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- PDB-8edk: Structure of C. elegans UNC-6 LamN and EGF domains -

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Basic information

Entry
Database: PDB / ID: 8edk
TitleStructure of C. elegans UNC-6 LamN and EGF domains
ComponentsNetrin unc-6
KeywordsSIGNALING PROTEIN / Secreted Protein / Axon Guidance Cue / Glycoprotein
Function / homology
Function and homology information


regulation of sensory neuron axon guidance / regulation of motor neuron axon guidance / interneuron axon guidance / positive regulation of anterior/posterior axon guidance / regulation of dorsal/ventral axon guidance / mesodermal cell migration / gonad morphogenesis / positive regulation of locomotion / nematode male tail tip morphogenesis / dorsal/ventral axon guidance ...regulation of sensory neuron axon guidance / regulation of motor neuron axon guidance / interneuron axon guidance / positive regulation of anterior/posterior axon guidance / regulation of dorsal/ventral axon guidance / mesodermal cell migration / gonad morphogenesis / positive regulation of locomotion / nematode male tail tip morphogenesis / dorsal/ventral axon guidance / netrin-activated signaling pathway / establishment or maintenance of actin cytoskeleton polarity / ventral cord development / sensory neuron axon guidance / tissue development / motor neuron axon guidance / positive regulation of synapse assembly / dendrite morphogenesis / negative regulation of microtubule polymerization / dendrite development / basement membrane / regulation of cell migration / animal organ morphogenesis / axon guidance / neuron projection development / axon / signaling receptor binding / extracellular region / cytoplasm
Similarity search - Function
Laminin, N-terminal / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Netrin C-terminal Domain ...Laminin, N-terminal / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / EGF-like domain signature 1. / EGF-like domain
Similarity search - Domain/homology
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPriest, J.M. / Ozkan, E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS097161 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM138826 United States
CitationJournal: To Be Published
Title: Structure of C. elegans UNC-6/Netrin LamN and 3 EGF Domains
Authors: Priest, J.M. / Ozkan, E.
History
DepositionSep 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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
A: Netrin unc-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2636
Polymers49,7691
Non-polymers1,4945
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.243, 70.243, 287.353
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Netrin unc-6 / Uncoordinated protein 6


Mass: 49769.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: unc-6, unc-106, F41C6.1 / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P34710

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Sugars , 2 types, 2 molecules

#2: 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)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1040.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-2/a3-b1_a4-c1_a6-f1_c4-d1_d6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 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.: 1 / Source method: obtained synthetically / 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 , 3 types, 34 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.56 Å3/Da / Density % sol: 65.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris, pH 8.0, 10% (w/v) Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→200 Å / Num. obs: 25806 / % possible obs: 98.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 76.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.09 / Rsym value: 0.087 / Net I/σ(I): 19.43
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 13.7 % / Rmerge(I) obs: 2.164 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 4008 / CC1/2: 0.7 / Rrim(I) all: 2.245 / Rsym value: 2.164 / % possible all: 98.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2 model for UNC-6

Resolution: 2.5→68.23 Å / SU ML: 0.4799 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.1919
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2588 1297 5.04 %
Rwork0.22 24451 -
obs0.222 25748 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.71 Å2
Refinement stepCycle: LAST / Resolution: 2.5→68.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 95 31 3304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793358
X-RAY DIFFRACTIONf_angle_d0.89864542
X-RAY DIFFRACTIONf_chiral_restr0.0497501
X-RAY DIFFRACTIONf_plane_restr0.0086591
X-RAY DIFFRACTIONf_dihedral_angle_d13.06281260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.55151380.46452632X-RAY DIFFRACTION98.16
2.6-2.720.36161320.3322628X-RAY DIFFRACTION98.68
2.72-2.860.31271520.27572631X-RAY DIFFRACTION98.93
2.86-3.040.31841220.28622707X-RAY DIFFRACTION98.88
3.04-3.280.37351530.28182645X-RAY DIFFRACTION98.31
3.28-3.610.27281230.22842718X-RAY DIFFRACTION99.2
3.61-4.130.25511620.21492751X-RAY DIFFRACTION99.52
4.13-5.20.20251480.16692756X-RAY DIFFRACTION99.32
5.2-68.230.23511670.20322983X-RAY DIFFRACTION99.65
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7709895045-0.109761838911.279991641722.647960082130.9352898660467.41768086747-0.268254590090.4488989325470.355352112073-0.0268079029056-0.195965441334-0.0893732365077-0.8135194394980.3224755004660.5435565560590.5273197222370.05984893693610.07833711027070.4372330738040.1437657141420.61343709455821.503931641631.859205834210.7128752787
22.10072327384-0.155220744818-0.5105080927571.971737620930.6564223573554.29395969305-0.0842590500480.140018448889-0.0663564798780.0982567144514-0.1736702909250.293952723671-0.125759204541-0.6445351603780.2761778375250.444286107668-0.05105058138530.03959450522150.456510609054-0.01378426422320.56951346873210.034202678630.750425676514.1032237825
32.42936922983-1.155784493231.204173552473.27992775143-4.335488411057.155117933530.0978572788067-0.1901917690730.04446602498680.190142582702-0.437742106448-0.451277413037-0.1267815438120.6679124018010.3164456352420.587598390855-0.104876970659-0.1001888796360.7681110902770.1240180900450.65385350739139.583289587616.779672526244.82902437
45.19361525651-3.563704119423.964466789526.82594496209-5.868741852585.335088529730.00913723106212-0.771369591731-0.08600853501860.01976378374470.9537301990440.76975204497-0.0946074802472-1.65271866173-1.095789132870.6601849819080.0328114641337-0.08027474839211.08929690820.2099731578270.88913467165256.3845481837-7.7841081691576.0933097423
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 33 through 92 )33 - 921 - 53
22chain 'A' and (resid 93 through 299 )93 - 29954 - 246
33chain 'A' and (resid 300 through 406 )300 - 406247 - 353
44chain 'A' and (resid 407 through 465 )407 - 465354 - 412

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