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- PDB-7y4q: Semaphorin 6D in complex with Plexin A1 -

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Basic information

Entry
Database: PDB / ID: 7y4q
TitleSemaphorin 6D in complex with Plexin A1
Components
  • Plexin-A1
  • Semaphorin 6D
KeywordsSIGNALING PROTEIN / signaling complex
Function / homology
Function and homology information


Other semaphorin interactions / olfactory nerve formation / dichotomous subdivision of terminal units involved in salivary gland branching / semaphorin receptor binding / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / Other semaphorin interactions / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of smooth muscle cell migration / negative regulation of axon extension involved in axon guidance / ventricular system development ...Other semaphorin interactions / olfactory nerve formation / dichotomous subdivision of terminal units involved in salivary gland branching / semaphorin receptor binding / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / Other semaphorin interactions / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of smooth muscle cell migration / negative regulation of axon extension involved in axon guidance / ventricular system development / semaphorin receptor complex / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / chemorepellent activity / semaphorin receptor activity / CRMPs in Sema3A signaling / negative regulation of cell adhesion / RHOD GTPase cycle / regulation of smooth muscle cell migration / RND1 GTPase cycle / neural crest cell migration / smooth muscle cell migration / neuron projection extension / negative chemotaxis / positive regulation of axonogenesis / regulation of GTPase activity / positive regulation of smooth muscle cell migration / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / regulation of cell migration / axon guidance / regulation of cell shape / positive regulation of cell migration / Golgi apparatus / extracellular space / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Plexin-A1, Sema domain / Semaphorin / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain ...Plexin-A1, Sema domain / Semaphorin / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / Rho GTPase activation protein / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Semaphorin 6D / Plexin-A1
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.7 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 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Plexin-A1
A: Plexin-A1
D: Semaphorin 6D
C: Semaphorin 6D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,21013
Polymers279,2034
Non-polymers3,0079
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11060 Å2
ΔGint25 kcal/mol
Surface area103480 Å2
Unit cell
Length a, b, c (Å)173.139, 198.508, 180.495
Angle α, β, γ (deg.)90.000, 117.827, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Plexin-A1 / Semaphorin receptor NOV


Mass: 77079.102 Da / Num. of mol.: 2 / Fragment: ectodomain fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNA1, NOV, PLXN1 / Cell line (production host): HEK293S GnT1- / Production host: Homo sapiens (human) / References: UniProt: Q9UIW2
#2: 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
#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.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: 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.: 4 / 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

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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: 9.82 Å3/Da / Density % sol: 87.48 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 150 mM NaCl and 10 mM Tris-Cl (pH 7.4)

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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: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 4.7→49.43 Å / Num. obs: 110174 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 155.92 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 6.1
Reflection shellResolution: 4.7→4.84 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.938 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4580 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998+SVNrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D07, 7CYT

7d07
PDB Unreleased entry

7cyt
PDB Unreleased entry


Resolution: 4.7→49.43 Å / SU ML: 0.6709 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 27.178 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.258 5052 4.81 %
Rwork0.2408 100070 -
obs0.2416 105122 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 200.63 Å2
Refinement stepCycle: LAST / Resolution: 4.7→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18879 0 196 0 19075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00619581
X-RAY DIFFRACTIONf_angle_d1.311926604
X-RAY DIFFRACTIONf_chiral_restr0.06782926
X-RAY DIFFRACTIONf_plane_restr0.00643454
X-RAY DIFFRACTIONf_dihedral_angle_d14.281511820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.7-4.750.3882030.35723323X-RAY DIFFRACTION96.21
4.75-4.810.33231630.34383419X-RAY DIFFRACTION95.78
4.81-4.870.4111840.33593265X-RAY DIFFRACTION95.04
4.87-4.930.29491900.32963272X-RAY DIFFRACTION94.69
4.93-4.990.29571990.32943304X-RAY DIFFRACTION94.17
4.99-5.060.30031370.31483362X-RAY DIFFRACTION94.47
5.06-5.130.34021760.32683312X-RAY DIFFRACTION95.56
5.13-5.210.32281740.32613408X-RAY DIFFRACTION96.68
5.21-5.290.32221970.3223370X-RAY DIFFRACTION96.61
5.29-5.380.34071670.31763406X-RAY DIFFRACTION95.84
5.38-5.470.34352180.3083295X-RAY DIFFRACTION96.01
5.47-5.570.32271670.30383373X-RAY DIFFRACTION97.01
5.57-5.680.31842010.31613381X-RAY DIFFRACTION97.28
5.68-5.790.32081600.29663414X-RAY DIFFRACTION97.04
5.79-5.920.32351930.30263376X-RAY DIFFRACTION97.12
5.92-6.060.30061790.28843417X-RAY DIFFRACTION97.27
6.06-6.210.29621520.27093440X-RAY DIFFRACTION97
6.21-6.380.25731440.25293426X-RAY DIFFRACTION96.77
6.38-6.560.20411070.24093475X-RAY DIFFRACTION97.26
6.56-6.770.26921750.23213392X-RAY DIFFRACTION96.56
6.77-7.020.24841710.22083367X-RAY DIFFRACTION96.51
7.02-7.30.18731560.20633329X-RAY DIFFRACTION93.68
7.3-7.630.23451500.1953299X-RAY DIFFRACTION94.52
7.63-8.030.22021560.18853379X-RAY DIFFRACTION96.32
8.03-8.530.20082180.18263317X-RAY DIFFRACTION95.49
8.53-9.180.19291600.17643329X-RAY DIFFRACTION94.53
9.18-10.10.17211860.15973207X-RAY DIFFRACTION91.26
10.1-11.550.16031190.14333152X-RAY DIFFRACTION89.27
11.55-14.480.1816880.17523153X-RAY DIFFRACTION87.81
14.48-49.430.27381620.25823108X-RAY DIFFRACTION88.88

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