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- PDB-6u7n: Crystal structure of neurotrimin (NTM) -

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Basic information

Entry
Database: PDB / ID: 6u7n
TitleCrystal structure of neurotrimin (NTM)
ComponentsNeurotrimin
KeywordsCELL ADHESION / synaptic organizer / IgLON / Ig domain-containing
Function / homology
Function and homology information


neuron recognition / Post-translational modification: synthesis of GPI-anchored proteins / side of membrane / cell adhesion / 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 ...: / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.321 Å
AuthorsMachius, M. / Venkannagari, H. / Misra, A. / Rudenko, G. / Rush, S.
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
DepositionSep 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurotrimin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,23614
Polymers34,8121
Non-polymers1,42413
Water00
1
A: Neurotrimin
hetero molecules

A: Neurotrimin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,47228
Polymers69,6252
Non-polymers2,84726
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1,z1
Buried area7250 Å2
ΔGint-102 kcal/mol
Surface area30230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.049, 106.049, 227.819
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Neurotrimin / hNT / IgLON family member 2


Mass: 34812.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTM, IGLON2, NT, UNQ297/PRO337 / Plasmid: pFastbac / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q9P121
#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.: 1
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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: Cl
Has ligand of interestN
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

Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Protein: 5.4 mg/ml NTM in 10 mM HEPES, pH 8.0, 150 mM sodium chloride Reservoir Solution: 2.5 M NaCl, 100 mM sodium acetate pH 4.5, 200 mM lithium sulfate Crystallization Drop: 2 micro- ...Details: Protein: 5.4 mg/ml NTM in 10 mM HEPES, pH 8.0, 150 mM sodium chloride Reservoir Solution: 2.5 M NaCl, 100 mM sodium acetate pH 4.5, 200 mM lithium sulfate Crystallization Drop: 2 micro-Liters NTM + 2 micro-Liters Reservoir Solution Single crystals grew to a size of ~250 x 150 micro-meters within 7-10 days. Crystals harvested from the crystallization drops were cryo-protected in reservoir solution containing 20% (v/v) ethylene glycol 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: ALS / Beamline: 8.2.1 / Wavelength: 0.99999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 3.32→46.431 Å / Num. obs: 18288 / % possible obs: 99.4 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.032 / Rrim(I) all: 0.07 / Χ2: 0.845 / Net I/σ(I): 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.32-3.383.61.3288170.4670.7761.5451.07993.4
3.38-3.444.11.0898920.6450.6021.2481.06997.2
3.44-3.54.40.9259070.7540.4971.0530.98699.6
3.5-3.584.60.7289360.8150.3790.8230.99799.9
3.58-3.654.70.6299090.8430.3240.7090.989100
3.65-3.744.70.4339320.9120.2250.4890.957100
3.74-3.834.70.39150.9520.1560.3390.857100
3.83-3.944.60.2459120.9690.1280.2770.869100
3.94-4.054.70.1689260.9750.0870.1890.759100
4.05-4.184.70.139150.9770.0680.1470.723100
4.18-4.334.70.0969060.9860.0490.1080.749100
4.33-4.514.70.0759360.9890.0390.0850.708100
4.51-4.714.70.0559290.990.0280.0620.628100
4.71-4.964.70.0519030.9890.0260.0580.713100
4.96-5.274.60.059240.9880.0260.0570.728100
5.27-5.684.60.0539260.9810.0280.060.896100
5.68-6.254.60.0559310.9810.0290.0620.9799.8
6.25-7.154.60.059200.9810.0260.0570.99999.9
7.15-9.014.50.0359160.9920.0180.0390.7999.9
9.01-1004.60.039360.9770.0150.0340.56498.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UV6

5uv6


Resolution: 3.321→46.43 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.56
RfactorNum. reflection% reflection
Rfree0.2501 504 3.31 %
Rwork0.2291 --
obs0.2298 15249 82.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 234.26 Å2 / Biso mean: 79.78 Å2 / Biso min: 27.76 Å2
Refinement stepCycle: final / Resolution: 3.321→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 165 0 2182
Biso mean--96.18 --
Num. residues----256
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.321-3.65460.2563540.2726159536
3.6546-4.18320.24981460.2363416794
4.1832-5.26920.22421510.20264481100
5.2692-46.430.27281530.23894502100
Refinement TLS params.Method: refined / Origin x: 5.2396 Å / Origin y: -38.7208 Å / Origin z: 4.6635 Å
111213212223313233
T0.4394 Å2-0.016 Å20.084 Å2-0.3001 Å20.0303 Å2--0.3636 Å2
L0.0064 °20.008 °20.2588 °2-1.3496 °2-1.7575 °2--2.1919 °2
S0.2008 Å °0.0871 Å °-0.1552 Å °-0.0934 Å °-0.141 Å °0.057 Å °0.0297 Å °0.3611 Å °0.0228 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA43 - 311
2X-RAY DIFFRACTION1allA401 - 708

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