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- PDB-6nrr: Crystal structure of Dpr11 IG1 bound to DIP-gamma IG+IG2 -

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Basic information

Entry
Database: PDB / ID: 6nrr
TitleCrystal structure of Dpr11 IG1 bound to DIP-gamma IG+IG2
Components
  • Defective proboscis extension response 11, isoform B
  • Dpr-interacting protein gamma
KeywordsCELL ADHESION / Immunoglobulin superfamily / Neuronal / Cell surface receptor / Glycoprotein
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 / sensory perception of chemical stimulus / synapse organization / neuron projection / plasma membrane
Similarity search - Function
Zwei Ig domain protein zig-8 / : / 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 ...Zwei Ig domain protein zig-8 / : / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Defective proboscis extension response 11, isoform B / Dpr-interacting protein gamma
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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: Advisory / Atomic model ...Advisory / 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_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 9, 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: Defective proboscis extension response 11, isoform B
B: Dpr-interacting protein gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4189
Polymers37,1162
Non-polymers1,3017
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-28 kcal/mol
Surface area15540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.364, 85.364, 103.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-905-

SO4

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Defective proboscis extension response 11, isoform B / Defective proboscis extension response 11 / isoform C / GH22307p


Mass: 13109.940 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: dpr11, BcDNA:GH22307, CG15181, CG15182, CG15183, CG31309, CT35098, Dmel\CG33202, Dpr-11, Dpr11, CG33202, Dmel_CG33202
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8MRE6
#2: 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
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9VAR6

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Sugars , 1 types, 1 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 75 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M sodium citrate, pH 5.5, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.96638 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 6, 2014
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96638 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13814 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 13.26 % / CC1/2: 0.998 / Rmerge(I) obs: 0.161 / Rrim(I) all: 0.168 / Net I/σ(I): 16.48
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 8.61 % / Rmerge(I) obs: 1.818 / Mean I/σ(I) obs: 1.17 / Num. unique obs: 2138 / CC1/2: 0.577 / Rrim(I) all: 1.931 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIXdev_3374refinement
XDSJanuary 10, 2014data reduction
XDSJanuary 10, 2014data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EO9

5eo9


Resolution: 2.5→44.279 Å / SU ML: 0.41 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / Phase error: 28.69
RfactorNum. reflection% reflectionSelection details
Rfree0.2607 707 5.14 %Random selection
Rwork0.2072 ---
obs0.21 13768 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→44.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 81 69 2451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052427
X-RAY DIFFRACTIONf_angle_d0.6993285
X-RAY DIFFRACTIONf_dihedral_angle_d11.7961494
X-RAY DIFFRACTIONf_chiral_restr0.049382
X-RAY DIFFRACTIONf_plane_restr0.004412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4996-2.69260.34561270.2972521X-RAY DIFFRACTION98
2.6926-2.96350.36391540.24282554X-RAY DIFFRACTION100
2.9635-3.39220.27621270.21542600X-RAY DIFFRACTION100
3.3922-4.27330.25031540.17952614X-RAY DIFFRACTION100
4.2733-44.28640.221450.19692772X-RAY DIFFRACTION100
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)
19.38675.2272-2.13884.6186-3.42953.4489-0.1918-0.507-0.20431.32470.4183-0.4527-1.504-1.0122-0.12250.59330.0894-0.02920.5733-0.11640.406610.841147.3444-11.2387
22.595-0.7715-2.85592.0308-2.10267.82770.6787-0.12580.10810.3347-0.2121-0.4337-0.45071.1629-0.16610.3003-0.0891-0.04590.3919-0.03150.379415.570346.3264-19.8275
33.4367-4.32484.00322.0086-7.63035.97270.2978-0.3403-0.0728-0.7383-0.2441-0.02510.7243-0.03110.12250.47080.05870.04820.36620.00540.43068.022930.6018-11.7942
42.491-2.9647-2.43564.24583.81623.5176-0.09580.9060.3275-1.148-0.26450.3751-0.7112-0.21180.37420.4425-0.0286-0.02790.4520.0240.47471.612336.2016-21.98
53.26223.7361-0.75655.8046-1.06666.1146-0.2422-0.3634-0.0681-0.6327-0.3214-0.20650.78861.02950.46070.42390.08440.11430.3946-0.01330.245810.224633.0957-25.9231
64.91182.0647-2.80524.79931.00172.8034-0.5174-0.1779-0.20450.69240.0404-0.72910.54021.85350.45680.50260.1476-0.07810.45230.0210.624215.998931.9475-13.7956
74.98113.9273-4.44059.0849-4.54717.66370.04460.4342-0.12410.14490.12420.2793-0.4371-0.7308-0.1780.23240.0042-0.05180.2914-0.07530.27727.007638.4434-17.957
88.83526.8461-5.83426.6903-3.03345.16570.1394-0.71551.02772.13930.57521.3786-1.85980.1773-0.78580.60790.05660.02750.5113-0.07140.29165.789844.397-13.0778
96.45261.6932-0.03322.9669-0.63386.3695-0.36090.554-0.2965-0.48470.3968-0.18380.5282-0.0447-0.03690.408-0.10850.03830.3004-0.06280.327-7.380323.4726-23.7851
107.2778-0.7447-5.78684.4750.93546.47860.7873-0.53791.14450.23440.2085-0.1467-1.21540.6947-0.90390.7501-0.10020.12620.4322-0.00150.5001-32.87626.45346.8764
116.7937-3.4253-2.0244.6175.79028.48890.3229-0.47440.8621-0.84460.31920.0552-1.4635-1.5302-0.42530.81580.15010.12150.79220.18730.8271-48.162928.29347.1412
125.1527-1.2226-3.60224.79231.28326.94170.67360.30841.03440.15850.09670.2056-1.3246-0.6659-0.70580.6105-0.00160.12510.45180.14090.5694-40.832826.19648.0644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 123 through 129 )
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 138 )
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 153 )
4X-RAY DIFFRACTION4chain 'A' and (resid 154 through 162 )
5X-RAY DIFFRACTION5chain 'A' and (resid 163 through 172 )
6X-RAY DIFFRACTION6chain 'A' and (resid 173 through 183 )
7X-RAY DIFFRACTION7chain 'A' and (resid 184 through 207 )
8X-RAY DIFFRACTION8chain 'A' and (resid 208 through 217 )
9X-RAY DIFFRACTION9chain 'B' and (resid 37 through 138 )
10X-RAY DIFFRACTION10chain 'B' and (resid 139 through 178 )
11X-RAY DIFFRACTION11chain 'B' and (resid 179 through 194 )
12X-RAY DIFFRACTION12chain 'B' and (resid 195 through 240 )

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