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- PDB-8edc: Structure of C. elegans UNC-5 IG 1+2 Domains -

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Basic information

Entry
Database: PDB / ID: 8edc
TitleStructure of C. elegans UNC-5 IG 1+2 Domains
ComponentsNetrin receptor unc-5
KeywordsPROTEIN BINDING / Cell surface receptor / Axon Guidance / Netrin Receptor / Signaling / Glycoprotein
Function / homology
Function and homology information


distal tip cell migration / Netrin-1 signaling / 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 / netrin receptor activity / dorsal/ventral axon guidance ...distal tip cell migration / Netrin-1 signaling / 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 / netrin receptor activity / dorsal/ventral axon guidance / chemorepulsion of axon / netrin-activated signaling pathway / establishment or maintenance of actin cytoskeleton polarity / ventral cord development / commissural neuron axon guidance / motor neuron axon guidance / negative regulation of microtubule polymerization / positive regulation of axon extension / axonal growth cone / protein tyrosine kinase binding / membrane raft / plasma membrane
Similarity search - Function
UPA domain / Netrin receptor UNC5 / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Thrombospondin type 1 domain / Death domain profile. / Thrombospondin type-1 (TSP1) repeat superfamily ...UPA domain / Netrin receptor UNC5 / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Thrombospondin type 1 domain / Death domain profile. / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Immunoglobulin domain / Death-like domain superfamily / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Netrin receptor unc-5
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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-5 IG 1+2 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 1.1Oct 25, 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

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Assembly

Deposited unit
A: Netrin receptor unc-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9494
Polymers23,1871
Non-polymers7633
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.282, 130.216, 97.549
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z

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Components

#1: Protein Netrin receptor unc-5 / Uncoordinated protein 5


Mass: 23186.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: unc-5, B0273.4 / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q26261
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

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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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.25 M (NH4)2SO4, 0.1 M Tris pH 8.5, 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 6114 / % possible obs: 98.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 72.71 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.114 / Rsym value: 0.104 / Net I/σ(I): 14.6
Reflection shellResolution: 2.89→3.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 894 / CC1/2: 0.722 / Rrim(I) all: 0.948 / Rsym value: 0.855 / % possible all: 92.8

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.20_4444refinement
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V2A

4v2a


Resolution: 2.89→48.77 Å / SU ML: 0.5812 / Cross valid method: FREE R-VALUE / Phase error: 31.6789
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2851 613 10.03 %
Rwork0.2459 5496 -
obs0.2498 6109 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.01 Å2
Refinement stepCycle: LAST / Resolution: 2.89→48.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1511 0 48 0 1559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00181581
X-RAY DIFFRACTIONf_angle_d0.41822150
X-RAY DIFFRACTIONf_chiral_restr0.0405259
X-RAY DIFFRACTIONf_plane_restr0.0027273
X-RAY DIFFRACTIONf_dihedral_angle_d11.9381583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-3.180.42571460.37841292X-RAY DIFFRACTION95.29
3.19-3.650.33861520.28461366X-RAY DIFFRACTION100
3.65-4.590.26061540.22291384X-RAY DIFFRACTION99.94
4.59-48.770.25031610.21881454X-RAY DIFFRACTION99.14
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)
16.16628626149-2.375115645041.521584699685.45372487321-0.8228513505367.57741366062-0.2040514996360.283461526145-0.0526731245544-0.093805481104-0.1265021833630.084856433045-0.2912652326940.1200458780920.4054055293020.427939861655-0.05693070299190.007024749977020.5087898290060.01383359368920.40292368297-20.700374018348.993518293210.8134973094
25.49540942372-2.24364093658-0.04170807449366.55038684834-3.011675655419.489768763730.0161566470148-0.4579891756820.3316051892540.4259508528410.00864215730687-0.117447102806-0.9886244994970.8176574886860.1938907304230.612226013162-0.109948125432-0.04792482760740.452448751088-0.1581521166410.511789111031-16.860109460552.136373268319.1909841651
36.32596675222-2.985251565813.626092805818.63608985768-5.679434624198.11217155162-0.313119378982-0.639671079242-0.1628743145930.0920183066047-0.0658731009744-0.5823528674410.3378254908220.4565198038340.3378864349550.3863927347820.05755715049210.05773178789590.697505130573-0.02988183850170.507262849895.0019934163121.007834449336.4761988945
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 2 through 68 )2 - 681 - 67
22chain 'A' and (resid 69 through 106 )69 - 10668 - 103
33chain 'A' and (resid 107 through 201 )107 - 201104 - 198

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