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- PDB-2qqm: Crystal Structure of the a2b1b2 Domains from Human Neuropilin-1 -

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Entry
Database: PDB / ID: 2qqm
TitleCrystal Structure of the a2b1b2 Domains from Human Neuropilin-1
ComponentsNeuropilin-1
KeywordsSIGNALING PROTEIN / VEGF receptor / semaphorin receptor / calcium-binding domain / 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 / regulation of vascular endothelial growth factor receptor signaling pathway / dorsal root ganglion morphogenesis ...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 / regulation of vascular endothelial growth factor receptor signaling pathway / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / neurofilament / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / branchiomotor neuron axon guidance / renal artery morphogenesis / postsynapse organization / negative regulation of axon extension involved in axon guidance / VEGF-activated neuropilin signaling pathway / axon extension involved in axon guidance / sympathetic neuron projection extension / vascular endothelial growth factor binding / Neurophilin interactions with VEGF and VEGFR / endothelial cell chemotaxis / 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 / CHL1 interactions / vascular endothelial growth factor receptor activity / outflow tract septum morphogenesis / regulation of vesicle-mediated transport / Signaling by ROBO receptors / semaphorin receptor complex / angiogenesis involved in coronary vascular morphogenesis / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / neuropilin signaling pathway / hepatocyte growth factor receptor signaling pathway / coronary artery morphogenesis / substrate-dependent cell migration, cell extension / semaphorin receptor activity / CRMPs in Sema3A signaling / commissural neuron axon guidance / axonal fasciculation / cell migration involved in sprouting angiogenesis / regulation of Cdc42 protein signal transduction / motor neuron axon guidance / sprouting angiogenesis / neural crest cell migration / positive regulation of filopodium assembly / artery morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / cellular response to hepatocyte growth factor stimulus / branching involved in blood vessel morphogenesis / retinal ganglion cell axon guidance / positive chemotaxis / positive regulation of smooth muscle cell migration / cytokine binding / growth factor binding / sorting endosome / positive regulation of focal adhesion assembly / Sema3A PAK dependent Axon repulsion / platelet-derived growth factor receptor signaling pathway / semaphorin-plexin signaling pathway / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / vascular endothelial growth factor receptor signaling pathway / coreceptor activity / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / GTPase activator activity / Signal transduction by L1 / axon guidance / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / animal organ morphogenesis / mitochondrial membrane / neuron migration / response to wounding / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell signaling / heparin binding / cytoplasmic vesicle / angiogenesis / postsynaptic membrane / negative regulation of neuron apoptotic process / positive regulation of ERK1 and ERK2 cascade / Attachment and Entry / early endosome / receptor complex / neuron projection
Similarity search - Function
Spermadhesin, CUB domain / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / : / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. ...Spermadhesin, CUB domain / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / MAM domain signature. / 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: 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 2.0Oct 25, 2017Group: Atomic model / Derived calculations / Refinement description
Category: atom_site / pdbx_struct_assembly_gen ...atom_site / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / software / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.occupancy / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Aug 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-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,29810
Polymers50,7441
Non-polymers1,5549
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.177, 68.178, 66.613
Angle α, β, γ (deg.)90.000, 102.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 50744.254 Da / Num. of mol.: 1 / Fragment: CUB 2, F5/8 type C 1, and F5/8 type C 2 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP1, NRP, VEGF165R / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O14786

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1-2/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 201 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES, 12% PEG 20000, pH 6.5, 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→50 Å / Num. obs: 30901 / % possible obs: 97.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 30.9 Å2 / Rsym value: 0.086 / Χ2: 1.038 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueΧ2% possible allRmerge(I) obs
2-2.0733.227940.3220.88788.7
2.07-2.153.229570.9694.40.299
2.15-2.253.430221.00296.20.268
2.25-2.373.531041.06298.20.243
2.37-2.523.631361.08199.40.205
2.52-2.713.731821.0599.80.169
2.71-2.993.631581.10599.90.129
2.99-3.423.631571.08699.80.091
3.42-4.313.531621.01499.20.067
4.31-503.532291.05999.30.053

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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: 2QQI (b1b2 domains), 2QQK (a2 domain)

2qqi

2qqk


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.623 / SU ML: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1558 5.1 %RANDOM
Rwork0.183 ---
obs0.186 29213 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.27 Å2
Baniso -1Baniso -2Baniso -3
1--2.38 Å20 Å22.16 Å2
2---1.22 Å20 Å2
3---4.51 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3456 0 101 194 3751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223649
X-RAY DIFFRACTIONr_bond_other_d0.0010.022572
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9814933
X-RAY DIFFRACTIONr_angle_other_deg0.8433.0036204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6315435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33523.727161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54615611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6991524
X-RAY DIFFRACTIONr_chiral_restr0.0830.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023949
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02737
X-RAY DIFFRACTIONr_nbd_refined0.1850.2644
X-RAY DIFFRACTIONr_nbd_other0.1950.22684
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21760
X-RAY DIFFRACTIONr_nbtor_other0.0960.21957
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2178
X-RAY DIFFRACTIONr_metal_ion_refined0.1050.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.24
X-RAY DIFFRACTIONr_mcbond_it3.5112.52250
X-RAY DIFFRACTIONr_mcbond_other0.8432.5889
X-RAY DIFFRACTIONr_mcangle_it4.66653507
X-RAY DIFFRACTIONr_scbond_it3.3142.51643
X-RAY DIFFRACTIONr_scangle_it4.57251425
LS refinement shellResolution: 2→2.041 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.311 85 -
Rwork0.242 1517 -
all-1602 -
obs--87.73 %
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)
12.67410.00450.28521.29020.15020.6469-0.00970.00410.07440.0125-0.060.0613-0.04170.03610.0697-0.0460.010.0187-0.02850.045-0.0869-10.72667.388314.6973
20.74620.4045-0.00581.09580.03011.49210.00230.02110.05430.0686-0.01280.1945-0.0696-0.09640.0105-0.01150.01610.0105-0.0334-0.0205-0.05933.49811.574843.143
31.9166-0.01-0.45673.1716-0.54140.6883-0.02330.0449-0.1335-0.05170.01690.02340.0717-0.01240.0064-0.0152-0.0095-0.0442-0.002-0.0097-0.189713.5363-13.158114.8863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A145 - 270
2X-RAY DIFFRACTION1A601
3X-RAY DIFFRACTION1A608 - 611
4X-RAY DIFFRACTION1A612 - 613
5X-RAY DIFFRACTION2A273 - 425
6X-RAY DIFFRACTION3A426 - 586

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