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- PDB-4of3: Crystal Structure of SYG-1 D1-D2, Glycosylated -

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Basic information

Entry
Database: PDB / ID: 4of3
TitleCrystal Structure of SYG-1 D1-D2, Glycosylated
ComponentsProtein SYG-1, isoform b
KeywordsCELL ADHESION / Immunoglobulin superfamily / Synaptogenesis / Protein binding / N-linked Glycosylation / Membrane / Extracellular / SIGNALING PROTEIN
Function / homology
Function and homology information


Nephrin family interactions / protein complex involved in cell adhesion / branching morphogenesis of a nerve / synaptic target recognition / collateral sprouting / actin filament bundle assembly / cell adhesion molecule binding / synapse assembly / synaptic membrane / synapse organization ...Nephrin family interactions / protein complex involved in cell adhesion / branching morphogenesis of a nerve / synaptic target recognition / collateral sprouting / actin filament bundle assembly / cell adhesion molecule binding / synapse assembly / synaptic membrane / synapse organization / cell-cell adhesion / cell-cell junction / cell-cell signaling / axon / synapse / protein-containing complex binding / plasma membrane
Similarity search - Function
CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Synaptogenesis protein syg-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOzkan, E. / Garcia, K.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: Extracellular Architecture of the SYG-1/SYG-2 Adhesion Complex Instructs Synaptogenesis.
Authors: Ozkan, E. / Chia, P.H. / Wang, R.R. / Goriatcheva, N. / Borek, D. / Otwinowski, Z. / Walz, T. / Shen, K. / Garcia, K.C.
History
DepositionJan 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_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.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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein SYG-1, isoform b
B: Protein SYG-1, isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6245
Polymers60,7512
Non-polymers1,8743
Water70339
1
A: Protein SYG-1, isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6623
Polymers30,3751
Non-polymers1,2872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein SYG-1, isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9622
Polymers30,3751
Non-polymers5871
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.648, 92.648, 129.014
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-905-

HOH

21A-911-

HOH

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Components

#1: Protein Protein SYG-1, isoform b


Mass: 30375.271 Da / Num. of mol.: 2 / Fragment: D1-D2, UNP residues 19-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: CELE_K02E10.8, K02E10.8, syg-1 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: B1Q236
#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: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1-2/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 200, 5% PEG 3,000, 0.1 M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2006
RadiationMonochromator: SINGLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 22777 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 66.91 Å2 / Rsym value: 0.057 / Net I/σ(I): 25.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4OF0

4of0


Resolution: 2.5→43.599 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 28.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 1164 5.13 %RANDOM
Rwork0.1963 ---
obs0.1992 22690 99.62 %-
all-22777 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→43.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3542 0 125 39 3706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073759
X-RAY DIFFRACTIONf_angle_d1.0765104
X-RAY DIFFRACTIONf_dihedral_angle_d12.6181414
X-RAY DIFFRACTIONf_chiral_restr0.044610
X-RAY DIFFRACTIONf_plane_restr0.006642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.61160.35711760.27552615X-RAY DIFFRACTION100
2.6116-2.74930.27861340.25692661X-RAY DIFFRACTION100
2.7493-2.92150.37311290.23992684X-RAY DIFFRACTION100
2.9215-3.14710.3061390.24372675X-RAY DIFFRACTION100
3.1471-3.46360.30821640.22732663X-RAY DIFFRACTION100
3.4636-3.96450.25491440.1962690X-RAY DIFFRACTION100
3.9645-4.99380.20261310.15122741X-RAY DIFFRACTION100
4.9938-43.60530.21871470.18942797X-RAY DIFFRACTION98
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)
11.46170.5314-0.10046.02160.15735.4638-0.2090.2696-0.025-0.35140.37420.1941-0.1301-0.4337-0.18380.36250.01530.07870.62520.09910.4767-43.741111.7559-43.9053
21.8898-0.43931.97863.209-0.28266.3037-0.2947-0.09510.56390.7798-0.3754-0.7794-0.75790.59670.49210.8182-0.1483-0.09470.5680.10490.7093-24.6599.976-8.8591
33.91060.25450.31534.239-0.95959.34640.1098-0.1728-0.08690.6774-0.4202-0.72090.04750.49190.30280.6319-0.1479-0.11680.42610.04890.612-23.13185.25-6.3469
44.6487-3.33042.41039.1145-4.85678.4938-0.3388-0.3365-0.20551.28270.3837-0.0672-0.73360.4982-0.06060.4919-0.0721-0.060.56810.09620.5733-20.046712.586-41.3401
53.0332-0.67932.52723.4069-0.83476.2233-0.1220.0721-0.1953-0.5859-0.08250.35660.2251-0.24850.21830.50420.0149-0.04630.3546-0.00870.5085-36.445312.979-78.2963
64.89670.7243-1.28816.68610.22715.98330.03760.062-0.39-0.5128-0.25560.18620.816-0.14020.18120.54660.0269-0.05310.35590.03330.4192-35.677811.1332-79.1961
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 119 )
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 175 )
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 268 )
4X-RAY DIFFRACTION4chain 'B' and (resid 21 through 119 )
5X-RAY DIFFRACTION5chain 'B' and (resid 120 through 186 )
6X-RAY DIFFRACTION6chain 'B' and (resid 187 through 267 )

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