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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-1Neuropilin 1
  • Plexin-A2
  • Semaphorin-3ASemaphorin
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 / synaptic target recognition / CRMPs in Sema3A signaling / basal dendrite development ...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 / synaptic target recognition / CRMPs in Sema3A signaling / basal dendrite development / protein localization to early endosome / otic placode development / neurofilament / basal dendrite arborization / Sema3A PAK dependent Axon repulsion / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / regulation of vascular endothelial growth factor receptor signaling pathway / vestibulocochlear nerve structural organization / semaphorin receptor binding / dorsal root ganglion morphogenesis / epithelial cell migration / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / cerebellar climbing fiber to Purkinje cell synapse / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / postsynapse organization / branchiomotor neuron axon guidance / renal artery morphogenesis / positive regulation of male gonad development / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin-plexin signaling pathway involved in axon guidance / maintenance of synapse structure / axon extension involved in axon guidance / VEGF-activated neuropilin signaling pathway / negative regulation of axon extension involved in axon guidance / retina vasculature development in camera-type eye / blood vessel endothelial cell migration / sympathetic neuron projection extension / negative regulation of epithelial cell migration / motor neuron migration / endothelial cell chemotaxis / vascular endothelial growth factor binding / sympathetic ganglion development / limb bud formation / axonogenesis involved in innervation / neural crest cell migration involved in autonomic nervous system development / positive regulation of axon extension involved in axon guidance / negative regulation of axon extension / vascular endothelial growth factor receptor activity / substrate-dependent cell migration, cell extension / nerve development / semaphorin receptor complex / positive regulation of neuron migration / angiogenesis involved in coronary vascular morphogenesis / olfactory bulb development / sympathetic nervous system development / hepatocyte growth factor receptor signaling pathway / pharyngeal system development / neuropilin signaling pathway / neuropilin binding / coronary artery morphogenesis / outflow tract septum morphogenesis / regulation of Cdc42 protein signal transduction / chemorepellent activity / semaphorin receptor activity / commissural neuron axon guidance / negative regulation of cell adhesion / axon extension / motor neuron axon guidance / retinal ganglion cell axon guidance / cell migration involved in sprouting angiogenesis / artery morphogenesis / axonal fasciculation / dendrite morphogenesis / sprouting angiogenesis / neural tube development / neural crest cell migration / positive regulation of filopodium assembly / centrosome localization / negative chemotaxis / cellular response to hepatocyte growth factor stimulus / branching involved in blood vessel morphogenesis / positive regulation of axonogenesis / positive regulation of cell migration involved in sprouting angiogenesis / positive chemotaxis / dendrite development / growth factor binding / sorting endosome / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / platelet-derived growth factor receptor signaling pathway / neuron development / endothelial cell migration / cellular response to vascular endothelial growth factor stimulus
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, TIG domain 1 / TIG domain / Neuropilin ...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, TIG domain 1 / TIG domain / Neuropilin / Neuropilin, C-terminal / Plexin, cytoplasmic RhoGTPase-binding domain / C-terminal domain of neuropilin glycoprotein / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / MAM domain signature. / 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. / Plexin family / 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. / Plexin repeat / Plexin repeat / Spermadhesin, CUB domain superfamily / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / 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 / F5/8 type C domain / Rho GTPase activation protein / PSI domain / domain found in Plexins, Semaphorins and Integrins / Coagulation factor 5/8 C-terminal domain / IPT domain / Galactose-binding-like domain superfamily / Immunoglobulin E-set / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin subtype / Immunoglobulin / 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

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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
Water0
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 / 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 / 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
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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