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

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Basic information

Entry
Database: PDB / ID: 2qqk
TitleNeuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab
Components
  • Antibody Heavy ChainImmunoglobulin heavy chain
  • Antibody Light ChainImmunoglobulin light chain
  • Neuropilin-2Neuropilin
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 / 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
Spermadhesin, CUB domain / 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 ...Spermadhesin, CUB domain / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 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 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0185
Polymers113,5763
Non-polymers4422
Water0
1
A: Neuropilin-2
hetero molecules

A: Neuropilin-2
hetero molecules

H: Antibody Heavy Chain
L: Antibody Light Chain

H: Antibody Heavy Chain
L: Antibody Light Chain


Theoretical massNumber of molelcules
Total (without water)228,03710
Polymers227,1526
Non-polymers8854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_453-x-1,y,-z-21
crystal symmetry operation3_444x-1/2,y-1/2,z-11
crystal symmetry operation4_444-x-1/2,y-1/2,-z-11
Buried area14470 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.277, 105.873, 92.400
Angle α, β, γ (deg.)90.000, 98.830, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Neuropilin-2 / Neuropilin / 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 / Immunoglobulin 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 / Immunoglobulin 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)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 3.16 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes, 22% polyacrylic acid 5100, 0.02 M MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / 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: 2.75→50 Å / Num. obs: 36321 / % possible obs: 99.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 75.4 Å2 / Rsym value: 0.104 / Χ2: 1.028 / Net I/σ(I): 10.9
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 3599 / Rsym value: 0.527 / Χ2: 0.852 / % possible all: 100

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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: 2QQJ (b1b2 domains), 2FJH (antibody), 1NT0 (a2 domain)

2qqj

2fjh

1nt0


Resolution: 2.75→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.922 / SU B: 25.301 / SU ML: 0.235 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.723 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1830 5 %RANDOM
Rwork0.186 ---
obs0.189 34487 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.912 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å2-2.82 Å2
2--4.17 Å20 Å2
3----7.13 Å2
Refinement stepCycle: LAST / Resolution: 2.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7593 0 28 0 7621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227828
X-RAY DIFFRACTIONr_bond_other_d0.0010.025317
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.95210646
X-RAY DIFFRACTIONr_angle_other_deg0.8263.00312901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8075962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05123.902346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.882151245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5131543
X-RAY DIFFRACTIONr_chiral_restr0.0770.21154
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028695
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021595
X-RAY DIFFRACTIONr_nbd_refined0.1930.21359
X-RAY DIFFRACTIONr_nbd_other0.1880.25162
X-RAY DIFFRACTIONr_nbtor_refined0.1850.23630
X-RAY DIFFRACTIONr_nbtor_other0.0840.24384
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2163
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.24
X-RAY DIFFRACTIONr_mcbond_it3.2562.56180
X-RAY DIFFRACTIONr_mcbond_other0.5042.51958
X-RAY DIFFRACTIONr_mcangle_it4.29757810
X-RAY DIFFRACTIONr_scbond_it2.9172.53592
X-RAY DIFFRACTIONr_scangle_it4.21252836
LS refinement shellResolution: 2.75→2.808 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.315 93 -
Rwork0.27 1786 -
all-1879 -
obs--88.01 %
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)
11.68290.2846-1.69841.839-1.25576.42-0.15410.231-0.06150.09190.0320.18791.3427-1.03270.12210.0566-0.28660.05050.014-0.0611-0.0872-4.7724-44.4553-42.877
27.9498-0.1591-0.13142.97080.11422.6234-0.33170.31910.6215-0.04120.07180.1517-0.67520.70010.25990.0352-0.7406-0.34330.006-0.1074-0.0622-24.2425-41.5606-72.3537
31.83490.00610.37972.26920.38473.42430.0855-0.0877-0.02370.1695-0.2087-0.09440.08390.55040.1232-0.1964-0.0668-0.03280.0478-0.0328-0.0975-33.7485-69.3803-73.9799
43.488-0.2208-0.47442.85140.20874.2845-0.2679-0.89280.35740.66090.1887-0.1353-0.43070.31440.07920.2543-0.0596-0.18250.1136-0.2654-0.209-40.5421-52.4504-47.1548
50.95850.31120.75981.12541.10243.1697-0.0821-0.0570.03820.09860.07070.00580.2444-0.0650.0114-0.0985-0.05710.0269-0.0461-0.0032-0.05395.0802-27.1663-10.9971
60.37230.57920.56044.3109-1.75317.8806-0.3555-0.41280.1967-0.06740.07590.1055-1.91420.08510.27950.2906-0.142-0.1572-0.1454-0.15710.079712.72948.2123-1.3523
70.9543-0.9180.11743.50760.86782.3485-0.1010.25970.1149-0.1978-0.0238-0.0062-0.18970.31170.1248-0.0989-0.1416-0.00140.01660.0416-0.10925.809-19.9234-31.2037
86.972-0.41356.78452.6717-1.873312.073-0.39010.64960.2698-0.48310.0649-0.3864-1.10041.71170.3252-0.0506-0.32530.05880.05060.0901-0.03319.63243.036-15.6522
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA27 - 1485 - 126
2X-RAY DIFFRACTION2AA149 - 272127 - 250
3X-RAY DIFFRACTION2AD11
4X-RAY DIFFRACTION2AE6021
5X-RAY DIFFRACTION3AA273 - 428251 - 406
6X-RAY DIFFRACTION4AA429 - 594407 - 572
7X-RAY DIFFRACTION5LC1 - 1091 - 109
8X-RAY DIFFRACTION6LC110 - 211110 - 211
9X-RAY DIFFRACTION7HB1 - 1141 - 125
10X-RAY DIFFRACTION8HB115 - 213126 - 224

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