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- PDB-6ns1: Crystal structure of DIP-gamma IG1+IG2 -

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Basic information

Entry
Database: PDB / ID: 6ns1
TitleCrystal structure of DIP-gamma IG1+IG2
ComponentsDpr-interacting protein gamma
KeywordsCELL ADHESION / Immunoglobulin superfamily / Glycoprotein / Neuronal / Cell surface receptor
Function / homology
Function and homology information


regulation of neuromuscular junction development / Degradation of the extracellular matrix / Non-integrin membrane-ECM interactions / ECM proteoglycans / HS-GAG biosynthesis / HS-GAG degradation / Integrin cell surface interactions / neuron projection membrane / Glycosaminoglycan-protein linkage region biosynthesis / photoreceptor cell axon guidance ...regulation of neuromuscular junction development / Degradation of the extracellular matrix / Non-integrin membrane-ECM interactions / ECM proteoglycans / HS-GAG biosynthesis / HS-GAG degradation / Integrin cell surface interactions / neuron projection membrane / Glycosaminoglycan-protein linkage region biosynthesis / photoreceptor cell axon guidance / establishment of synaptic specificity at neuromuscular junction / synapse organization / neuron projection / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / 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 domain / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Dpr-interacting protein gamma
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsCheng, S. / Park, Y.J. / 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)R01 NS097161 United States
CitationJournal: Elife / Year: 2019
Title: Molecular basis of synaptic specificity by immunoglobulin superfamily receptors in Drosophila.
Authors: Cheng, S. / Ashley, J. / Kurleto, J.D. / Lobb-Rabe, M. / Park, Y.J. / Carrillo, R.A. / Ozkan, E.
History
DepositionJan 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 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 / 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 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
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
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dpr-interacting protein gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5772
Polymers24,0071
Non-polymers5711
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.330, 43.440, 86.140
Angle α, β, γ (deg.)90.00, 90.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dpr-interacting protein gamma / GH08175p


Mass: 24006.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: DIP-gamma, 14521, anon-WO0140519.196, CT34248, Dmel\CG14521, CG14521, Dmel_CG14521
Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9VAR6
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.15 M ammonium sulfate, 0.1 M MES, pH 5.5, 25% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 24, 2015
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 18742 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.32 % / Biso Wilson estimate: 26.72 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.146 / Rrim(I) all: 0.158 / Net I/σ(I): 8.81
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3.79 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1366 / CC1/2: 0.828 / Rrim(I) all: 0.833 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIXdev_2932refinement
XDSOct 15, 2015data reduction
XDSOct 15, 2015data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EO9

5eo9


Resolution: 1.85→43.069 Å / SU ML: 0.21 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / Phase error: 26.8
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 933 4.99 %Random selection
Rwork0.2045 ---
obs0.2059 18695 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→43.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1605 0 38 179 1822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081696
X-RAY DIFFRACTIONf_angle_d0.9562305
X-RAY DIFFRACTIONf_dihedral_angle_d10.8261064
X-RAY DIFFRACTIONf_chiral_restr0.056267
X-RAY DIFFRACTIONf_plane_restr0.006297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.94760.30551320.25712518X-RAY DIFFRACTION99
1.9476-2.06960.33821280.24682504X-RAY DIFFRACTION100
2.0696-2.22940.24181350.22312525X-RAY DIFFRACTION100
2.2294-2.45370.24471370.2152533X-RAY DIFFRACTION100
2.4537-2.80870.22541320.21652518X-RAY DIFFRACTION100
2.8087-3.53840.23961310.20062548X-RAY DIFFRACTION100
3.5384-43.08030.20661380.18292616X-RAY DIFFRACTION100

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