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- PDB-6on6: Crystal Structure of the RIG-5 IG1 homodimer -

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Basic information

Entry
Database: PDB / ID: 6on6
TitleCrystal Structure of the RIG-5 IG1 homodimer
ComponentsNeuRonal IgCAM-5
KeywordsCELL ADHESION / Cell surface receptor / Immunoglobulin superfamily / Nervous system / Homodimer
Function / homology
Function and homology information


Degradation of the extracellular matrix / Glycosaminoglycan-protein linkage region biosynthesis / HS-GAG biosynthesis / HS-GAG degradation / Integrin cell surface interactions / Laminin interactions / Non-integrin membrane-ECM interactions / Formation of the dystrophin-glycoprotein complex (DGC) / ECM proteoglycans / neuron projection
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...: / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / 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
Ig-like domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.423 Å
AuthorsCheng, S. / Kurleto, J.D. / Ozkan, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS097161 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Family of neural wiring receptors in bilaterians defined by phylogenetic, biochemical, and structural evidence.
Authors: Cheng, S. / Park, Y. / Kurleto, J.D. / Jeon, M. / Zinn, K. / Thornton, J.W. / Ozkan, E.
History
DepositionApr 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NeuRonal IgCAM-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5563
Polymers13,2431
Non-polymers3132
Water1,74797
1
A: NeuRonal IgCAM-5
hetero molecules

A: NeuRonal IgCAM-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1126
Polymers26,4862
Non-polymers6274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area2560 Å2
ΔGint-8 kcal/mol
Surface area10920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.610, 46.610, 196.849
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-201-

GOL

21A-353-

HOH

31A-379-

HOH

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Components

#1: Protein NeuRonal IgCAM-5


Mass: 13242.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: rig-5, C36F7.4, CELE_C36F7.4 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five cells / References: UniProt: C6KRM7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: 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: isolated from a genetically manipulated source
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 1 M Sodium citrate

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2018
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. obs: 24835 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 17.7 % / Biso Wilson estimate: 29.76 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.027 / Rrim(I) all: 0.028 / Net I/σ(I): 55.51
Reflection shellResolution: 1.42→1.51 Å / Redundancy: 15.2 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 9.46 / Num. unique obs: 3827 / CC1/2: 0.996 / Rrim(I) all: 0.209 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.15rc3_3435refinement
XDS20180409data reduction
PHASER2.8.2phasing
Cootmodel building
XDS20180409data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NRX

6nrx


Resolution: 1.423→40.365 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.84
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 1240 5 %Random selection
Rwork0.197 ---
obs0.1985 24788 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.423→40.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms841 0 20 97 958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013876
X-RAY DIFFRACTIONf_angle_d1.3021189
X-RAY DIFFRACTIONf_dihedral_angle_d16.546332
X-RAY DIFFRACTIONf_chiral_restr0.103140
X-RAY DIFFRACTIONf_plane_restr0.009155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4233-1.48030.24181280.17632441X-RAY DIFFRACTION96
1.4803-1.54760.25381350.16942568X-RAY DIFFRACTION100
1.5476-1.62920.23461340.17382536X-RAY DIFFRACTION100
1.6292-1.73130.25691350.16742585X-RAY DIFFRACTION100
1.7313-1.8650.21681370.16512590X-RAY DIFFRACTION100
1.865-2.05260.25451380.16812599X-RAY DIFFRACTION100
2.0526-2.34960.23461390.1852637X-RAY DIFFRACTION100
2.3496-2.96020.2421400.22242686X-RAY DIFFRACTION100
2.9602-40.38170.20881540.20512906X-RAY DIFFRACTION100

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