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- PDB-5lf5: Myelin-associated glycoprotein (MAG) deglycosylated full extracel... -

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Basic information

Entry
Database: PDB / ID: 5lf5
TitleMyelin-associated glycoprotein (MAG) deglycosylated full extracellular domain with co-purified ligand
ComponentsMyelin-associated glycoprotein
KeywordsCELL ADHESION / Myelin / Signaling
Function / homology
Function and homology information


mesaxon / Axonal growth inhibition (RHOA activation) / Basigin interactions / ganglioside GT1b binding / sialic acid binding / central nervous system myelination / central nervous system myelin formation / positive regulation of myelination / myelin sheath adaxonal region / cell-cell adhesion via plasma-membrane adhesion molecules ...mesaxon / Axonal growth inhibition (RHOA activation) / Basigin interactions / ganglioside GT1b binding / sialic acid binding / central nervous system myelination / central nervous system myelin formation / positive regulation of myelination / myelin sheath adaxonal region / cell-cell adhesion via plasma-membrane adhesion molecules / negative regulation of axon extension / paranode region of axon / Schmidt-Lanterman incisure / positive regulation of astrocyte differentiation / axon regeneration / transmission of nerve impulse / negative regulation of neuron differentiation / myelination / cellular response to mechanical stimulus / myelin sheath / negative regulation of neuron projection development / carbohydrate binding / negative regulation of neuron apoptotic process / cell adhesion / membrane raft / signaling receptor binding / protein kinase binding / protein homodimerization activity / plasma membrane
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Myelin-associated glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsPronker, M.F. / Janssen, B.J.C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research723.012.002 Netherlands
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis of myelin-associated glycoprotein adhesion and signalling.
Authors: Matti F Pronker / Suzanne Lemstra / Joost Snijder / Albert J R Heck / Dominique M E Thies-Weesie / R Jeroen Pasterkamp / Bert J C Janssen /
Abstract: Myelin-associated glycoprotein (MAG) is a myelin-expressed cell-adhesion and bi-directional signalling molecule. MAG maintains the myelin-axon spacing by interacting with specific neuronal ...Myelin-associated glycoprotein (MAG) is a myelin-expressed cell-adhesion and bi-directional signalling molecule. MAG maintains the myelin-axon spacing by interacting with specific neuronal glycolipids (gangliosides), inhibits axon regeneration and controls myelin formation. The mechanisms underlying MAG adhesion and signalling are unresolved. We present crystal structures of the MAG full ectodomain, which reveal an extended conformation of five Ig domains and a homodimeric arrangement involving membrane-proximal domains Ig4 and Ig5. MAG-oligosaccharide complex structures and biophysical assays show how MAG engages axonal gangliosides at domain Ig1. Two post-translational modifications were identified-N-linked glycosylation at the dimerization interface and tryptophan C-mannosylation proximal to the ganglioside binding site-that appear to have regulatory functions. Structure-guided mutations and neurite outgrowth assays demonstrate MAG dimerization and carbohydrate recognition are essential for its regeneration-inhibiting properties. The combination of trans ganglioside binding and cis homodimerization explains how MAG maintains the myelin-axon spacing and provides a mechanism for MAG-mediated bi-directional signalling.
History
DepositionJun 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / pdbx_validate_close_contact / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.1Jan 10, 2024Group: 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
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myelin-associated glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3008
Polymers55,1931
Non-polymers2,1077
Water00
1
A: Myelin-associated glycoprotein
hetero molecules

A: Myelin-associated glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,60016
Polymers110,3862
Non-polymers4,21414
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+4/31
Buried area9360 Å2
ΔGint31 kcal/mol
Surface area53000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)278.868, 278.868, 62.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Myelin-associated glycoprotein / Siglec-4a


Mass: 55192.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The two C-terminal residues of the construct and the cloning sites and purification tag are not observed in the electron density, probably because of disorder
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mag / Plasmid: pUPE107.03 / Cell (production host): HEK293ES / Cell line (production host): HEK293 / Organ (production host): kidney / Production host: Homo sapiens (human) / Variant (production host): GnTI-/- and EBNA1-expressing / References: UniProt: P20917
#2: 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
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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 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

CrystalDensity Matthews: 12.7 Å3/Da / Density % sol: 90.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM NaCl, 20 mM Tris/HCl pH 7.0, 7.7 % PEG 4000 (w/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 3.8→52.7 Å / Num. obs: 27623 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.233 / Net I/σ(I): 9.3
Reflection shellResolution: 3.8→4.03 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.685 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.565 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1URL, 4FRW, 1CS6, 3P3Y, 2YD6

1url

4frw

1cs6

3p3y

2yd6


Resolution: 3.8→52.701 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 1407 5.1 %Random selection
Rwork0.199 ---
obs0.2005 27582 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→52.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3750 0 137 0 3887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063998
X-RAY DIFFRACTIONf_angle_d1.3975474
X-RAY DIFFRACTIONf_dihedral_angle_d14.0341453
X-RAY DIFFRACTIONf_chiral_restr0.192644
X-RAY DIFFRACTIONf_plane_restr0.013703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8001-3.93590.41921360.4252588X-RAY DIFFRACTION99
3.9359-4.09340.30511440.28882599X-RAY DIFFRACTION100
4.0934-4.27960.26751350.22882581X-RAY DIFFRACTION100
4.2796-4.50510.20991340.19132632X-RAY DIFFRACTION100
4.5051-4.78720.20681530.17132597X-RAY DIFFRACTION100
4.7872-5.15650.18561480.16792587X-RAY DIFFRACTION100
5.1565-5.67490.19961520.16412628X-RAY DIFFRACTION100
5.6749-6.49480.25761260.1922612X-RAY DIFFRACTION100
6.4948-8.17790.20891390.18742643X-RAY DIFFRACTION100
8.1779-52.70610.20241400.17262708X-RAY DIFFRACTION100
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)
13.07072.8206-0.00965.624-0.19567.64830.15330.3321-0.2428-0.2551-0.1452-0.07640.1020.64950.03870.61170.2995-0.04920.85280.02541.031572.6668131.770116.8174
27.0678-6.45011.07396.61580.62321.3226-0.21730.05710.3476-0.3686-0.09330.9175-1.0455-0.92210.22371.61880.6964-0.16111.2655-0.15341.750746.095151.099913.5661
37.735-3.471-4.30715.17137.05682.19820.55130.1822-0.0957-0.6329-0.55110.2605-0.48040.09810.01272.25490.72870.01071.12010.05022.249837.2755192.779220.7303
49.06031.64932.74297.7618-3.96374.2039-0.07390.1602-0.4965-1.40820.1647-0.45761.25171.1894-0.06091.47870.20540.28260.6951-0.11271.228415.0655226.784327.6531
57.30451.14250.39537.3137-2.56726.2890.1201-0.60361.4817-0.4675-0.1667-0.1823-1.84140.025-0.04191.52250.04040.01170.591-0.01371.35816.7747263.631939.6996
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 138 )
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 238 )
3X-RAY DIFFRACTION3chain 'A' and (resid 239 through 323 )
4X-RAY DIFFRACTION4chain 'A' and (resid 324 through 409 )
5X-RAY DIFFRACTION5chain 'A' and (resid 410 through 506 )

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