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- PDB-5xeq: Crystal Structure of human MDGA1 and human neuroligin-2 complex -

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Basic information

Entry
Database: PDB / ID: 5xeq
TitleCrystal Structure of human MDGA1 and human neuroligin-2 complex
Components
  • MAM domain-containing glycosylphosphatidylinositol anchor protein 1
  • Neuroligin-2
KeywordsCELL ADHESION / Immunogloubulin-like domain
Function / homology
Function and homology information


neurotransmitter-gated ion channel clustering / jump response / positive regulation of t-SNARE clustering / symmetric, GABA-ergic, inhibitory synapse / cerebral cortex radially oriented cell migration / spinal cord association neuron differentiation / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / postsynaptic membrane assembly ...neurotransmitter-gated ion channel clustering / jump response / positive regulation of t-SNARE clustering / symmetric, GABA-ergic, inhibitory synapse / cerebral cortex radially oriented cell migration / spinal cord association neuron differentiation / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / postsynaptic membrane assembly / cell-cell junction maintenance / positive regulation of synaptic vesicle clustering / presynaptic membrane assembly / positive regulation of inhibitory postsynaptic potential / thigmotaxis / ribbon synapse / Post-translational modification: synthesis of GPI-anchored proteins / inhibitory synapse / neuron cell-cell adhesion / insulin metabolic process / regulation of respiratory gaseous exchange by nervous system process / neurexin family protein binding / dopaminergic synapse / presynapse assembly / inhibitory synapse assembly / protein localization to synapse / glycinergic synapse / regulation of AMPA receptor activity / postsynaptic specialization membrane / synaptic transmission, GABAergic / protein localization to cell surface / Neurexins and neuroligins / positive regulation of synapse assembly / positive regulation of protein localization to synapse / regulation of synaptic membrane adhesion / positive regulation of dendritic spine development / locomotory exploration behavior / social behavior / positive regulation of excitatory postsynaptic potential / neuromuscular process controlling balance / regulation of presynapse assembly / excitatory synapse / synaptic vesicle endocytosis / GABA-ergic synapse / side of membrane / sensory perception of pain / synapse assembly / cell adhesion molecule binding / positive regulation of synaptic transmission, glutamatergic / dendritic shaft / positive regulation of synaptic transmission, GABAergic / synapse organization / brain development / neuron migration / modulation of chemical synaptic transmission / positive regulation of insulin secretion / cell-cell adhesion / signaling receptor activity / presynaptic membrane / nervous system development / chemical synaptic transmission / postsynaptic membrane / synapse / positive regulation of cell population proliferation / Golgi apparatus / cell surface / extracellular space / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Neuroligin / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Immunoglobulin domain ...Neuroligin / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / 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 / Alpha/Beta hydrolase fold, catalytic domain / Concanavalin A-like lectin/glucanase domain superfamily / Alpha/Beta hydrolase fold / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MAM domain-containing glycosylphosphatidylinositol anchor protein 1 / Neuroligin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.136 Å
AuthorsKim, H.M. / Kim, J.A. / Kim, D.
CitationJournal: Neuron / Year: 2017
Title: Structural Insights into Modulation of Neurexin-Neuroligin Trans-synaptic Adhesion by MDGA1/Neuroligin-2 Complex
Authors: Kim, J.A. / Kim, D. / Won, S.Y. / Han, K.A. / Park, D. / Cho, E. / Yun, N. / An, H.J. / Um, J.W. / Kim, E. / Lee, J.O. / Ko, J. / Kim, H.M.
History
DepositionApr 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
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.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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 2.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuroligin-2
B: MAM domain-containing glycosylphosphatidylinositol anchor protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2286
Polymers99,1402
Non-polymers1,0884
Water0
1
A: Neuroligin-2
B: MAM domain-containing glycosylphosphatidylinositol anchor protein 1
hetero molecules

A: Neuroligin-2
B: MAM domain-containing glycosylphosphatidylinositol anchor protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,45612
Polymers198,2804
Non-polymers2,1768
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area11420 Å2
ΔGint-15 kcal/mol
Surface area68810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.875, 69.134, 108.843
Angle α, β, γ (deg.)90.000, 115.310, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Neuroligin-2 /


Mass: 64101.059 Da / Num. of mol.: 1 / Fragment: UNP residues 42-610 / Mutation: N98Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLGN2, KIAA1366 / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: Q8NFZ4
#2: Protein MAM domain-containing glycosylphosphatidylinositol anchor protein 1 / GPI and MAM protein / GPIM / Glycosylphosphatidylinositol-MAM / MAM domain-containing protein 3


Mass: 35038.707 Da / Num. of mol.: 1 / Fragment: UNP residues 19-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDGA1, MAMDC3 / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: Q8NFP4
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}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.: 3
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: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 300mM Ammonium citrate tribasic, pH 7.0, 13% 1,3-Butanediol and 18%(v/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.14→49.2 Å / Num. obs: 18485 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 77.18 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.022 / Rrim(I) all: 0.078 / Net I/σ(I): 22.9 / Num. measured all: 236647 / Scaling rejects: 171
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.14-3.3512.90.26142385329232920.9930.0750.2728.4100
8.87-49.211.80.04103098730.9780.0130.04246.199.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BL8

3bl8


Resolution: 3.136→49.199 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2779 1847 10.01 %
Rwork0.2341 16609 -
obs0.2385 18456 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.18 Å2 / Biso mean: 75.0805 Å2 / Biso min: 32.37 Å2
Refinement stepCycle: final / Resolution: 3.136→49.199 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6380 0 70 0 6450
Biso mean--115.39 --
Num. residues----817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046618
X-RAY DIFFRACTIONf_angle_d0.689024
X-RAY DIFFRACTIONf_chiral_restr0.0571005
X-RAY DIFFRACTIONf_plane_restr0.0041176
X-RAY DIFFRACTIONf_dihedral_angle_d10.9573928
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1357-3.22050.40171380.318412301368
3.2205-3.31520.41411420.301212911433
3.3152-3.42220.32181380.289512391377
3.4222-3.54450.35491430.276412791422
3.5445-3.68630.35821430.275712861429
3.6863-3.8540.30581430.247612861429
3.854-4.05710.29061410.238412631404
4.0571-4.31120.26431400.221112631403
4.3112-4.64380.28291400.209112611401
4.6438-5.11070.26951430.20812861429
5.1107-5.84920.24691430.220712921435
5.8492-7.36540.25611440.243412971441
7.3654-49.20470.21011490.202213361485

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