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- PDB-7y4o: Rat Semaphorin 6D extracellular region -

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Basic information

Entry
Database: PDB / ID: 7y4o
TitleRat Semaphorin 6D extracellular region
ComponentsSemaphorin 6D
KeywordsSIGNALING PROTEIN / Receptor ligand
Function / homology
Function and homology information


Other semaphorin interactions / semaphorin receptor binding / negative regulation of smooth muscle cell migration / ventricular system development / chemorepellent activity / neural crest cell migration / smooth muscle cell migration / negative chemotaxis / positive regulation of smooth muscle cell migration / semaphorin-plexin signaling pathway ...Other semaphorin interactions / semaphorin receptor binding / negative regulation of smooth muscle cell migration / ventricular system development / chemorepellent activity / neural crest cell migration / smooth muscle cell migration / negative chemotaxis / positive regulation of smooth muscle cell migration / semaphorin-plexin signaling pathway / axon guidance / positive regulation of cell migration / Golgi apparatus / plasma membrane / cytoplasm
Similarity search - Function
Semaphorin / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTanaka, T. / Neyazaki, M. / Nogi, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP17K19206 Japan
Japan Society for the Promotion of Science (JSPS)JP23121520 Japan
Japan Society for the Promotion of Science (JSPS)JP25121729 Japan
CitationJournal: Protein Sci. / Year: 2022
Title: Hybrid in vitro/in silico analysis of low-affinity protein-protein interactions that regulate signal transduction by Sema6D.
Authors: Tanaka, T. / Ekimoto, T. / Nagatomo, M. / Neyazaki, M. / Shimoji, E. / Yamane, T. / Kanagawa, S. / Oi, R. / Mihara, E. / Takagi, J. / Akashi, S. / Ikeguchi, M. / Nogi, T.
History
DepositionJun 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 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: Semaphorin 6D
B: Semaphorin 6D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,4884
Polymers125,0452
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-2 kcal/mol
Surface area45910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.147, 213.147, 191.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Semaphorin 6D


Mass: 62522.633 Da / Num. of mol.: 2 / Fragment: ectodomain fragment / Mutation: S332G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Sema6d / Cell line (production host): CHO-lec 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: A0A0G2JZC4
#2: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
Has ligand of interestY
Has protein modificationY

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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: 8.69 Å3/Da / Density % sol: 85.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 12%(wt./vol.) PEG3350, 100 mM CaCl2, 400 mM sodium formate and 100 mM sodium acetate buffer (pH 4.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→47.66 Å / Num. obs: 169234 / % possible obs: 99.2 % / Redundancy: 5.1 % / CC1/2: 0.985 / Rmerge(I) obs: 0.151 / Net I/σ(I): 7.6
Reflection shellResolution: 3→3.06 Å / Rmerge(I) obs: 0.693 / Num. unique obs: 4516 / CC1/2: 0.71

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PHENIX1.13_2998+SVNrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AFC

3afc


Resolution: 3→47.66 Å / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 30.8989 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2443 8626 5.26 %
Rwork0.2241 155292 -
obs0.2631 163918 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.46 Å2
Refinement stepCycle: LAST / Resolution: 3→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8515 0 28 0 8543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00238767
X-RAY DIFFRACTIONf_angle_d0.549111889
X-RAY DIFFRACTIONf_chiral_restr0.04431285
X-RAY DIFFRACTIONf_plane_restr0.00341539
X-RAY DIFFRACTIONf_dihedral_angle_d13.89275285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.050.3684290.37267912X-RAY DIFFRACTION93.7
3.05-3.110.42324330.36717831X-RAY DIFFRACTION93.62
3.11-3.170.36824140.35187954X-RAY DIFFRACTION93.97
3.17-3.230.32753320.33038046X-RAY DIFFRACTION94.9
3.23-3.30.38733760.32967969X-RAY DIFFRACTION94.3
3.3-3.380.38134240.3127887X-RAY DIFFRACTION93.54
3.38-3.460.32854530.30417732X-RAY DIFFRACTION92.78
3.46-3.560.31893660.29997942X-RAY DIFFRACTION93.68
3.56-3.660.30963900.30117829X-RAY DIFFRACTION93.01
3.66-3.780.29983820.29157809X-RAY DIFFRACTION92.62
3.78-3.910.28733710.28297750X-RAY DIFFRACTION92.31
3.91-4.070.30344660.26887669X-RAY DIFFRACTION90.41
4.07-4.260.30634150.26777623X-RAY DIFFRACTION90.37
4.26-4.480.28654550.24337559X-RAY DIFFRACTION89.88
4.48-4.760.234420.23117561X-RAY DIFFRACTION89.72
4.76-5.130.25744640.22377600X-RAY DIFFRACTION90.22
5.13-5.640.23493840.21827715X-RAY DIFFRACTION91.44
5.64-6.460.22924680.22097646X-RAY DIFFRACTION91.06
6.46-8.130.25744270.21837784X-RAY DIFFRACTION91.71
8.13-44.490.27994580.23917745X-RAY DIFFRACTION92.01

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