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- PDB-4ofy: Crystal Structure of the Complex of SYG-1 D1-D2 and SYG-2 D1-D4 -

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Basic information

Entry
Database: PDB / ID: 4ofy
TitleCrystal Structure of the Complex of SYG-1 D1-D2 and SYG-2 D1-D4
Components
  • Protein SYG-1, isoform b
  • Protein SYG-2
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 / protein localization to synapse / actin filament bundle assembly / synapse assembly / cell adhesion molecule binding / synaptic membrane ...Nephrin family interactions / protein complex involved in cell adhesion / branching morphogenesis of a nerve / synaptic target recognition / collateral sprouting / protein localization to synapse / actin filament bundle assembly / synapse assembly / cell adhesion molecule binding / synaptic membrane / cell-cell adhesion / synapse organization / cell-cell junction / cell-cell signaling / axon / synapse / protein-containing complex binding / protein homodimerization activity / plasma membrane
Similarity search - Function
: / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain ...: / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / 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
ETHYL MERCURY ION / Synaptogenesis protein syg-1 / Synaptogenesis protein syg-2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 15, 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_conn_angle / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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_seq_id / _struct_conn.ptnr2_label_asym_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
Revision 2.2Nov 20, 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: Protein SYG-1, isoform b
B: Protein SYG-1, isoform b
C: Protein SYG-1, isoform b
D: Protein SYG-2
E: Protein SYG-2
F: Protein SYG-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,77231
Polymers227,9986
Non-polymers6,77525
Water00
1
A: Protein SYG-1, isoform b
D: Protein SYG-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,18410
Polymers75,9992
Non-polymers2,1848
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein SYG-1, isoform b
E: Protein SYG-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,18410
Polymers75,9992
Non-polymers2,1848
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein SYG-1, isoform b
F: Protein SYG-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,40511
Polymers75,9992
Non-polymers2,4069
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)286.786, 116.144, 98.032
Angle α, β, γ (deg.)90.00, 107.62, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein Protein SYG-1, isoform b


Mass: 29085.717 Da / Num. of mol.: 3 / Fragment: D1-D2, UNP residues 19-271
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: Protein Protein SYG-2


Mass: 46913.484 Da / Num. of mol.: 3 / Fragment: D1-D4, UNP residues 20-430 / Mutation: N391C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: C26G2.1, CELE_C26G2.1, syg-2 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q9U3P2
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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.: 16
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
#5: Chemical ChemComp-EMC / ETHYL MERCURY ION


Mass: 229.651 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5Hg
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: 3.41 Å3/Da / Density % sol: 63.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 16% PEG 3,350, 0.2 M Triammonium citrate, 0.1 M MES pH 6.4, 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: 1.0088 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 5, 2008
RadiationMonochromator: Single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0088 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 44725 / Num. obs: 44580 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 90.89 Å2 / Rsym value: 0.098 / Net I/σ(I): 13.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_1593)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entries 4OF3, 4OFP

4of3

4ofp


Resolution: 3.3→41.061 Å / SU ML: 0.5 / σ(F): 0 / Phase error: 39.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3059 2262 5.07 %Random
Rwork0.2594 ---
all0.2619 46764 --
obs0.2619 44580 95.33 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→41.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14415 0 401 0 14816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415175
X-RAY DIFFRACTIONf_angle_d0.90420703
X-RAY DIFFRACTIONf_dihedral_angle_d12.2795445
X-RAY DIFFRACTIONf_chiral_restr0.0372458
X-RAY DIFFRACTIONf_plane_restr0.0042676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.36010.41341070.37391971X-RAY DIFFRACTION71
3.3601-3.43830.42021010.34122296X-RAY DIFFRACTION83
3.4383-3.52420.37591130.32352423X-RAY DIFFRACTION87
3.5242-3.61940.38051320.31782578X-RAY DIFFRACTION93
3.6194-3.72590.34581390.32482641X-RAY DIFFRACTION97
3.7259-3.8460.39231500.30652710X-RAY DIFFRACTION98
3.846-3.98340.35711600.28222753X-RAY DIFFRACTION100
3.9834-4.14270.33821390.25332772X-RAY DIFFRACTION100
4.1427-4.33110.29371500.23542747X-RAY DIFFRACTION100
4.3311-4.55920.30551540.22712765X-RAY DIFFRACTION100
4.5592-4.84440.28551420.22182778X-RAY DIFFRACTION100
4.8444-5.21770.26911560.21082752X-RAY DIFFRACTION100
5.2177-5.74160.23951330.23712803X-RAY DIFFRACTION100
5.7416-6.56950.3051860.25892742X-RAY DIFFRACTION100
6.5695-8.26570.28441360.25182809X-RAY DIFFRACTION100
8.2657-41.06420.27071640.25462778X-RAY DIFFRACTION98

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