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- PDB-4gza: Complex of mouse Plexin A2 - Semaphorin 3A - Neuropilin-1 -

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Basic information

Entry
Database: PDB / ID: 4gza
TitleComplex of mouse Plexin A2 - Semaphorin 3A - Neuropilin-1
Components
  • Neuropilin-1
  • Plexin-A2
  • Semaphorin-3A
KeywordsSIGNALING PROTEIN / ternary complex / multi-domain / mammalian / cell-cell signaling / glycosilation / transmembrane
Function / homology
Function and homology information


Neurophilin interactions with VEGF and VEGFR / neural crest cell migration involved in sympathetic nervous system development / cell migration involved in coronary vasculogenesis / trigeminal nerve morphogenesis / Signal transduction by L1 / cerebellar granule cell precursor tangential migration / regulation of axon extension involved in axon guidance / basal dendrite development / otic placode development / CRMPs in Sema3A signaling ...Neurophilin interactions with VEGF and VEGFR / neural crest cell migration involved in sympathetic nervous system development / cell migration involved in coronary vasculogenesis / trigeminal nerve morphogenesis / Signal transduction by L1 / cerebellar granule cell precursor tangential migration / regulation of axon extension involved in axon guidance / basal dendrite development / otic placode development / CRMPs in Sema3A signaling / protein localization to early endosome / Sema3A PAK dependent Axon repulsion / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / positive regulation of smooth muscle cell chemotaxis / 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 / epithelial cell migration / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / branchiomotor neuron axon guidance / semaphorin receptor binding / positive regulation of male gonad development / negative regulation of axon extension involved in axon guidance / axon extension involved in axon guidance / blood vessel endothelial cell migration / renal artery morphogenesis / VEGF-activated neuropilin signaling pathway / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / neurofilament / cerebellar climbing fiber to Purkinje cell synapse / maintenance of synapse structure / sympathetic neuron projection extension / synaptic target recognition / vascular endothelial growth factor binding / negative regulation of epithelial cell migration / angiogenesis involved in coronary vascular morphogenesis / limb bud formation / motor neuron migration / neural crest cell migration involved in autonomic nervous system development / retina vasculature development in camera-type eye / sympathetic ganglion development / negative regulation of axon extension / positive regulation of axon extension involved in axon guidance / endothelial cell chemotaxis / axonogenesis involved in innervation / vascular endothelial growth factor receptor activity / nerve development / positive regulation of neuron migration / neuropilin signaling pathway / olfactory bulb development / sympathetic nervous system development / neuropilin binding / pharyngeal system development / substrate-dependent cell migration, cell extension / hepatocyte growth factor receptor signaling pathway / positive regulation of platelet-derived growth factor receptor signaling pathway / coronary artery morphogenesis / semaphorin receptor activity / chemorepellent activity / commissural neuron axon guidance / outflow tract septum morphogenesis / motor neuron axon guidance / positive regulation of vascular associated smooth muscle cell migration / axonal fasciculation / retinal ganglion cell axon guidance / sprouting angiogenesis / cell migration involved in sprouting angiogenesis / axon extension / regulation of Cdc42 protein signal transduction / positive regulation of filopodium assembly / positive regulation of cell migration involved in sprouting angiogenesis / neural tube development / artery morphogenesis / centrosome localization / negative chemotaxis / cellular response to hepatocyte growth factor stimulus / growth factor binding / branching involved in blood vessel morphogenesis / dendrite morphogenesis / positive chemotaxis / sorting endosome / platelet-derived growth factor receptor signaling pathway / dendrite development / semaphorin-plexin signaling pathway / positive regulation of phosphorylation / cellular response to vascular endothelial growth factor stimulus / positive regulation of focal adhesion assembly / vascular endothelial growth factor receptor signaling pathway / endothelial cell migration / neuron development / somitogenesis
Similarity search - Function
Semaphorin-3A, sema domain / Plexin-A2, sema domain / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Semaphorin / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin A/B, PSI domain / Plexin, TIG domain 1 / TIG domain ...Semaphorin-3A, sema domain / Plexin-A2, sema domain / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Semaphorin / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin A/B, PSI domain / Plexin, TIG domain 1 / TIG domain / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / : / Plexin family / Coagulation factors 5/8 type C domain (FA58C) signature 2. / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Plexin repeat / Plexin repeat / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / 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 / IPT/TIG domain / Coagulation factors 5/8 type C domain (FA58C) profile. / ig-like, plexins, transcription factors / Rho GTPase activation protein / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / IPT domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / Galactose-binding-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin E-set / Concanavalin A-like lectin/glucanase domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Semaphorin-3A / Plexin-A2 / Neuropilin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7 Å
AuthorsJanssen, B.J.C. / Malinauskas, T. / Siebold, C. / Jones, E.Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Neuropilins lock secreted semaphorins onto plexins in a ternary signaling complex.
Authors: Janssen, B.J.C. / Malinauskas, T. / Weir, G.A. / Cader, M.Z. / Siebold, C. / Jones, E.Y.
History
DepositionSep 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plexin-A2
B: Plexin-A2
C: Plexin-A2
D: Plexin-A2
E: Plexin-A2
F: Plexin-A2
G: Semaphorin-3A
H: Neuropilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)582,3649
Polymers582,3248
Non-polymers401
Water00
1
A: Plexin-A2
B: Plexin-A2
C: Plexin-A2
D: Plexin-A2
E: Plexin-A2
F: Plexin-A2
G: Semaphorin-3A
H: Neuropilin-1
hetero molecules

A: Plexin-A2
B: Plexin-A2
C: Plexin-A2
D: Plexin-A2
E: Plexin-A2
F: Plexin-A2
G: Semaphorin-3A
H: Neuropilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,164,72818
Polymers1,164,64816
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Unit cell
Length a, b, c (Å)191.632, 293.604, 252.176
Angle α, β, γ (deg.)90.00, 106.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Plexin-A2 / Plex 2 / Plexin-2


Mass: 75934.914 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 33-703
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plxna2, Kiaa0463 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P70207
#2: Protein Semaphorin-3A / Semaphorin III / Sema III / Semaphorin-D / Sema D


Mass: 61246.945 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-555
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sema3a, Semad, SemD / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O08665
#3: Protein Neuropilin-1 / A5 protein


Mass: 65467.652 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 22-586
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nrp1, Nrp / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P97333
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY
Sequence detailsTHE SEQUENCE OF CHAIN G IS BASED ON NCBI REFERENCE SEQUENCE: NP_033178.2. RESIDUE 475 IS A VAL IN ...THE SEQUENCE OF CHAIN G IS BASED ON NCBI REFERENCE SEQUENCE: NP_033178.2. RESIDUE 475 IS A VAL IN THIS DATABASE SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
15.8478.95
2
3
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop7.570mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2932vapor diffusion, sitting drop7.570mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, 1% v/v ethyl acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2933vapor diffusion, sitting drop7.570mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, 8% v/v acetonitrile , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
31003
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I04-110.9173
SYNCHROTRONDiamond I0321.0719
SYNCHROTRONDiamond I0230.9795
Detector
TypeIDDetectorDate
DECTRIS PILATUS 2M1PIXELApr 15, 2011
DECTRIS PILATUS 6M2PIXELApr 20, 2011
ADSC QUANTUM 315r3CCDMay 5, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single bounce monochromatorSINGLE WAVELENGTHMx-ray1
2Double crystal monochromatorSINGLE WAVELENGTHMx-ray1
3Double crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91731
21.07191
30.97951
ReflectionResolution: 7→126 Å / Num. all: 20190 / Num. obs: 20176 / % possible obs: 95.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OKT, 1Q47, 4GZ9

3okt

1q47

4gz9


Resolution: 7→125.506 Å / SU ML: 1.03 / Cross valid method: THROUGHOUT / σ(F): -3 / Phase error: 29.14 / Stereochemistry target values: MLHL
Details: AUTHORS STATE THAT DUE TO THE LOW RESOLUTION OF THE DIFFRACTION DATA THE STRUCTURE WAS ONLY SUBJECTED TO RIGID BODY REFINEMENT WITH EACH DOMAIN AS RIGID BODY USING (PARTS OF) THE COORDINATES ...Details: AUTHORS STATE THAT DUE TO THE LOW RESOLUTION OF THE DIFFRACTION DATA THE STRUCTURE WAS ONLY SUBJECTED TO RIGID BODY REFINEMENT WITH EACH DOMAIN AS RIGID BODY USING (PARTS OF) THE COORDINATES OF PDB ENTRIES 3OKT, 1Q47 AND 4GZ9. AUTHORS HAVE NOT FURTHER REFINED THE RESULTING COORDINATES NOR CORRECTED RESULTING CLASHES BETWEEN ATOMS AND DEVIATING PEPTIDE LINKAGES BETWEEN DOMAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2848 1009 5.05 %RANDOM
Rwork0.2847 ---
obs0.2847 20176 95.6 %-
all-20176 --
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 283.537 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-84.1244 Å2-0 Å2119.0039 Å2
2--17.4558 Å2-0 Å2
3---22.6768 Å2
Refinement stepCycle: LAST / Resolution: 7→125.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35654 0 1 0 35655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01436622
X-RAY DIFFRACTIONf_angle_d1.20249584
X-RAY DIFFRACTIONf_dihedral_angle_d13.07413337
X-RAY DIFFRACTIONf_chiral_restr0.0635452
X-RAY DIFFRACTIONf_plane_restr0.0086434
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
7.0004-7.17550.36191190.3727260894
7.1755-7.36950.36681680.3578266094
7.3695-7.58630.31881490.3447263194
7.5863-7.83110.30611580.3451258393
7.8311-8.1110.31851340.3312256590
8.111-8.43570.32091210.3213228781
8.4357-8.81950.31881330.2921239485
8.8195-9.28430.28781390.2803270095
9.2843-9.86580.26911320.2596265795
9.8658-10.62720.22871500.2527266795
10.6272-11.69590.25181270.2403273195
11.6959-13.38670.27641210.253264393
13.3867-16.85940.281300.2752245588
16.8594-125.52630.27391410.2832257591

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