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- PDB-6on9: Crystal Structure of the ZIG-8-RIG-5 IG1-IG1 heterodimer, tetrago... -

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Basic information

Entry
Database: PDB / ID: 6on9
TitleCrystal Structure of the ZIG-8-RIG-5 IG1-IG1 heterodimer, tetragonal form
Components
  • NeuRonal IgCAM-5
  • Zwei Ig domain protein zig-8
KeywordsCELL ADHESION / Cell surface receptor / Immunoglobulin superfamily / Nervous system / heterodimer
Function / homology
Function and homology information


Signaling by ROBO receptors / : / : / SLIT2:ROBO1 increases RHOA activity / neuron projection membrane / side of membrane / synapse organization / neuron projection / extracellular region / plasma membrane
Similarity search - Function
Zwei Ig domain protein zig-8 / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...Zwei Ig domain protein zig-8 / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like domain-containing protein / Zwei Ig domain protein zig-8
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.995 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 / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zwei Ig domain protein zig-8
B: NeuRonal IgCAM-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0275
Polymers27,5412
Non-polymers4863
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-3 kcal/mol
Surface area11630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.078, 80.078, 166.622
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-903-

SO4

21B-1089-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Zwei Ig domain protein zig-8 / 2 Ig domain protein zig-8


Mass: 14297.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: zig-8, Y39E4B.8 / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G5ED00
#2: 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 / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C6KRM7

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Sugars , 1 types, 1 molecules

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


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 182 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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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: 5.25 Å3/Da / Density % sol: 76.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M disodium hydrogen phosphate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 27, 2019
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.995→100 Å / Num. obs: 37606 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Biso Wilson estimate: 50 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.178 / Rrim(I) all: 0.185 / Net I/σ(I): 7.94
Reflection shellResolution: 2→2.12 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.693 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 5835 / CC1/2: 0.672 / Rrim(I) all: 1.764 / % possible all: 97.6

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Processing

Software
NameVersionClassification
XDS20180808data reduction
PHENIX(1.15rc3_3435: ???)refinement
PHASER2.8.3phasing
XDS20180808data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ON6

6on6


Resolution: 1.995→72.175 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.65
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 1961 5.23 %Random selection
Rwork0.1742 ---
obs0.1759 37511 99.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.995→72.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 30 180 1977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181837
X-RAY DIFFRACTIONf_angle_d1.3672505
X-RAY DIFFRACTIONf_dihedral_angle_d12.0971133
X-RAY DIFFRACTIONf_chiral_restr0.091290
X-RAY DIFFRACTIONf_plane_restr0.009327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9954-2.04530.30811290.28652339X-RAY DIFFRACTION94
2.0453-2.10060.26961230.25952541X-RAY DIFFRACTION100
2.1006-2.16240.25341450.22492495X-RAY DIFFRACTION100
2.1624-2.23220.24471290.20612495X-RAY DIFFRACTION100
2.2322-2.3120.25111280.21532529X-RAY DIFFRACTION100
2.312-2.40460.22721190.18052522X-RAY DIFFRACTION100
2.4046-2.5140.20151590.16822508X-RAY DIFFRACTION100
2.514-2.64650.1991430.17532527X-RAY DIFFRACTION100
2.6465-2.81240.22541440.18442529X-RAY DIFFRACTION100
2.8124-3.02950.23041520.18162539X-RAY DIFFRACTION100
3.0295-3.33440.21671600.17082553X-RAY DIFFRACTION100
3.3344-3.81690.20151440.16142562X-RAY DIFFRACTION100
3.8169-4.80870.14981290.14252641X-RAY DIFFRACTION100
4.8087-72.22260.21651570.17982770X-RAY DIFFRACTION99
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)
14.83730.4908-1.46815.73460.25723.6902-0.0321-0.3980.32450.2928-0.1713-0.0279-0.08860.3660.1960.2942-0.0099-0.06180.729-0.08540.44798.565320.353-20.8587
25.38551.17950.41852.61810.13814.93310.068-0.2083-0.6819-0.00280.027-0.20230.54110.6585-0.08640.30470.102-0.02620.4463-0.01740.46187.227810.9467-30.0338
33.6934-0.0930.21560.08990.40994.8179-0.0091-0.179-0.2152-0.1226-0.1107-0.03480.19640.18620.10640.32090.0612-0.01540.4041-0.01140.4006-4.523310.9296-33.9423
47.5606-2.98512.97697.543-2.21936.94670.02360.1986-0.90930.35990.2144-0.4720.89670.8341-0.25380.45530.1441-0.07960.5428-0.06580.56287.08375.8149-32.0517
53.22611.14450.49284.142-0.04253.1206-0.11750.1058-0.0234-0.21060.12240.1782-0.02180.22330.03810.24990.0499-0.00570.4577-0.03540.37264.287316.7672-30.1076
64.1289-3.5471-3.05963.96243.68153.4666-0.04920.1364-0.2744-0.4467-0.55690.7565-0.7028-2.21940.54220.31310.0601-0.01320.4738-0.07810.389-23.776214.7491-35.8772
70.8012-0.919-0.88071.13660.8862.9294-0.0228-0.3693-0.05920.05810.0210.0888-0.0129-0.1970.01690.2887-0.0087-0.00470.4911-0.03570.4194-18.536613.7018-21.397
83.5318-0.62-2.52642.2907-2.80176.6124-0.0349-1.1079-0.53170.264-0.0815-0.34920.72230.77310.06280.32610.0344-0.0050.55420.07470.4109-9.26445.4083-18.9751
97.7239-0.50464.13625.00340.11312.2669-0.0244-0.9068-0.7810.05920.0850.42130.908-1.1246-0.03610.4018-0.09270.02160.46760.06670.4378-21.97565.2565-23.0152
101.5313-0.0485-1.16711.5196-0.92855.3982-0.0325-0.44760.06530.18860.0386-0.0824-0.23450.170.00020.2339-0.0035-0.03490.4874-0.04660.3408-13.439415.5487-19.6822
112.3726-0.08880.49723.35492.32131.9407-0.2343-0.76370.19830.2584-0.0286-0.0372-1.0885-0.01580.21380.31580.0138-0.03180.6011-0.08670.4545-17.736620.1176-13.9811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 71 )
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 90 )
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 105 )
5X-RAY DIFFRACTION5chain 'A' and (resid 106 through 137 )
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 27 )
7X-RAY DIFFRACTION7chain 'B' and (resid 28 through 65 )
8X-RAY DIFFRACTION8chain 'B' and (resid 66 through 80 )
9X-RAY DIFFRACTION9chain 'B' and (resid 81 through 98 )
10X-RAY DIFFRACTION10chain 'B' and (resid 99 through 118 )
11X-RAY DIFFRACTION11chain 'B' and (resid 119 through 130 )

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