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- PDB-5lfv: Crystal structure of glycosylated Myelin-associated glycoprotein ... -

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Basic information

Entry
Database: PDB / ID: 5lfv
TitleCrystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 with soaked trisaccharide ligand
ComponentsMyelin-associated glycoprotein
KeywordsCELL ADHESION / Myelin / Signaling
Function / homology
Function and homology information


mesaxon / Axonal growth inhibition (RHOA activation) / Basigin interactions / myelin sheath adaxonal region / ganglioside GT1b binding / sialic acid binding / central nervous system myelination / central nervous system myelin formation / : / negative regulation of axon extension ...mesaxon / Axonal growth inhibition (RHOA activation) / Basigin interactions / myelin sheath adaxonal region / ganglioside GT1b binding / sialic acid binding / central nervous system myelination / central nervous system myelin formation / : / negative regulation of axon extension / paranode region of axon / positive regulation of astrocyte differentiation / positive regulation of myelination / Schmidt-Lanterman incisure / axon regeneration / negative regulation of neuron differentiation / transmission of nerve impulse / 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
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: 2.3 Å
AuthorsPronker, M.F. / Janssen, B.J.C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organization for Scientific Research721.012.004 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
DepositionJul 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_unobs_or_zero_occ_atoms / 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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myelin-associated glycoprotein
B: Myelin-associated glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,62422
Polymers70,0292
Non-polymers4,59520
Water61334
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A: Myelin-associated glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,17912
Polymers35,0141
Non-polymers2,16511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myelin-associated glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,44410
Polymers35,0141
Non-polymers2,4309
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.605, 60.115, 79.471
Angle α, β, γ (deg.)71.86, 86.51, 82.95
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 35014.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mag / Plasmid: pUPE107.03 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Variant (production host): GnTI-/- and EBNA1-expressing / References: UniProt: P20917

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Sugars , 4 types, 10 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a6-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+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.: 2
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.: 5
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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Non-polymers , 3 types, 44 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.05 M tri-sodium citrate, 1.2 M ammonium sulfate, 3 % (w/v) isopropanol
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.3→56.79 Å / Num. obs: 32993 / % possible obs: 97.5 % / Redundancy: 4.5 % / CC1/2: 0.985 / Rmerge(I) obs: 0.157 / Net I/σ(I): 5.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.565 / % possible all: 95.7

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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

1url

4frw

1cs6


Resolution: 2.3→56.786 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.64
RfactorNum. reflection% reflectionSelection details
Rfree0.2541 1639 4.98 %Random selection
Rwork0.2238 ---
obs0.2253 32887 97.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→56.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4785 0 276 34 5095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025207
X-RAY DIFFRACTIONf_angle_d0.5837137
X-RAY DIFFRACTIONf_dihedral_angle_d12.3391862
X-RAY DIFFRACTIONf_chiral_restr0.026822
X-RAY DIFFRACTIONf_plane_restr0.003902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36770.3881180.35092503X-RAY DIFFRACTION94
2.3677-2.44410.37091420.33682653X-RAY DIFFRACTION98
2.4441-2.53150.3881230.32062617X-RAY DIFFRACTION98
2.5315-2.63280.35351420.3172583X-RAY DIFFRACTION98
2.6328-2.75270.3581490.30672625X-RAY DIFFRACTION98
2.7527-2.89780.3571440.28492574X-RAY DIFFRACTION96
2.8978-3.07930.32031380.26382614X-RAY DIFFRACTION98
3.0793-3.31710.24291360.23942663X-RAY DIFFRACTION99
3.3171-3.65080.24281620.21632518X-RAY DIFFRACTION96
3.6508-4.1790.22351140.20182663X-RAY DIFFRACTION99
4.179-5.26450.2041370.16892642X-RAY DIFFRACTION99
5.2645-56.80360.20341340.19392593X-RAY DIFFRACTION97
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)
18.95550.7714-3.14672.1893-1.06734.8718-0.01640.00020.13960.17720.06940.0233-0.0044-0.0682-0.03870.3725-0.0153-0.05380.24740.00240.2459-7.178332.597461.1127
20.14450.44512.47368.2313-4.34354.81250.0467-0.0417-0.0223-0.1357-0.0833-0.3404-0.11540.33710.08470.30830.0220.04650.51260.01890.38714.786945.207741.1094
31.4610.6929-2.19730.4721-1.21284.7497-0.29020.2129-0.1032-0.17640.1051-0.04440.2988-0.23630.1410.5780.02740.0890.39120.00610.439119.244849.78623.7845
45.7616-0.18122.44476.08790.54628.03060.16290.62430.3774-0.2926-0.1214-0.0487-1.08260.3339-0.05510.58790.02840.02770.48060.03150.38940.603768.838819.9636
53.74210.6809-3.26.0363-4.43645.64650.0187-0.36550.05880.4081-0.0662-0.0502-0.52320.53530.00440.5175-0.11660.04670.5483-0.17060.45234.411163.822352.1513
61.4928-0.3243-1.12550.8009-0.14975.4489-0.1931-0.3807-0.27560.43430.10190.13490.1385-0.20030.12070.85730.0660.18870.4582-0.01870.5856-15.497953.772683.967
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 138)
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 237)
3X-RAY DIFFRACTION3chain 'A' and (resid 238 through 329 )
4X-RAY DIFFRACTION4chain 'B' and (resid 19 through 138 )
5X-RAY DIFFRACTION5chain 'B' and (resid 139 through 237 )
6X-RAY DIFFRACTION6chain 'B' and (resid 238 through 329 )

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