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- PDB-6nrx: Crystal structure of DIP-eta IG1 homodimer -

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Basic information

Entry
Database: PDB / ID: 6nrx
TitleCrystal structure of DIP-eta IG1 homodimer
ComponentsDpr-interacting protein eta, isoform B
KeywordsCELL ADHESION / Immunoglobulin superfamily / Glycoprotein / Neuronal / Cell surface receptor
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 / A tetrasaccharide linker sequence is required for GAG synthesis / 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 eta, isoform B
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 11, 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 1.4Oct 9, 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 eta, isoform B
B: Dpr-interacting protein eta, isoform B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5086
Polymers25,8822
Non-polymers6274
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-4 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.426, 67.133, 61.012
Angle α, β, γ (deg.)90.00, 128.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Dpr-interacting protein eta, isoform B / Dpr-interacting protein eta / isoform D


Mass: 12940.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: DIP-eta, 14010, CT33567, Dmel\CG14010, CG14010, Dmel_CG14010
Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9VMN9
#2: 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.: 2
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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M sodium citrate, pH 5.5, 45% (w/v) PEG 200

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2017
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 21928 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 38.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.049 / Net I/σ(I): 12.33
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.32 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 1.99 / Num. unique obs: 1506 / CC1/2: 0.901 / Rrim(I) all: 0.668 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX1.13rc2_2986refinement
XDSNov 11, 2017data reduction
XDSNov 11, 2017data scaling
PHASER2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EO9

5eo9


Resolution: 1.9→48.08 Å / SU ML: 0.16 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / Phase error: 43.37
RfactorNum. reflection% reflectionSelection details
Rfree0.2693 1081 4.96 %Random selection
Rwork0.2321 ---
obs0.2339 21783 98.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 40 21 1751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031766
X-RAY DIFFRACTIONf_angle_d0.6362397
X-RAY DIFFRACTIONf_dihedral_angle_d10.9791071
X-RAY DIFFRACTIONf_chiral_restr0.049281
X-RAY DIFFRACTIONf_plane_restr0.003296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8957-1.98190.45881170.37572510X-RAY DIFFRACTION96
1.9819-2.08640.37171370.32672533X-RAY DIFFRACTION98
2.0864-2.21710.31211340.28862603X-RAY DIFFRACTION99
2.2171-2.38830.3511430.26092571X-RAY DIFFRACTION99
2.3883-2.62870.32221220.25692604X-RAY DIFFRACTION99
2.6287-3.0090.30121490.25282598X-RAY DIFFRACTION99
3.009-3.79080.27181400.22552610X-RAY DIFFRACTION99
3.7908-48.09760.21461390.1992673X-RAY DIFFRACTION99
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)
14.13942.24994.20871.46632.11014.3932-0.53660.77150.88351.04480.4021-0.5088-0.81960.60490.32640.8002-0.0058-0.29410.65440.02780.602746.694624.360259.0662
25.7139-0.11012.13813.3507-3.52234.445-0.04720.5519-0.71010.53380.1123-0.5888-0.09040.3169-0.28320.6116-0.0068-1.04490.6439-0.35121.404160.865315.550570.7863
33.8982-2.50185.2327.8851-2.14457.2116-0.2187-0.30570.31590.56150.6212-0.3638-0.3456-0.0310.2340.82290.0788-0.33660.5763-0.05920.536146.347321.419364.8986
46.48870.03241.18646.14141.35091.9257-0.577-0.16020.3024-0.09180.55810.3715-0.7201-0.20450.11810.61710.0951-0.20640.6002-0.04740.413338.717615.733261.4657
56.10271.60181.19478.17890.44595.2807-0.3160.0758-0.799-0.10810.4789-0.87750.42080.1284-0.3390.57840.0729-0.05960.581-0.10780.504447.07786.467460.2881
65.53160.27762.68684.8256-0.04922.2552-0.2478-0.7894-0.50921.1710.424-0.4688-0.0607-0.4441-0.0950.8350.0729-0.26120.72270.09680.568344.1659.430170.7728
72.3298-0.64621.79492.12451.74694.0356-0.4371-1.0645-0.03930.51470.6273-0.2853-0.4418-0.4492-0.10360.85430.0902-0.23140.6719-0.01720.57243.451219.298869.0034
87.81722.31191.63262.10462.56795.57370.3046-0.5543-0.96650.79690.24-1.11120.32980.4019-0.45570.81610.0885-0.70450.657-0.32771.425759.21148.245368.4829
94.04930.51651.91014.48950.0462.2813-0.42961.13820.0139-0.28870.42580.1217-0.91070.2657-0.12990.665-0.0347-0.17780.6748-0.06260.419642.813114.138155.8702
104.021-1.5718-0.49193.8125-0.81040.3625-0.19331.14820.1754-0.02730.3614-1.0085-0.21250.71160.19280.6733-0.0754-0.11140.8708-0.17220.516853.649616.433559.1027
112-8.419522222.325810.90962.0887-0.3475-1.39482.1575-6.17983.5755-0.92741.24320.4220.1251.4373-0.04231.285569.64511.644766.5137
123.80750.52213.08493.9123-0.09875.8020.23970.1159-0.778-0.10050.2324-0.30150.51580.1629-0.45160.5501-0.0273-0.25920.5569-0.03270.712137.5626-8.404954.1109
130.7221-0.54182.01153.5032-1.3086.36680.4397-0.0525-0.70780.18790.3415-0.13381.1056-0.2364-1.030.7786-0.0555-0.40580.65930.06780.888336.4363-7.931860.6515
144.81012.82881.77138.05881.3345.89580.2042-0.0066-0.3518-0.12950.19280.1049-0.119-0.0806-0.34940.49570.0459-0.13210.59010.01470.432333.78663.620555.4708
152.57411.66092.61784.37030.61839.5508-0.05350.2207-0.4667-0.12440.5879-0.19770.04590.0639-0.68730.5134-0.0174-0.21230.5401-0.05310.644436.7397-2.110251.2926
166.43881.17794.40525.45510.53814.5287-0.49090.91960.5218-1.20330.2811.4667-0.1216-0.61730.06270.95310.1566-0.31720.73410.01480.768327.895922.892954.0962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 44 through 51 )
2X-RAY DIFFRACTION2chain 'B' and (resid 52 through 59 )
3X-RAY DIFFRACTION3chain 'B' and (resid 60 through 67 )
4X-RAY DIFFRACTION4chain 'B' and (resid 68 through 78 )
5X-RAY DIFFRACTION5chain 'B' and (resid 79 through 87 )
6X-RAY DIFFRACTION6chain 'B' and (resid 88 through 103 )
7X-RAY DIFFRACTION7chain 'B' and (resid 104 through 112 )
8X-RAY DIFFRACTION8chain 'B' and (resid 113 through 120 )
9X-RAY DIFFRACTION9chain 'B' and (resid 121 through 132 )
10X-RAY DIFFRACTION10chain 'B' and (resid 133 through 142 )
11X-RAY DIFFRACTION11chain 'B' and (resid 143 through 143 )
12X-RAY DIFFRACTION12chain 'A' and (resid 38 through 59 )
13X-RAY DIFFRACTION13chain 'A' and (resid 60 through 73 )
14X-RAY DIFFRACTION14chain 'A' and (resid 74 through 103 )
15X-RAY DIFFRACTION15chain 'A' and (resid 104 through 143 )
16X-RAY DIFFRACTION16chain 'B' and (resid 38 through 43 )

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