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- PDB-8ivx: Crystal structure of NRP2 in complex with aNRP2-14 Fab fragment -

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Basic information

Entry
Database: PDB / ID: 8ivx
TitleCrystal structure of NRP2 in complex with aNRP2-14 Fab fragment
Components
  • Heavy chain of antibody 14V4 Fab fragment
  • Light chain of antibody 14V4 Fab fragment
  • aNRP2-14
KeywordsMEMBRANE PROTEIN / Complex / Antibody
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-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGeng, Y. / Zhai, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Transl Med / Year: 2023
Title: Inhibition of VEGF binding to neuropilin-2 enhances chemosensitivity and inhibits metastasis in triple-negative breast cancer.
Authors: Xu, Z. / Goel, H.L. / Burkart, C. / Burman, L. / Chong, Y.E. / Barber, A.G. / Geng, Y. / Zhai, L. / Wang, M. / Kumar, A. / Menefee, A. / Polizzi, C. / Eide, L. / Rauch, K. / Rahman, J. / ...Authors: Xu, Z. / Goel, H.L. / Burkart, C. / Burman, L. / Chong, Y.E. / Barber, A.G. / Geng, Y. / Zhai, L. / Wang, M. / Kumar, A. / Menefee, A. / Polizzi, C. / Eide, L. / Rauch, K. / Rahman, J. / Hamel, K. / Fogassy, Z. / Klopp-Savino, S. / Paz, S. / Zhang, M. / Cubitt, A. / Nangle, L.A. / Mercurio, A.M.
History
DepositionMar 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_planes
Item: _pdbx_validate_planes.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: aNRP2-14
H: Heavy chain of antibody 14V4 Fab fragment
L: Light chain of antibody 14V4 Fab fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5454
Polymers114,4833
Non-polymers621
Water7,494416
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.501, 89.411, 130.877
Angle α, β, γ (deg.)90.00, 94.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-565-

HOH

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Components

#1: Protein aNRP2-14 / Vascular endothelial cell growth factor 165 receptor 2


Mass: 65954.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP2, VEGF165R2 / Production host: Homo sapiens (human) / References: UniProt: O60462
#2: Antibody Heavy chain of antibody 14V4 Fab fragment


Mass: 24742.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Light chain of antibody 14V4 Fab fragment


Mass: 23785.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 30% PEG300, 0.1M Sodium acetate trihydrate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2019
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 78778 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.033 / Rrim(I) all: 0.082 / Χ2: 0.96 / Net I/σ(I): 23.28
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.41 / Num. unique obs: 3849 / CC1/2: 0.816 / Rpim(I) all: 0.264 / Rrim(I) all: 0.649 / Χ2: 0.633 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.65 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.705 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22547 4067 5.2 %RANDOM
Rwork0.191 ---
obs0.19284 74703 97.13 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.361 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å2-1.04 Å2
2--0.72 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6527 0 4 416 6947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0166709
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165903
X-RAY DIFFRACTIONr_angle_refined_deg1.0571.8039123
X-RAY DIFFRACTIONr_angle_other_deg0.3651.55913817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5795.203861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.247101074
X-RAY DIFFRACTIONr_chiral_restr0.0590.2999
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027577
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021351
X-RAY DIFFRACTIONr_mcbond_it3.1452.3333334
X-RAY DIFFRACTIONr_mcbond_other3.1422.3333334
X-RAY DIFFRACTIONr_mcangle_it4.2133.4684150
X-RAY DIFFRACTIONr_mcangle_other4.2173.4694151
X-RAY DIFFRACTIONr_scbond_it4.5972.7433375
X-RAY DIFFRACTIONr_scbond_other4.5962.7443376
X-RAY DIFFRACTIONr_scangle_other6.3133.9474974
X-RAY DIFFRACTIONr_long_range_B_refined7.86131.0827104
X-RAY DIFFRACTIONr_long_range_B_other7.8529.7767027
LS refinement shellResolution: 1.9→1.949 Å
RfactorNum. reflection% reflection
Rfree0.325 256 -
Rwork0.3 5286 -
obs--92.78 %
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)
11.004-0.1166-0.29861.4313-0.05831.5840.0574-0.35880.00450.4828-0.0140.0931-0.1024-0.0588-0.04350.3291-0.06320.03310.35150.00030.0071-23.218-15.15150.332
20.37630.0871-0.18150.8114-0.35531.8510.00740.0388-0.0053-0.1311-0.0384-0.02650.04490.01890.0310.0790.0120.00370.0735-0.00560.0018-21.882-8.9021.859
30.24690.0584-0.14380.6032-0.07741.8325-0.00230.0419-0.0004-0.064-0.03370.0540.00370.00280.0360.11860.0195-0.00960.1063-0.0030.0332-19.968.322-4.711
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A149 - 595
2X-RAY DIFFRACTION2H1 - 221
3X-RAY DIFFRACTION3L1 - 213

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