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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) / compact myelin / ganglioside GT1b binding / central nervous system myelination / sialic acid binding / myelin sheath adaxonal region / positive regulation of myelination / central nervous system myelin formation / negative regulation of axon extension ...mesaxon / Axonal growth inhibition (RHOA activation) / compact myelin / ganglioside GT1b binding / central nervous system myelination / sialic acid binding / myelin sheath adaxonal region / positive regulation of myelination / central nervous system myelin formation / negative regulation of axon extension / cell-cell adhesion via plasma-membrane adhesion molecules / 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 / negative regulation of neuron projection development / myelin sheath / 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 / 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: Pronker, M.F. / Lemstra, S. / Snijder, J. / Heck, A.J. / Thies-Weesie, D.M. / Pasterkamp, R.J. / Janssen, B.J.
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

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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 / 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 / N-Acetylglucosamine


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 / Glycerol


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


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


Mass: 18.015 Da / Num. of mol.: 34 / 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: 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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