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- PDB-4gz8: Mouse Semaphorin 3A, domains Sema-PSI-IG -

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Entry
Database: PDB / ID: 4gz8
TitleMouse Semaphorin 3A, domains Sema-PSI-IG
ComponentsSemaphorin-3ASemaphorin
KeywordsSIGNALING PROTEIN / sema / multi-domain / cell-cell signaling / plexin / glycosilated / extracellular
Function / homology
Function and homology information


neural crest cell migration involved in sympathetic nervous system development / regulation of axon extension involved in axon guidance / synaptic target recognition / CRMPs in Sema3A signaling / basal dendrite arborization / Sema3A PAK dependent Axon repulsion / dichotomous subdivision of terminal units involved in salivary gland branching / semaphorin receptor binding / epithelial cell migration / ventral trunk neural crest cell migration ...neural crest cell migration involved in sympathetic nervous system development / regulation of axon extension involved in axon guidance / synaptic target recognition / CRMPs in Sema3A signaling / basal dendrite arborization / Sema3A PAK dependent Axon repulsion / dichotomous subdivision of terminal units involved in salivary gland branching / semaphorin receptor binding / 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 / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / branchiomotor neuron axon guidance / positive regulation of male gonad development / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / maintenance of synapse structure / axon extension involved in axon guidance / negative regulation of axon extension involved in axon guidance / sympathetic neuron projection extension / negative regulation of epithelial cell migration / sympathetic ganglion development / axonogenesis involved in innervation / neural crest cell migration involved in autonomic nervous system development / negative regulation of axon extension / nerve development / positive regulation of neuron migration / olfactory bulb development / neuropilin binding / chemorepellent activity / axon extension / motor neuron axon guidance / axonal fasciculation / dendrite morphogenesis / neural crest cell migration / negative chemotaxis / semaphorin-plexin signaling pathway / regulation of heart rate / axon guidance / neuron migration / negative regulation of neuron projection development / nervous system development / axon / dendrite / glutamatergic synapse / extracellular space / extracellular region
Similarity search - Function
Semaphorin-3A, sema domain / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Semaphorin / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily ...Semaphorin-3A, sema domain / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Semaphorin / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / PSI domain / domain found in Plexins, Semaphorins and Integrins / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Semaphorin-3A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 2.0Jul 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Semaphorin-3A
B: Semaphorin-3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,29413
Polymers144,8322
Non-polymers2,46111
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-35 kcal/mol
Surface area48340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.630, 126.170, 161.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: UNK / End label comp-ID: UNK / Refine code: 0

Dom-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1AA27 - 66410 - 647
2BB27 - 66510 - 648

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Semaphorin-3A / Semaphorin / Semaphorin III / Sema III / Semaphorin-D / Sema D


Mass: 72416.078 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 21-675
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

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Sugars , 4 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}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
#4: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: 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.: 1
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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Non-polymers , 2 types, 7 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2

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Details

Sequence details(1) THE SEQUENCE IS BASED ON NCBI REFERENCE SEQUENCE: NP_033178.2. RESIDUE 475 IS A VAL IN THIS ...(1) THE SEQUENCE IS BASED ON NCBI REFERENCE SEQUENCE: NP_033178.2. RESIDUE 475 IS A VAL IN THIS DATABASE SEQUENCE. (2) RESIDUES 551 AND 555 WERE BOTH MUTATED FROM ARG TO ALA TO PREVENT PROTEOLYTIC CLEAVAGE IN THE FURIN SITE AT RESIDUES 551-555. (3) THE AUTHORS KNOW THE SEQUENCE BUT ARE UNSURE OF THE ASSIGNMENT OF RESIDUES IN THE SEGMENT 598 TO 666. THE ONE LETTER CODE SEQUENCE IS LQHHDNHHGPSLEERIIYGVENSSTFLECSPKSQRALVYWQFQRRNEDRKEEIRMGDHIIRTEQGLLLRSLQKKDSGNYLCHAVEHGFMQTLLKVTLEVIDTEHLEGTKHHHHHH.

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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: 3.43 Å3/Da / Density % sol: 64.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M sodium cacodylate, 0.1M calcium acetate, 12% w/v PEG 8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 14, 2011
RadiationMonochromator: Single bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 3.3→99.42 Å / Num. all: 30776 / Num. obs: 29876 / % possible obs: 97.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q47

1q47


Resolution: 3.3→77 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.867 / SU B: 23.111 / SU ML: 0.375 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R Free: 0.503 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26499 1505 5 %RANDOM
Rwork0.21321 ---
all0.21585 29876 --
obs0.21585 28371 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.898 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å2-0 Å20 Å2
2--2.49 Å2-0 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 3.3→77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8731 0 155 0 8886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.029152
X-RAY DIFFRACTIONr_bond_other_d0.0040.028533
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.96312441
X-RAY DIFFRACTIONr_angle_other_deg0.901319340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.74751098
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66923.619431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.074151406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4541558
X-RAY DIFFRACTIONr_chiral_restr0.0860.21370
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110284
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022127
Refine LS restraints NCS

Ens-ID: 1 / Number: 33450 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 105 -
Rwork0.293 1930 -
obs--99.03 %

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