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- PDB-6u6t: Neuronal growth regulator 1 (NEGR1) -

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Basic information

Entry
Database: PDB / ID: 6u6t
TitleNeuronal growth regulator 1 (NEGR1)
ComponentsNeuronal growth regulator 1
KeywordsCELL ADHESION / synaptic organizer / IgLON / Ig domain-containing
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 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
Neuronal growth regulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.01 Å
AuthorsMachius, M. / Venkannagari, H. / Misra, A. / Rudenko, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01MH077303 United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Highly Conserved Molecular Features in IgLONs Contrast Their Distinct Structural and Biological Outcomes.
Authors: Venkannagari, H. / Kasper, J.M. / Misra, A. / Rush, S.A. / Fan, S. / Lee, H. / Sun, H. / Seshadrinathan, S. / Machius, M. / Hommel, J.D. / Rudenko, G.
History
DepositionAug 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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 / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuronal growth regulator 1
B: Neuronal growth regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8738
Polymers64,0322
Non-polymers1,8426
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.569, 97.218, 252.424
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-407-

CA

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 47 through 50 or resid 52...
21(chain B and (resid 47 through 50 or resid 52...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 47 through 50 or resid 52...A47 - 50
121(chain A and (resid 47 through 50 or resid 52...A52 - 60
131(chain A and (resid 47 through 50 or resid 52...A62
141(chain A and (resid 47 through 50 or resid 52...A0
151(chain A and (resid 47 through 50 or resid 52...A0
161(chain A and (resid 47 through 50 or resid 52...A64
171(chain A and (resid 47 through 50 or resid 52...A166 - 172
181(chain A and (resid 47 through 50 or resid 52...A46 - 602
191(chain A and (resid 47 through 50 or resid 52...A201 - 206
1101(chain A and (resid 47 through 50 or resid 52...A212 - 230
1111(chain A and (resid 47 through 50 or resid 52...A232 - 223
1121(chain A and (resid 47 through 50 or resid 52...A241 - 258
1131(chain A and (resid 47 through 50 or resid 52...A294 - 312
1141(chain A and (resid 47 through 50 or resid 52...A313
1151(chain A and (resid 47 through 50 or resid 52...A46 - 602
1161(chain A and (resid 47 through 50 or resid 52...A46 - 602
1171(chain A and (resid 47 through 50 or resid 52...A46 - 602
1181(chain A and (resid 47 through 50 or resid 52...A46 - 602
1191(chain A and (resid 47 through 50 or resid 52...A46 - 602
1201(chain A and (resid 47 through 50 or resid 52...A46 - 602
1211(chain A and (resid 47 through 50 or resid 52...A46 - 602
1221(chain A and (resid 47 through 50 or resid 52...A46 - 602
211(chain B and (resid 47 through 50 or resid 52...B47 - 50
221(chain B and (resid 47 through 50 or resid 52...B52 - 60
231(chain B and (resid 47 through 50 or resid 52...B62
241(chain B and (resid 47 through 50 or resid 52...B68 - 94
251(chain B and (resid 47 through 50 or resid 52...B0
261(chain B and (resid 47 through 50 or resid 52...B64
271(chain B and (resid 47 through 50 or resid 52...B166 - 172
281(chain B and (resid 47 through 50 or resid 52...B43 - 501
291(chain B and (resid 47 through 50 or resid 52...B184 - 199
2101(chain B and (resid 47 through 50 or resid 52...B201 - 20
2111(chain B and (resid 47 through 50 or resid 52...B212 - 230
2121(chain B and (resid 47 through 50 or resid 52...B232 - 23
2131(chain B and (resid 47 through 50 or resid 52...B241 - 258
2141(chain B and (resid 47 through 50 or resid 52...B271 - 283
2151(chain B and (resid 47 through 50 or resid 52...B294 - 501

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Components

#1: Protein Neuronal growth regulator 1 / IgLON family member 4


Mass: 32015.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEGR1, IGLON4, UNQ2433/PRO4993 / Plasmid: pFastbac / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q7Z3B1
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Ca
#5: 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.: 1
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
Has ligand of interestN

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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: 3.53 Å3/Da / Density % sol: 65.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Protein: 2.5 mg/ml NEGR1 in 10 mM HEPES, pH 8.0, 150 mM NaCl. Reservoir Solution: 20% (w/v) PEG 3350, 0.1 M Tris pH 9.0, 0.2 M MgCl2, 0.6 M NaI. Crystallization Drop: 1 micro-Liter NEGR1 + 1 ...Details: Protein: 2.5 mg/ml NEGR1 in 10 mM HEPES, pH 8.0, 150 mM NaCl. Reservoir Solution: 20% (w/v) PEG 3350, 0.1 M Tris pH 9.0, 0.2 M MgCl2, 0.6 M NaI. Crystallization Drop: 1 micro-Liter NEGR1 + 1 micro-Liter Reservoir Solution Single crystals were obtained via microseeding, and their size improved to ~600 x 200 micro-meters by macroseeding. Crystals harvested from the crystallization drops were cryo-protected in reservoir solution containing 20% (v/v) MPD and then flash cooled by plunging into liquid nitrogen

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 3.01→31.81 Å / Num. obs: 16011 / % possible obs: 86.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.029 / Rrim(I) all: 0.077 / Χ2: 1.036 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.01-3.064.10.4844640.8750.2510.550.87850.2
3.06-3.124.60.4324960.9610.210.4830.86656.6
3.12-3.1850.4195500.9540.1960.4650.95259.7
3.18-3.245.30.3625760.930.1640.3990.9162.7
3.24-3.315.30.326200.9750.1430.3520.9670.5
3.31-3.395.50.2626670.9740.1140.2870.91971.6
3.39-3.475.80.2427290.9830.1030.2640.89380.7
3.47-3.575.90.2228090.9840.0920.2410.97288.4
3.57-3.676.60.28570.9880.080.2160.96293.5
3.67-3.796.70.1718920.9840.0680.1850.9798.1
3.79-3.9370.1469050.9830.0590.1581.03199.9
3.93-4.096.70.1189360.9710.0490.1281.05699.2
4.09-4.277.30.1028910.9840.040.1091.143100
4.27-4.57.20.0849130.9860.0330.091.17599.7
4.5-4.787.70.0749410.9960.0280.0791.10499.9
4.78-5.157.50.079300.9950.0270.0761.139100
5.15-5.667.20.0679380.9870.0260.0731.107100
5.66-6.487.60.0669340.9920.0250.0711.083100
6.48-8.177.30.0589650.9930.0230.0631.057100
8.17-1006.90.0549980.990.0220.0590.97897.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.08 Å31.88 Å
Translation3.08 Å31.88 Å

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
HKL-2000718data reduction
HKL-2000718data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UV6

5uv6


Resolution: 3.01→31.81 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.97
RfactorNum. reflection% reflection
Rfree0.2856 498 3.48 %
Rwork0.2338 --
obs0.2357 14290 77.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 239.75 Å2 / Biso mean: 62.6765 Å2 / Biso min: 20.92 Å2
Refinement stepCycle: final / Resolution: 3.01→31.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4158 0 223 0 4381
Biso mean--83.07 --
Num. residues----539
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1220X-RAY DIFFRACTION2.622TORSIONAL
12B1220X-RAY DIFFRACTION2.622TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.01-3.30670.359690.2931192844
3.3067-3.78460.31441110.2571306669
3.7846-4.76560.24811520.2151420495
4.7656-31.810.29171660.22854594100
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)
11.83140.2661-2.12312.57810.72186.03020.17770.85120.1577-0.42620.14520.46-0.3324-0.47020.64810.3785-0.0947-0.08090.51-0.16870.4667-35.46372.996387.3949
22.7379-0.7493-2.4790.51150.59283.5882-0.1830.1025-0.01010.224-0.05720.07960.5377-0.27940.2530.2996-0.1404-0.04190.2949-0.0680.305-16.0855-10.982366.5234
32.91010.1208-1.03412.49450.1190.3791-0.09170.4667-0.0762-0.47720.0709-0.47160.18770.6229-0.04230.29250.03860.11720.79990.04620.39198.7013-15.559320.3931
42.0634-0.23710.06652.8814-0.43814.734-0.1666-0.3941-0.49650.1892-0.04050.09470.3649-0.1044-0.03040.2902-0.00990.05230.6040.29850.4792-6.5584-50.7798-15.8214
51.1784-0.46580.56123.37181.45042.3609-0.00190.3129-0.0885-0.5367-0.09250.4578-0.3434-0.2769-0.26160.35540.0796-0.03980.88970.18790.3123-12.5815-17.702211.0782
62.6815-0.8662-0.36064.44550.0456.65210.3254-0.03630.45010.0553-0.2954-0.1809-0.8701-0.0351-0.03860.3122-0.0254-0.06780.29190.06760.457-12.77962.677446.5717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 101 )A46 - 101
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 222 )A102 - 222
3X-RAY DIFFRACTION3chain 'A' and (resid 223 through 313 )A223 - 313
4X-RAY DIFFRACTION4chain 'B' and (resid 43 through 136 )B43 - 136
5X-RAY DIFFRACTION5chain 'B' and (resid 137 through 222 )B137 - 222
6X-RAY DIFFRACTION6chain 'B' and (resid 223 through 313 )B223 - 313

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