[English] 日本語
Yorodumi
- PDB-5llk: Crystal structure of human alpha-dystroglycan -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5llk
TitleCrystal structure of human alpha-dystroglycan
ComponentsDystroglycan
KeywordsCELL ADHESION / Dystroglycan / Extraellular Matrix Adhesion
Function / homology
Function and homology information


Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / dystroglycan complex / nerve maturation / muscle attachment / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / regulation of embryonic cell shape / retrograde trans-synaptic signaling by trans-synaptic protein complex / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / O-linked glycosylation ...Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / dystroglycan complex / nerve maturation / muscle attachment / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / regulation of embryonic cell shape / retrograde trans-synaptic signaling by trans-synaptic protein complex / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / O-linked glycosylation / contractile ring / regulation of gastrulation / calcium-dependent cell-matrix adhesion / microtubule anchoring / morphogenesis of an epithelial sheet / dystrophin-associated glycoprotein complex / laminin-1 binding / response to denervation involved in regulation of muscle adaptation / basement membrane organization / positive regulation of myelination / regulation of epithelial to mesenchymal transition / dystroglycan binding / branching involved in salivary gland morphogenesis / nerve development / skeletal muscle tissue regeneration / cellular response to cholesterol / photoreceptor ribbon synapse / vinculin binding / EGR2 and SOX10-mediated initiation of Schwann cell myelination / myelination in peripheral nervous system / node of Ranvier / costamere / angiogenesis involved in wound healing / commissural neuron axon guidance / response to muscle activity / axon regeneration / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / structural constituent of muscle / positive regulation of cell-matrix adhesion / postsynaptic cytosol / epithelial tube branching involved in lung morphogenesis / positive regulation of oligodendrocyte differentiation / regulation of synapse organization / alpha-actinin binding / plasma membrane raft / membrane protein ectodomain proteolysis / Non-integrin membrane-ECM interactions / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / ECM proteoglycans / negative regulation of MAPK cascade / heart morphogenesis / GABA-ergic synapse / laminin binding / tubulin binding / SH2 domain binding / nuclear periphery / negative regulation of cell migration / filopodium / axon guidance / morphogenesis of an epithelium / adherens junction / regulation of synaptic plasticity / sarcolemma / response to peptide hormone / Regulation of expression of SLITs and ROBOs / cellular response to mechanical stimulus / Golgi lumen / protein transport / lamellipodium / virus receptor activity / actin binding / basolateral plasma membrane / collagen-containing extracellular matrix / postsynaptic membrane / cytoskeleton / endoplasmic reticulum lumen / external side of plasma membrane / intracellular membrane-bounded organelle / focal adhesion / glutamatergic synapse / calcium ion binding / protein-containing complex binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dystroglycan, domain 2 / Dystroglycan-type cadherin-like / Dystroglycan, C-terminal / Alpha-dystroglycan domain 2 / DG-type SEA domain / Alpha-dystroglycan N-terminal domain 2 / Dystroglycan (Dystrophin-associated glycoprotein 1) / Alpha-Dystroglycan N-terminal domain 2 / DG-type SEA domain profile. / Dystroglycan-type cadherin-like domains. ...Dystroglycan, domain 2 / Dystroglycan-type cadherin-like / Dystroglycan, C-terminal / Alpha-dystroglycan domain 2 / DG-type SEA domain / Alpha-dystroglycan N-terminal domain 2 / Dystroglycan (Dystrophin-associated glycoprotein 1) / Alpha-Dystroglycan N-terminal domain 2 / DG-type SEA domain profile. / Dystroglycan-type cadherin-like domains. / Putative Ig domain / Cadherin-like superfamily / Alpha-Beta Plaits / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCovaceuszach, S. / Cassetta, A. / Lamba, D. / Brancaccio, A. / Bozzi, M. / Sciandra, F. / Bigotti, M.G. / Konarev, P.V.
CitationJournal: FEBS Open Bio / Year: 2017
Title: Structural flexibility of human alpha-dystroglycan.
Authors: Covaceuszach, S. / Bozzi, M. / Bigotti, M.G. / Sciandra, F. / Konarev, P.V. / Brancaccio, A. / Cassetta, A.
History
DepositionJul 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dystroglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6793
Polymers28,5541
Non-polymers1242
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint6 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.520, 71.520, 144.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-616-

HOH

-
Components

#1: Protein Dystroglycan / Dystrophin-associated glycoprotein 1


Mass: 28554.453 Da / Num. of mol.: 1 / Fragment: UNP residues 52-315 / Mutation: R168H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAG1 / Organ: Skeletal Muscle / Plasmid: pHis-Trx / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14118
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.8 M Sodium Citrate / PH range: 6.8-7.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 22, 2016 / Details: Pt-coated mirror
RadiationMonochromator: Si(111) Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48 Å / Num. obs: 25220 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 32 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 21.6
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 1.61 / CC1/2: 0.868 / % possible all: 94.5

-
Processing

Software
NameVersionClassification
PHENIX(dev_2328: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U2C

1u2c


Resolution: 1.8→35.76 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 24.21
Details: Refined: Bulk Solvent + coordinates + TLS + ADP + occupancies Refinement Target: ML TLS refinement: 6 groups Occupancies: selected residues with low electron density
RfactorNum. reflection% reflection
Rfree0.1947 1258 5 %
Rwork0.1633 --
obs0.1649 25153 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→35.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1702 0 8 129 1839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011747
X-RAY DIFFRACTIONf_angle_d1.0122377
X-RAY DIFFRACTIONf_dihedral_angle_d17.8991051
X-RAY DIFFRACTIONf_chiral_restr0.063277
X-RAY DIFFRACTIONf_plane_restr0.007305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.87210.36451340.37012523X-RAY DIFFRACTION94
1.8721-1.95730.29841380.24872622X-RAY DIFFRACTION98
1.9573-2.06050.27771400.20152667X-RAY DIFFRACTION99
2.0605-2.18960.19271400.18382681X-RAY DIFFRACTION100
2.1896-2.35860.19531410.17062672X-RAY DIFFRACTION100
2.3586-2.59590.21881400.17712673X-RAY DIFFRACTION99
2.5959-2.97140.22971420.17662679X-RAY DIFFRACTION100
2.9714-3.7430.17871420.15352698X-RAY DIFFRACTION100
3.743-35.7670.15671410.13272680X-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)
11.45110.27730.43541.20590.12721.6474-0.0096-0.0661-0.3679-0.0374-0.1813-0.22860.43060.27140.00020.4999-0.0777-0.04290.41430.03220.4416-20.9156-13.968238.0541
20.96560.0302-0.67080.83430.44011.03380.04790.0254-0.181-0.0593-0.2874-0.0730.02320.42170.0010.388-0.0462-0.05490.3016-0.01260.36-26.1584-11.416139.4008
30.493-0.19950.7350.1944-0.00381.8464-0.0788-0.12060.11240.1731-0.1001-0.0614-0.50430.0623-0.08570.4632-0.11-0.04220.34640.01050.3416-23.8242-3.21125.7148
40.28730.10820.13930.38850.31470.31250.2509-0.3606-0.01170.4518-0.0815-0.13580.3294-0.09420.00030.4038-0.0209-0.04290.28480.0220.3176-26.2663-13.489917.5766
52.48570.70240.0662.8537-0.60793.14270.02510.07370.123-0.0823-0.081-0.1171-0.19460.17-0.00010.2608-0.0018-0.00870.20820.03390.263-27.7025-4.43327.6753
60.8071-0.60530.03620.46140.02230.33110.303-0.27330.35310.2097-0.3537-0.1587-0.56960.25650.01350.4063-0.0936-0.0090.26060.03380.321-26.53280.98067.1826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 61 through 115 )
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 143 )
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 203 )
4X-RAY DIFFRACTION4chain 'A' and (resid 204 through 218 )
5X-RAY DIFFRACTION5chain 'A' and (resid 219 through 292 )
6X-RAY DIFFRACTION6chain 'A' and (resid 293 through 304 )

+
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