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- PDB-8edi: Structure of C. elegans UNC-5 IG 1+2 Domains bound to Heparin dp4 -

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Basic information

Entry
Database: PDB / ID: 8edi
TitleStructure of C. elegans UNC-5 IG 1+2 Domains bound to Heparin dp4
ComponentsNetrin receptor unc-5
KeywordsPROTEIN BINDING / Cell surface receptor / Axon Guidance / Signaling / Glycoprotein
Function / homology
Function and homology information


distal tip cell migration / Netrin-1 signaling / Netrin mediated repulsion signals / positive regulation of anterior/posterior axon guidance / regulation of dorsal/ventral axon guidance / gonad morphogenesis / nematode male tail tip morphogenesis / mesodermal cell migration / netrin receptor activity / dorsal/ventral axon guidance ...distal tip cell migration / Netrin-1 signaling / Netrin mediated repulsion signals / positive regulation of anterior/posterior axon guidance / regulation of dorsal/ventral axon guidance / gonad morphogenesis / nematode male tail tip morphogenesis / mesodermal cell migration / netrin receptor activity / dorsal/ventral axon guidance / chemorepulsion of axon / netrin-activated signaling pathway / positive regulation of locomotion / ventral cord development / establishment or maintenance of actin cytoskeleton polarity / commissural neuron axon guidance / motor neuron axon guidance / negative regulation of microtubule polymerization / axonal growth cone / positive regulation of axon extension / 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 / Immunoglobulin domain / Death 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Netrin receptor unc-5
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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: Sci Adv / Year: 2024
Title: Structural insights into the formation of repulsive netrin guidance complexes.
Authors: Priest, J.M. / Nichols, E.L. / Smock, R.G. / Hopkins, J.B. / Mendoza, J.L. / Meijers, R. / Shen, K. / 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
Revision 1.2Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 20, 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

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Assembly

Deposited unit
A: Netrin receptor unc-5
B: Netrin receptor unc-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6705
Polymers46,3742
Non-polymers2,2963
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint35 kcal/mol
Surface area22220 Å2
Unit cell
Length a, b, c (Å)69.460, 69.460, 424.990
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 2 and (name N or name...
d_2ens_1(chain "B" and (resid 2 through 159 or resid 161 through 903))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPILEA1 - 158
d_12ens_1ALAHISA160 - 200
d_13ens_1NAGNAGB
d_14ens_1NAGNAGC
d_15ens_1FUCFUCD
d_21ens_1ASPILEE1 - 158
d_22ens_1ALAHISE160 - 200
d_23ens_1NAGNAGF
d_24ens_1NAGNAGG
d_25ens_1FUCFUCC

NCS oper: (Code: givenMatrix: (-0.535665366599, -0.842344850865, 0.0593107683968), (-0.841123208806, 0.526039550849, -0.125674733142), (0.0746616543779, -0.117207265831, -0.990296972732)Vector: 4. ...NCS oper: (Code: given
Matrix: (-0.535665366599, -0.842344850865, 0.0593107683968), (-0.841123208806, 0.526039550849, -0.125674733142), (0.0746616543779, -0.117207265831, -0.990296972732)
Vector: 4.67759319331, 8.15166607083, 65.6829015097)

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Components

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


Mass: 23186.814 Da / Num. of mol.: 2
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.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)- ...4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1154.940 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O][a21eEA-1a_1-5_2*OSO/3=O/3=O]/1-2-1-3/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-4-deoxy-IdopA2SO3]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
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: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 4% (v/v) Pentaerythritol ethoxylate (3/4 EO/OH), 0.1 M sodium acetate pH 4.6, 16% (w/v) PEG 8000, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.11→49.1 Å / Num. obs: 21299 / % possible obs: 58 % / Redundancy: 18.4 % / Biso Wilson estimate: 53.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.014 / Rrim(I) all: 0.061 / Rsym value: 0.059 / Net I/σ(I): 27
Reflection shellResolution: 2.11→2.3 Å / Redundancy: 14.8 % / Rmerge(I) obs: 1.66 / Mean I/σ(I) obs: 2 / Num. unique obs: 1065 / CC1/2: 0.724 / Rpim(I) all: 0.43 / Rrim(I) all: 1.72 / Rsym value: 1.66 / % possible all: 24.6

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Processing

Software
NameVersionClassification
XDSdata reduction
STARANISOdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8EDC

8edc


Resolution: 2.11→49.1 Å / SU ML: 0.3186 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.3254
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2723 1065 5 %
Rwork0.2402 20234 -
obs0.2419 21299 58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.13 Å2
Refinement stepCycle: LAST / Resolution: 2.11→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3079 0 146 18 3243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00983359
X-RAY DIFFRACTIONf_angle_d1.17814587
X-RAY DIFFRACTIONf_chiral_restr0.0987569
X-RAY DIFFRACTIONf_plane_restr0.0076570
X-RAY DIFFRACTIONf_dihedral_angle_d13.03631317
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.957894604009 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.20.5373190.3742367X-RAY DIFFRACTION8.73
2.2-2.320.4148410.3996765X-RAY DIFFRACTION17.95
2.32-2.460.4423580.35521097X-RAY DIFFRACTION25.94
2.46-2.650.4354840.39171604X-RAY DIFFRACTION37.53
2.65-2.920.33551500.3392867X-RAY DIFFRACTION66.38
2.92-3.340.35972290.3274347X-RAY DIFFRACTION99.59
3.34-4.210.2882330.22884414X-RAY DIFFRACTION99.94
4.21-49.10.20812510.18824773X-RAY DIFFRACTION99.8
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)
16.40127831556-0.883226587357-0.4025280912016.626452712542.987482981276.400870094290.123799061704-1.018963732310.4497879529590.626562189087-0.424716055981.2323482783-0.0620738552887-0.8790118048190.2358270027670.44732007597-0.212702519972-0.01672331061170.865214231459-0.1016296585010.773897855827-3.1895601506-21.508789094147.7083683105
24.043043116210.543262132691-0.804261198531.42398917921-1.416953282125.38334782283-0.1810813730680.6839658445780.226652883877-0.1447565307340.0870906479042-0.135210536268-0.1919922877350.03962619614550.06308802109920.511827712002-0.259295331896-0.1603915099540.5212318402720.08378830328250.41400196914212.9416570734-21.48841488678.67095415824
35.1105736158-1.155522782091.440817270089.13141366039-6.305294311147.15493801591-0.5965394843780.1111470580690.945954634003-0.1119866030030.4452260492910.215163003265-0.900487156633-0.846091538424-0.008723924288780.724854239283-0.0706027827309-0.2764999274680.4123043215060.01579044272010.60430217901623.7416588719-5.6503627201724.7039551635
45.62088469506-2.5517734889-0.1486566635048.29999963654-1.119818326625.90363402883-0.3823200073990.6723900851011.038134860130.137497006778-0.236341138676-0.971428563849-0.4628455409370.7333674583420.5065901074170.609096494021-0.20286973447-0.2800213148480.4605065332730.08842190602720.67541009260629.4105466558-7.1946006997419.225347111
51.703171920450.275262279738-0.7006478340423.165764238160.1423492588475.373800121360.15241805839-0.5602441351520.1541352594610.794521941192-0.466792142290.7002377940680.240250565833-0.4014082458910.3256415015470.688447752459-0.2032984494220.03999517211640.578950413108-0.1726398338510.49222017705816.1766845953-15.957004574360.9515095003
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 2 through 103 )BE2 - 1031 - 102
22chain 'B' and (resid 104 through 201 )BE104 - 201103 - 200
33chain 'A' and (resid 2 through 28 )AA2 - 281 - 27
44chain 'A' and (resid 29 through 103 )AA29 - 10328 - 102
55chain 'A' and (resid 104 through 201 )AA104 - 201103 - 200

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