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- PDB-5v5w: Molecular Mechanism of MDGA1: Regulation of Neuroligin 2:Neurexin... -

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Basic information

Entry
Database: PDB / ID: 5v5w
TitleMolecular Mechanism of MDGA1: Regulation of Neuroligin 2:Neurexin Trans-synaptic Bridges
ComponentsMAM domain-containing glycosylphosphatidylinositol anchor protein 1
KeywordsCELL ADHESION / synaptic organizer / regulatory molecule / MDGAs
Function / homology
Function and homology information


cerebral cortex radially oriented cell migration / spinal cord association neuron differentiation / Post-translational modification: synthesis of GPI-anchored proteins / regulation of synaptic membrane adhesion / regulation of presynapse assembly / GABA-ergic synapse / side of membrane / neuron migration / brain development / nervous system development ...cerebral cortex radially oriented cell migration / spinal cord association neuron differentiation / Post-translational modification: synthesis of GPI-anchored proteins / regulation of synaptic membrane adhesion / regulation of presynapse assembly / GABA-ergic synapse / side of membrane / neuron migration / brain development / nervous system development / Golgi apparatus / extracellular space / extracellular region / plasma membrane
Similarity search - Function
: / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type ...: / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
MAM domain-containing glycosylphosphatidylinositol anchor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.718 Å
AuthorsMachius, M. / Gangwar, S.P. / Rudenko, G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01MH077303 United States
UT Brain Pilot United States
Brain and Behavior Research Foundation United States
CitationJournal: Neuron / Year: 2017
Title: Molecular Mechanism of MDGA1: Regulation of Neuroligin 2:Neurexin Trans-synaptic Bridges.
Authors: Gangwar, S.P. / Zhong, X. / Seshadrinathan, S. / Chen, H. / Machius, M. / Rudenko, G.
History
DepositionMar 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

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Assembly

Deposited unit
A: MAM domain-containing glycosylphosphatidylinositol anchor protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2194
Polymers25,9311
Non-polymers2883
Water1629
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, protein is consistent with a monomeric species in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MAM domain-containing glycosylphosphatidylinositol anchor protein 1
hetero molecules

A: MAM domain-containing glycosylphosphatidylinositol anchor protein 1
hetero molecules

A: MAM domain-containing glycosylphosphatidylinositol anchor protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,65812
Polymers77,7933
Non-polymers8659
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area5520 Å2
ΔGint-131 kcal/mol
Surface area32940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.068, 139.068, 139.068
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein MAM domain-containing glycosylphosphatidylinositol anchor protein 1 / GPI and MAM protein / GPIM / Glycosylphosphatidylinositol-MAM / MAM domain-containing protein 3


Mass: 25931.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDGA1, MAMDC3 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8NFP4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 4.32 Å3/Da / Density % sol: 75.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.5 M ammonium sulfate, 3.72% (v/v) 2-propanol, 25% (v/v) glycerol

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.71→32.78 Å / Num. obs: 12205 / % possible obs: 99.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 26
Reflection shellResolution: 2.71→2.76 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.945 / Num. unique obs: 617 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bih

1bih


Resolution: 2.718→32.779 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2555 597 4.92 %
Rwork0.2139 --
obs0.216 12127 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.718→32.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 16 9 1597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051615
X-RAY DIFFRACTIONf_angle_d0.7162193
X-RAY DIFFRACTIONf_dihedral_angle_d10.298983
X-RAY DIFFRACTIONf_chiral_restr0.049249
X-RAY DIFFRACTIONf_plane_restr0.004279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.718-2.99130.33121450.2692830X-RAY DIFFRACTION98
2.9913-3.42380.26951360.22982875X-RAY DIFFRACTION100
3.4238-4.3120.24911510.20312877X-RAY DIFFRACTION100
4.312-32.7810.23341650.19722948X-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)
13.3303-0.93810.65846.22041.93353.5370.22330.01520.52930.3588-0.20080.2287-0.4491-0.41050.15230.39460.01520.12850.2519-0.00840.352739.7771-12.771545.0766
27.66297.5156-5.25577.4356-5.39544.5102-0.9448-0.5366-0.7617-1.26620.22370.11370.97540.360.6680.71730.08310.13860.6189-0.07260.807142.7754-4.697633.6202
32.935-2.1102-0.31435.23950.8631.33910.31750.05170.46250.2317-0.1942-0.4154-0.4044-0.15240.14840.40310.01590.12010.18390.0560.328142.4307-12.422438.5113
43.0363-0.2136-0.95422.50780.36322.1574-0.0799-0.0704-0.29140.20050.1783-0.71220.56670.7280.24240.31570.115-0.04430.37-0.07240.452459.3828-43.958227.4954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 92 )
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 127 )
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 234 )

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