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- PDB-2qqn: Neuropilin-1 b1 Domain in Complex with a VEGF-Blocking Fab -

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Basic information

Entry
Database: PDB / ID: 2qqn
TitleNeuropilin-1 b1 Domain in Complex with a VEGF-Blocking Fab
Components
  • Antibody heavy chain
  • Antibody light chain
  • Neuropilin-1
KeywordsSIGNALING PROTEIN / VEGF receptor / semaphorin receptor / Phage-Derived Antibody / Angiogenesis / Developmental protein / Differentiation / Glycoprotein / Heparan sulfate / Membrane / Neurogenesis / Proteoglycan / Secreted / Transmembrane / HORMONE
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 / angiogenesis involved in coronary vascular morphogenesis / 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 / vascular endothelial growth factor receptor activity / endothelial cell chemotaxis / CHL1 interactions / regulation of vesicle-mediated transport / semaphorin receptor complex / neuropilin signaling pathway / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Signaling by ROBO receptors / substrate-dependent cell migration, cell extension / hepatocyte growth factor receptor signaling pathway / coronary artery morphogenesis / CRMPs in Sema3A signaling / semaphorin receptor activity / commissural neuron axon guidance / outflow tract septum morphogenesis / motor neuron axon guidance / axonal fasciculation / retinal ganglion cell axon guidance / sprouting angiogenesis / cell migration involved in sprouting angiogenesis / regulation of Cdc42 protein signal transduction / neural crest cell migration / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of filopodium assembly / artery morphogenesis / positive regulation of smooth muscle cell migration / cellular response to hepatocyte growth factor stimulus / growth factor binding / branching involved in blood vessel morphogenesis / positive chemotaxis / sorting endosome / cytokine binding / platelet-derived growth factor receptor signaling pathway / semaphorin-plexin signaling pathway / positive regulation of phosphorylation / 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 / 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 / response to wounding / neuron migration / positive regulation of angiogenesis / cell-cell signaling / heparin binding / cytoplasmic vesicle / angiogenesis / negative regulation of neuron apoptotic process / postsynaptic membrane / Attachment and Entry / early endosome / positive regulation of ERK1 and ERK2 cascade / receptor complex / neuron projection
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 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 / molecular replacement / Resolution: 2.2 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 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-1
H: Antibody heavy chain
L: Antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7866
Polymers65,5993
Non-polymers1863
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.115, 214.115, 45.465
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Neuropilin-1 / Vascular endothelial cell growth factor 165 receptor / CD304 antigen


Mass: 18004.369 Da / Num. of mol.: 1 / Fragment: F5/8 type C 1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP1, NRP, VEGF165R / Production host: Escherichia coli (E. coli) / References: UniProt: O14786
#2: Antibody Antibody heavy chain


Mass: 24289.260 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: 23305.840 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)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 3.06 Å3/Da / Density % sol: 59.77 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 25% PEG 1500, 4% tert-butanol, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 39195 / % possible obs: 99 % / Redundancy: 4.4 % / Biso Wilson estimate: 41.1 Å2 / Rsym value: 0.096 / Χ2: 1.014 / Net I/σ(I): 14.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 3893 / Rsym value: 0.485 / Χ2: 0.913 / % possible all: 98

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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: 1KEX (b1 domain), 2FJH (Fab)

1kex

2fjh


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 8.831 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1976 5.1 %RANDOM
Rwork0.159 ---
obs0.162 37085 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.243 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4540 0 12 249 4801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224660
X-RAY DIFFRACTIONr_bond_other_d0.0010.023149
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9556330
X-RAY DIFFRACTIONr_angle_other_deg0.8863.0037684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9065590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91824.208183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80515754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2851520
X-RAY DIFFRACTIONr_chiral_restr0.090.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025180
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02921
X-RAY DIFFRACTIONr_nbd_refined0.1780.2652
X-RAY DIFFRACTIONr_nbd_other0.1960.23001
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22163
X-RAY DIFFRACTIONr_nbtor_other0.0840.22484
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2202
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.216
X-RAY DIFFRACTIONr_mcbond_it3.5232.53758
X-RAY DIFFRACTIONr_mcbond_other0.7132.51201
X-RAY DIFFRACTIONr_mcangle_it4.33554777
X-RAY DIFFRACTIONr_scbond_it3.612.52064
X-RAY DIFFRACTIONr_scangle_it5.05151553
LS refinement shellResolution: 2.2→2.245 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.26 96 -
Rwork0.198 2202 -
all-2298 -
obs--98.21 %
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)
11.7157-0.0839-0.24842.1146-0.02261.7441-0.00610.10520.0355-0.00850.01330.2172-0.0175-0.1307-0.0072-0.15270.0181-0.0076-0.1501-0.0071-0.1672-53.642962.4083-11.6637
22.3012-1.2923-0.50672.3639-0.27011.3631-0.07030.08-0.1456-0.0074-0.02090.00380.10770.00490.0912-0.0212-0.05510.0157-0.1244-0.0104-0.0713-43.67726.5672-14.4336
33.288-0.08241.36422.0779-0.98160.99840.06330.5723-0.4991-0.2188-0.0139-0.17180.19150.0765-0.04940.26350.00710.03750.0168-0.11330.0713-43.3867-4.17556.0656
41.23810.779-0.80712.1344-1.231.8455-0.1057-0.0943-0.08650.1840.08370.10950.0943-0.11970.022-0.0122-0.03960.0476-0.11340.0053-0.0781-58.071330.21291.4371
54.5361-0.80910.25551.29530.16422.02920.03780.0511-0.20230.0118-0.0222-0.12250.21360.2593-0.01560.1515-0.02920.0416-0.15110.0169-0.0042-42.11733.879719.7137
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA274 - 4276 - 159
2X-RAY DIFFRACTION2HB1 - 1131 - 123
3X-RAY DIFFRACTION3HB114 - 220124 - 230
4X-RAY DIFFRACTION4LC1 - 1091 - 109
5X-RAY DIFFRACTION5LC110 - 214110 - 214

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