[English] 日本語
Yorodumi
- PDB-5oj2: Crystal structure of the chicken MDGA1 ectodomain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oj2
TitleCrystal structure of the chicken MDGA1 ectodomain
ComponentsMAM domain-containing glycosylphosphatidylinositol anchor protein 1
KeywordsCELL ADHESION / neuroligin-neurexin / synapse formation / austism spectrum disorders (ASDs) / synaptic transmission
Function / homology
Function and homology information


neuron migration / plasma membrane
Similarity search - Function
Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
MAM domain-containing glycosylphosphatidylinositol anchor protein 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsElegheert, J. / Clayton, A.J. / Aricescu, A.R.
Funding support United Kingdom, Canada, United States, 12items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G0700232 United Kingdom
Medical Research Council (United Kingdom)L009609 United Kingdom
Medical Research Council (United Kingdom)MC_UP_1201/15 United Kingdom
CIHRFDN-143206 Canada
CIHRNDD-144222 Canada
National Institutes of HealthR00 DC013805 United States
European Molecular Biology OrganizationALTF 1116-2012 United Kingdom
Marie-CurieFP7-328531 United Kingdom
Cancer Research UKC375/A10976 United Kingdom
National Institutes of HealthMH085926 United States
National Institutes of HealthGM105730 United States
Wellcome Trust090532/Z/09/Z United Kingdom
CitationJournal: Neuron / Year: 2017
Title: Structural Mechanism for Modulation of Synaptic Neuroligin-Neurexin Signaling by MDGA Proteins.
Authors: Elegheert, J. / Cvetkovska, V. / Clayton, A.J. / Heroven, C. / Vennekens, K.M. / Smukowski, S.N. / Regan, M.C. / Jia, W. / Smith, A.C. / Furukawa, H. / Savas, J.N. / de Wit, J. / Begbie, J. ...Authors: Elegheert, J. / Cvetkovska, V. / Clayton, A.J. / Heroven, C. / Vennekens, K.M. / Smukowski, S.N. / Regan, M.C. / Jia, W. / Smith, A.C. / Furukawa, H. / Savas, J.N. / de Wit, J. / Begbie, J. / Craig, A.M. / Aricescu, A.R.
History
DepositionJul 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
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_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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)210,34819
Polymers205,6952
Non-polymers4,65317
Water0
1
A: MAM domain-containing glycosylphosphatidylinositol anchor protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,20410
Polymers102,8471
Non-polymers2,3569
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MAM domain-containing glycosylphosphatidylinositol anchor protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1449
Polymers102,8471
Non-polymers2,2978
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.180, 109.040, 208.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein MAM domain-containing glycosylphosphatidylinositol anchor protein 1


Mass: 102847.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: MDGA1 / Plasmid: pHLsec / Cell line (production host): HEK293S GnTI-/- / Production host: Homo sapiens (human) / References: UniProt: Q0WYX8
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15
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: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES pH7.5, 3% w/v polyethylene glycol 8000

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97938 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 3.2→96.651 Å / Num. obs: 39616 / % possible obs: 100 % / Redundancy: 11 % / Rrim(I) all: 0.155 / Net I/σ(I): 13.6
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2874 / CC1/2: 0.622 / Rrim(I) all: 1.415 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX(dev_2044)refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→96.651 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.78
RfactorNum. reflection% reflection
Rfree0.2514 3851 5.14 %
Rwork0.2144 --
obs0.2163 39613 99.86 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Refinement stepCycle: LAST / Resolution: 3.2→96.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10788 0 299 0 11087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411348
X-RAY DIFFRACTIONf_angle_d0.98615499
X-RAY DIFFRACTIONf_dihedral_angle_d12.1116943
X-RAY DIFFRACTIONf_chiral_restr0.0421837
X-RAY DIFFRACTIONf_plane_restr0.0051980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.2390.38081220.37672522X-RAY DIFFRACTION99
3.239-3.280.39221640.34952525X-RAY DIFFRACTION100
3.28-3.32320.39831240.32882594X-RAY DIFFRACTION100
3.3232-3.36870.34051430.31192505X-RAY DIFFRACTION100
3.3687-3.41680.34461360.30242579X-RAY DIFFRACTION100
3.4168-3.46780.35991480.28172513X-RAY DIFFRACTION100
3.4678-3.5220.30631270.2832555X-RAY DIFFRACTION100
3.522-3.57980.28621290.26722553X-RAY DIFFRACTION100
3.5798-3.64150.31451300.26712536X-RAY DIFFRACTION100
3.6415-3.70770.26411340.26192534X-RAY DIFFRACTION100
3.7077-3.77910.36411330.25532549X-RAY DIFFRACTION100
3.7791-3.85620.31281430.25842569X-RAY DIFFRACTION100
3.8562-3.940.30521430.25482503X-RAY DIFFRACTION100
3.94-4.03170.28341400.24462548X-RAY DIFFRACTION100
4.0317-4.13250.27731520.21922538X-RAY DIFFRACTION100
4.1325-4.24430.19971850.18922482X-RAY DIFFRACTION100
4.2443-4.36910.21411440.18942537X-RAY DIFFRACTION100
4.3691-4.51020.21921210.17442586X-RAY DIFFRACTION100
4.5102-4.67140.16861300.1712559X-RAY DIFFRACTION100
4.6714-4.85840.20531540.17482504X-RAY DIFFRACTION100
4.8584-5.07950.23461600.16682494X-RAY DIFFRACTION100
5.0795-5.34730.1771150.15962594X-RAY DIFFRACTION100
5.3473-5.68230.2111440.1752541X-RAY DIFFRACTION100
5.6823-6.12090.2471530.18822529X-RAY DIFFRACTION100
6.1209-6.73680.2512890.20042576X-RAY DIFFRACTION100
6.7368-7.71120.26771370.21452543X-RAY DIFFRACTION100
7.7112-9.71390.22151250.18362543X-RAY DIFFRACTION100
9.7139-96.69510.23261260.21312508X-RAY DIFFRACTION98
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)
1-0.00021.1202-0.57764.755-1.49260.3104-0.0512-0.10830.04270.358-0.068-0.3653-0.0986-0.10640.15220.7712-0.0121-0.17230.65210.11550.78932.9703-62.21159.7875
21.91411.08741.94421.351.24233.4927-0.11480.3901-0.1233-0.31760.4559-0.3798-0.47540.3891-0.32740.6674-0.03870.1510.56540.14960.9616.0926-52.8006-28.5843
35.47123.5565-3.40654.0692-0.57984.9375-0.13840.23370.7831-0.26220.1192-0.1629-0.1710.48470.11050.376-0.0047-0.02840.60050.06040.4905-14.5186-74.9063-43.9547
41.98880.4825-0.12751.98692.04685.03450.516-0.39-0.14910.3774-0.3155-0.1470.2788-0.6874-0.12460.5614-0.07960.00340.49450.17760.4829-6.5598-109.026313.9906
50.169-0.9662-0.63764.0647-0.2948-0.1909-0.14070.18140.0497-0.60240.01750.11510.15430.03090.16830.9925-0.083-0.28640.7286-0.03460.9246-2.1136-67.0068-15.1495
61.2032-0.76052.47950.6598-1.72675.943-0.137-0.36010.04330.06560.49350.3115-0.1365-0.8357-0.35890.60530.0472-0.10290.7796-0.0050.852-6.4676-49.327819.9209
73.04-2.5793-1.62765.05561.79593.4917-0.086-0.1518-0.128-0.0856-0.11140.3747-0.2989-0.460.17980.52360.0276-0.09170.55170.03510.392913.9645-67.649940.7171
81.8323-0.20140.12982.81572.09785.38710.34140.2639-0.1012-0.23740.0998-0.4434-0.14390.1301-0.42080.36870.06480.11430.3297-0.01060.53228.1529-111.8448-8.5611
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 19:201)
2X-RAY DIFFRACTION2(chain A and resid 202:382)
3X-RAY DIFFRACTION3(chain A and resid 383:535)
4X-RAY DIFFRACTION4(chain A and resid 536:735)
5X-RAY DIFFRACTION5(chain B and resid 19:191)
6X-RAY DIFFRACTION6(chain B and resid 192:388)
7X-RAY DIFFRACTION7(chain B and resid 389:535)
8X-RAY DIFFRACTION8chain b and resid 734 and name SE

+
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