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- PDB-6dld: Crystal structure of IgLON5/NEGR1 heterodimer -

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Basic information

Entry
Database: PDB / ID: 6dld
TitleCrystal structure of IgLON5/NEGR1 heterodimer
Components
  • IgLON family member 5
  • Neuronal growth regulator 1
KeywordsCELL ADHESION / Ig / Complex / heterodimer / cell surface / neuronal
Function / homology
Function and homology information


Post-translational modification: synthesis of GPI-anchored proteins / feeding behavior / regulation of synapse assembly / locomotory behavior / brain development / cell-cell adhesion / positive regulation of neuron projection development / neuron projection development / neuronal cell body / dendrite ...Post-translational modification: synthesis of GPI-anchored proteins / feeding behavior / regulation of synapse assembly / locomotory behavior / brain development / cell-cell adhesion / positive regulation of neuron projection development / neuron projection development / neuronal cell body / dendrite / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin / Immunoglobulin 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 / Immunoglobulin 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
Similarity search - Domain/homology
IgLON family member 5 / Neuronal growth regulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsRanaivoson, F.M. / Turk, L.S. / Ozkan, E. / Montelione, G.T. / Comoletti, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1450895 United States
CitationJournal: Structure / Year: 2019
Title: Structure of a heterodimer of neuronal cell surface proteins
Authors: Ranaivoson, F.M. / Turk, L.S. / Ozkan, E. / Montelione, G.T. / Comoletti, D.
History
DepositionJun 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IgLON family member 5
B: Neuronal growth regulator 1
C: IgLON family member 5
D: Neuronal growth regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,94620
Polymers133,8804
Non-polymers4,06716
Water0
1
A: IgLON family member 5
B: Neuronal growth regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,23710
Polymers66,9402
Non-polymers2,2978
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint24 kcal/mol
Surface area30030 Å2
MethodPISA
2
C: IgLON family member 5
D: Neuronal growth regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,70910
Polymers66,9402
Non-polymers1,7708
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint15 kcal/mol
Surface area30500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.341, 305.799, 60.029
Angle α, β, γ (deg.)90.00, 100.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein IgLON family member 5


Mass: 33543.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGLON5 / Production host: Homo sapiens (human) / References: UniProt: A6NGN9
#2: Protein Neuronal growth regulator 1 / IgLON family member 4


Mass: 33396.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEGR1, IGLON4, UNQ2433/PRO4993 / Production host: Homo sapiens (human) / References: UniProt: Q7Z3B1
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15
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

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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: 4.05 Å3/Da / Density % sol: 69.65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: MES-NaOH pH6.5, MgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.3→48.6 Å / Num. obs: 31695 / % possible obs: 98.82 % / Redundancy: 3.5 % / CC1/2: 0.996 / Net I/σ(I): 7.92
Reflection shellResolution: 3.3→3.5 Å / Num. unique all: 4988 / CC1/2: 0.397

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EO9

5eo9


Resolution: 3.3→48.596 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.68
RfactorNum. reflection% reflectionSelection details
Rfree0.2859 1579 5.01 %Random
Rwork0.2449 ---
obs0.247 31534 98.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→48.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7596 0 260 0 7856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038039
X-RAY DIFFRACTIONf_angle_d0.56911071
X-RAY DIFFRACTIONf_dihedral_angle_d10.4554742
X-RAY DIFFRACTIONf_chiral_restr0.0441356
X-RAY DIFFRACTIONf_plane_restr0.0041440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3002-3.40670.40691330.372522X-RAY DIFFRACTION92
3.4067-3.52840.37031460.33182757X-RAY DIFFRACTION100
3.5284-3.66970.35881430.3172716X-RAY DIFFRACTION100
3.6697-3.83660.34141440.29062741X-RAY DIFFRACTION100
3.8366-4.03880.31441450.25372757X-RAY DIFFRACTION100
4.0388-4.29170.27761470.22682775X-RAY DIFFRACTION100
4.2917-4.62280.2531440.20512745X-RAY DIFFRACTION100
4.6228-5.08760.25111430.19742707X-RAY DIFFRACTION100
5.0876-5.82270.27931430.2152743X-RAY DIFFRACTION100
5.8227-7.3320.28161460.27532753X-RAY DIFFRACTION100
7.332-48.60080.25891450.22912739X-RAY DIFFRACTION98
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)
17.92071.4573.66581.6826-1.94527.9099-0.2525-0.5128-0.54950.2977-0.3427-0.1583-0.38730.34920.71520.6160.02940.05740.4464-0.00021.006123.3683-43.180910.8425
29.06431.0127-2.42447.46634.3489.00750.2097-0.20480.2470.2403-0.3449-0.08-0.096-0.43580.22760.45710.0138-0.07920.63240.16310.676813.6412-47.87677.3393
37.4869-0.43463.76514.15832.8224.3542-0.01420.4743-0.3458-0.11890.6282-0.69720.79380.5099-0.49110.4883-0.07090.01911.065-0.1080.76647.32-42.920838.4137
45.6818-2.55930.8716.13981.34940.7228-0.453-0.25042.3062-1.1294-0.80050.1206-1.4892-0.82310.80121.15070.0077-0.39341.63770.11110.941341.6143-36.230431.6736
58.04591.79376.65650.40830.60997.2224-0.92-0.6740.7262-0.38290.2297-0.0923-1.3151-0.340.57240.88860.1519-0.0410.5866-0.04070.708366.1646-28.342364.8672
62.2041-0.563-1.52664.9458-1.17291.6768-0.4415-2.57480.62880.3333-0.3828-0.8381-0.601-0.77040.71251.05270.0989-0.18461.0135-0.41880.676173.2729-29.74971.4658
73.98680.72920.66136.362.23783.2859-0.0436-0.5244-1.22611.67250.64480.05881.5141-0.0075-1.08550.739-0.046-0.38930.82850.20931.16469.2758-73.1410.3583
82.7384-2.01170.51285.71742.33196.42590.3730.2366-0.17220.25430.7618-0.34811.19830.1118-0.92370.617-0.0091-0.35540.81350.05941.08689.4984-66.41146.1954
91.94130.7197-1.58547.12831.32393.06890.0552-0.3196-0.7848-2.11070.1003-0.5215-0.1739-0.0846-0.04661.57540.4094-0.31071.0478-0.25291.467935.2976-94.1901-9.8838
102.08390.3185-0.08973.45623.38883.32510.0764-1.9324-0.95670.5672-0.2777-2.451-1.3619-0.6420.19391.18810.408-0.3091.04360.27091.46236.943-102.902-1.7504
112.74731.0123-1.22860.75250.5893.4746-0.2335-0.62961.1731-1.316-0.3618-0.403-0.0616-0.5676-0.4312.06471.0492-0.58430.5019-0.29882.24944.4321-104.9102-8.9211
122.759-0.339-0.29742.53050.44483.3893-0.32380.153-0.0997-0.4073-0.1275-0.8621.0617-0.76370.00831.3660.1636-0.21310.6463-0.32811.787833.8252-104.1135-8.713
131.8438-0.86380.61890.3713-0.17820.18520.89560.7149-0.68020.0228-0.3838-0.474-1.0342-1.312-0.27571.94880.29720.10910.6186-0.24841.735941.7145-133.4773-26.4366
141.71630.36261.74733.9719-1.49463.5887-0.39030.5531-3.3168-0.1711-0.2635-2.80862.5099-0.21330.06112.7122-1.00970.29951.00180.0062.478349.2402-130.9166-25.0958
155.0215-2.7322.33744.47-0.34719.0130.34340.025-1.4915-0.53250.56840.2192-0.03720.0042-0.85820.5724-0.0133-0.30940.9198-0.09311.181834.5477-71.657-6.8402
168.22-2.7911.5074.9842-1.30825.45010.0521.0497-0.56570.62270.288-0.3037-0.28270.5244-0.35360.8027-0.0461-0.34121.04560.12931.108164.1078-75.80623.7954
175.17540.07922.57472.3206-1.90125.31870.4212-0.3059-0.96310.3815-0.20380.93640.66191.5980.39511.18120.4311-0.50511.0849-0.19941.774794.2408-89.803444.3522
181.8327-2.7605-0.37755.2647-1.98267.65930.0968-1.25570.360.3174-0.33850.54321.8799-0.6-0.67441.05090.0515-0.85951.24480.22322.089396.8978-91.114244.2299
190.4253-0.326-0.18613.6332-4.37747.20620.0587-0.40661.22960.0056-0.0922-0.6111-1.59741.4543-0.43320.7757-0.1612-0.16391.15030.23050.25133.9857-40.5663-14.0464
207.36970.61460.16339.3194-0.24548.01940.57390.8615-0.2365-1.91161.1054-0.57060.014-0.3755-0.40230.7209-0.0635-0.15810.7215-0.15470.819434.5258-56.8561-16.2796
217.5753-0.9656-0.71575.90860.77796.42230.0159-0.2317-0.3341-0.62120.26920.5429-0.5261-0.4852-0.60390.5499-0.1176-0.1380.65010.03880.488131.351-49.3082-15.6242
224.778-0.7161-0.15922.3384-0.85051.9567-0.2482-0.29350.79790.10330.83280.6956-0.02060.9348-0.55930.7479-0.08190.10681.4316-0.22480.360740.7346-52.6416-9.6714
234.2323-4.7012-3.52768.30975.47126.65420.36270.11850.58550.7032-0.4079-0.24-0.5080.217-0.04550.9889-0.12650.00930.69830.00561.400117.2131-20.2639.176
241.83452.5581-3.4633.3392-4.60346.36410.0517-1.5229-0.16151.6157-2.5577-1.01-0.3433-0.87040.42231.56830.0022-0.00720.4289-0.35661.93265.454811.302513.215
255.7673.7457-0.62845.0128-3.38214.30470.54810.11980.7133-1.88851.091-0.35171.049-1.09730.61671.84770.2261-0.09790.81120.13732.0856-1.483316.91037.6869
261.7021-0.8886-0.82580.48760.68343.2520.5084-0.12030.0582-1.9693-0.11420.17-4.3784-1.11110.12282.61381.38910.4727-0.9769-0.36611.74880.012523.893913.0047
272.44282.8167-1.42653.7075-0.96362.0797-1.21060.01781.32721.0217-1.22080.9964-2.1134-0.5123-1.1991.9343-0.3618-0.11180.5949-0.00871.94733.124812.219418.6889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 130 )
3X-RAY DIFFRACTION3chain 'A' and (resid 131 through 190 )
4X-RAY DIFFRACTION4chain 'A' and (resid 191 through 207 )
5X-RAY DIFFRACTION5chain 'A' and (resid 208 through 278 )
6X-RAY DIFFRACTION6chain 'A' and (resid 279 through 308 )
7X-RAY DIFFRACTION7chain 'B' and (resid 43 through 67 )
8X-RAY DIFFRACTION8chain 'B' and (resid 68 through 136 )
9X-RAY DIFFRACTION9chain 'B' and (resid 137 through 171 )
10X-RAY DIFFRACTION10chain 'B' and (resid 172 through 186 )
11X-RAY DIFFRACTION11chain 'B' and (resid 187 through 198 )
12X-RAY DIFFRACTION12chain 'B' and (resid 199 through 229 )
13X-RAY DIFFRACTION13chain 'B' and (resid 230 through 292 )
14X-RAY DIFFRACTION14chain 'B' and (resid 293 through 312 )
15X-RAY DIFFRACTION15chain 'C' and (resid 38 through 130 )
16X-RAY DIFFRACTION16chain 'C' and (resid 131 through 215 )
17X-RAY DIFFRACTION17chain 'C' and (resid 216 through 261 )
18X-RAY DIFFRACTION18chain 'C' and (resid 262 through 304 )
19X-RAY DIFFRACTION19chain 'D' and (resid 37 through 59 )
20X-RAY DIFFRACTION20chain 'D' and (resid 60 through 88 )
21X-RAY DIFFRACTION21chain 'D' and (resid 89 through 120 )
22X-RAY DIFFRACTION22chain 'D' and (resid 121 through 136 )
23X-RAY DIFFRACTION23chain 'D' and (resid 137 through 222 )
24X-RAY DIFFRACTION24chain 'D' and (resid 223 through 259 )
25X-RAY DIFFRACTION25chain 'D' and (resid 260 through 282 )
26X-RAY DIFFRACTION26chain 'D' and (resid 283 through 300 )
27X-RAY DIFFRACTION27chain 'D' and (resid 301 through 312 )

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