[English] 日本語
Yorodumi
- PDB-5lfu: Myelin-associated glycoprotein (MAG) glycosylated and lysine-meth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lfu
TitleMyelin-associated glycoprotein (MAG) glycosylated and lysine-methylated full extracellular domain
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: 4.3 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: 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 1.1Sep 13, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / 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 / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _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 / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myelin-associated glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7398
Polymers55,1931
Non-polymers2,5467
Water0
1
A: Myelin-associated glycoprotein
hetero molecules

A: Myelin-associated glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,47916
Polymers110,3862
Non-polymers5,09314
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_776-y+2,-x+2,-z+7/61
Buried area9330 Å2
ΔGint49 kcal/mol
Surface area56230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.237, 101.237, 687.477
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 55192.984 Da / Num. of mol.: 1
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 / Organ (production host): Kidney / Production host: Homo sapiens (human) / Variant (production host): GntI-/- and EBNA1-expressing / References: UniProt: P20917

-
Sugars , 5 types, 7 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: 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
#4: 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
#5: 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.: 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
#6: 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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 7.9 Å3/Da
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Crystals were grown from protein that was modified by reductive lysine methylation. Protein was concentrated to 8.4 mg/mL, which was mixed 1:1 with reservoir solution. Crystals grew in a ...Details: Crystals were grown from protein that was modified by reductive lysine methylation. Protein was concentrated to 8.4 mg/mL, which was mixed 1:1 with reservoir solution. Crystals grew in a condition containing 200 mM NaOAc and 20 % PEG3350 (w/v).
PH range: 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97553 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97553 Å / Relative weight: 1
ReflectionResolution: 4.3→114.62 Å / Num. obs: 15430 / % possible obs: 100 % / Redundancy: 35.7 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 15.6
Reflection shellResolution: 4.3→4.81 Å / Redundancy: 36.9 % / Rmerge(I) obs: 3.937 / Mean I/σ(I) obs: 1.3 / % possible all: 100

-
Processing

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

1url

4frw

1cs6

3p3y

2yd6


Resolution: 4.3→114.579 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2955 769 4.99 %Random selection
Rwork0.2855 ---
obs0.2859 15425 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.3→114.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3776 0 166 0 3942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084058
X-RAY DIFFRACTIONf_angle_d1.3315563
X-RAY DIFFRACTIONf_dihedral_angle_d14.1551489
X-RAY DIFFRACTIONf_chiral_restr0.198663
X-RAY DIFFRACTIONf_plane_restr0.008710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3001-4.63210.44311410.43432849X-RAY DIFFRACTION100
4.6321-5.09820.39251670.38722800X-RAY DIFFRACTION100
5.0982-5.83590.36571500.34382875X-RAY DIFFRACTION100
5.8359-7.35250.41891520.37772940X-RAY DIFFRACTION100
7.3525-114.62010.23921590.23673192X-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)
18.27121.70361.44362.1991-2.00627.71790.11190.71590.03880.1285-0.79530.43871.2813-0.84250.62035.28220.59360.76092.5203-0.95533.641662.591923.2026297.4901
20.93122.60230.90611.68641.87950.07961.67191.0315-0.0485-3.5439-0.8248-1.8726-2.3557-1.9117-0.99385.61651.81390.30985.2793-0.37533.76642.688742.7499314.3286
35.7541-0.9896-3.27074.5132-0.04815.79932.22410.8717-1.7177-1.7769-1.2918-1.6013-1.8774-0.2881-0.53463.61110.29710.1512.8134-0.73913.526546.653467.5689349.7693
47.14.74614.91636.73930.39385.9158-0.46461.05331.951-0.6839-0.10131.2024-1.30350.67131.01744.2633-0.5651-0.05413.1353-0.24883.311738.807394.2976380.3178
54.7203-1.4771-0.58555.4335-2.43151.6125-0.7647-1.14340.8782-0.60870.82240.571-1.46742.0893-0.0614.6946-0.9515-0.57353.8163-0.1233.046239.8625113.3425416.1318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 139 )
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 238 )
3X-RAY DIFFRACTION3chain 'A' and (resid 239 through 323 )
4X-RAY DIFFRACTION4chain 'A' and (resid 324 through 411)
5X-RAY DIFFRACTION5chain 'A' and (resid 412 through 506)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more