0.46847.5403-41.46921.4651
58.27143.4176-4.445.3646-2.34842.70940.7525-0.7261-0.63980.7973-0.4331-0.1953-0.0224-0.1138-0.3194-0.2212-0.26530.0939-0.40970.1126-0.49621.7522-98.1904-16.3692
610.6088-4.3172-0.10264.22320.25561.826-0.6133-0.1961-1.45630.95150.1814-0.58410.96020.4480.43190.5898-0.12660.0397-0.26760.35040.459729.3067-134.2768-13.6348
77.723-0.274-1.51456.8541-1.27283.21360.63060.3292-1.10920.6364-0.215-0.59090.09350.5995-0.4157-0.5203-0.22140.0267-0.39630.0737-0.323240.7316-95.6262-26.3287
86.5796-0.8473-1.78473.41820.46442.2855-0.09031.4945-0.83780.0969-0.2636-1.14631.1225-0.23940.3540.1147-0.1129-0.02120.13130.08580.429135.0288-129.0442-27.7922
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA26 - 1484 - 126
2X-RAY DIFFRACTION2AA149 - 272127 - 250
3X-RAY DIFFRACTION3AA273 - 428251 - 406
4X-RAY DIFFRACTION4AA429 - 595407 - 573
5X-RAY DIFFRACTION5LC1 - 1091 - 109
6X-RAY DIFFRACTION6LC110 - 214110 - 214
7X-RAY DIFFRACTION7HB1 - 1141 - 125
8X-RAY DIFFRACTION8HB115 - 216126 - 227

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