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- PDB-6efy: Crystal Structure of DIP-Alpha Ig1-3 -

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Basic information

Entry
Database: PDB / ID: 6efy
TitleCrystal Structure of DIP-Alpha Ig1-3
ComponentsDpr-interacting protein alpha, isoform A
KeywordsCELL ADHESION / Immunoglobulin Super-Family / Synaptic specification / nervous system development / cell-surface protein
Function / homology
Function and homology information


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 / synapse organization / neuron projection / plasma membrane
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
Dpr-interacting protein alpha, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsCosmanescu, F. / Shapiro, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Neuron / Year: 2018
Title: Neuron-Subtype-Specific Expression, Interaction Affinities, and Specificity Determinants of DIP/Dpr Cell Recognition Proteins.
Authors: Cosmanescu, F. / Katsamba, P.S. / Sergeeva, A.P. / Ahlsen, G. / Patel, S.D. / Brewer, J.J. / Tan, L. / Xu, S. / Xiao, Q. / Nagarkar-Jaiswal, S. / Nern, A. / Bellen, H.J. / Zipursky, S.L. / ...Authors: Cosmanescu, F. / Katsamba, P.S. / Sergeeva, A.P. / Ahlsen, G. / Patel, S.D. / Brewer, J.J. / Tan, L. / Xu, S. / Xiao, Q. / Nagarkar-Jaiswal, S. / Nern, A. / Bellen, H.J. / Zipursky, S.L. / Honig, B. / Shapiro, L.
History
DepositionAug 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: 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 2.2Nov 20, 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 alpha, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1663
Polymers34,5031
Non-polymers6632
Water905
1
A: Dpr-interacting protein alpha, isoform A
hetero molecules

A: Dpr-interacting protein alpha, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3316
Polymers69,0062
Non-polymers1,3254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area3540 Å2
ΔGint7 kcal/mol
Surface area32020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.578, 104.578, 102.195
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z

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Components

#1: Protein Dpr-interacting protein alpha, isoform A / DDIP-Alpha / pr-interacting protein alpha / isoform C / RE16159p


Mass: 34503.098 Da / Num. of mol.: 1 / Fragment: UNP residues 40-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: DIP-alpha, 32791, CG13019, CG13020, Dmel\CG32791, CG32791, Dmel_CG32791
Production host: Homo sapiens (human) / References: UniProt: Q9W4R3
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 5 / 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: 4.77 Å3/Da / Density % sol: 74.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 2% PEG3350, 17% Tacsimate, pH 7.0, 0.1 M HEPES, pH 7.0, cryoprotectant: 30% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2016
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→67.78 Å / Num. obs: 14611 / % possible obs: 99.7 % / Redundancy: 4.6 % / Biso Wilson estimate: 79.9577746632 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.3
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.784 / Num. unique obs: 2349 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EO9

5eo9


Resolution: 2.9→19.938 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.57
RfactorNum. reflection% reflection
Rfree0.2437 725 4.99 %
Rwork0.2156 --
obs0.217 14535 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 44 5 2420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032471
X-RAY DIFFRACTIONf_angle_d0.6933358
X-RAY DIFFRACTIONf_dihedral_angle_d11.4951500
X-RAY DIFFRACTIONf_chiral_restr0.048386
X-RAY DIFFRACTIONf_plane_restr0.004428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.12320.40581430.35972692X-RAY DIFFRACTION98
3.1232-3.43610.41191440.30882727X-RAY DIFFRACTION99
3.4361-3.930.26561440.24772762X-RAY DIFFRACTION100
3.93-4.93890.19991470.192764X-RAY DIFFRACTION100
4.9389-19.93810.1941470.17482865X-RAY DIFFRACTION99

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