[English] 日本語
Yorodumi
- PDB-7kdv: Murine core lysosomal multienzyme complex (LMC) composed of acid ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kdv
TitleMurine core lysosomal multienzyme complex (LMC) composed of acid beta-galactosidase (GLB1) and protective protein cathepsin A (PPCA, CTSA)
Components
  • Beta-galactosidase
  • Lysosomal protective protein
KeywordsHYDROLASE / glycosidase / protease / lysosome
Function / homology
Function and homology information


Keratan sulfate degradation / HS-GAG degradation / keratan sulfate proteoglycan catabolic process / response to cortisone / Sialic acid metabolism / response to Thyroglobulin triiodothyronine / carboxypeptidase C / Glycosphingolipid catabolism / galactose catabolic process / serine-type carboxypeptidase activity ...Keratan sulfate degradation / HS-GAG degradation / keratan sulfate proteoglycan catabolic process / response to cortisone / Sialic acid metabolism / response to Thyroglobulin triiodothyronine / carboxypeptidase C / Glycosphingolipid catabolism / galactose catabolic process / serine-type carboxypeptidase activity / galactoside binding / glycoprotein catabolic process / beta-galactosidase / MHC class II antigen presentation / ganglioside catabolic process / beta-galactosidase activity / negative regulation of chaperone-mediated autophagy / Neutrophil degranulation / regulation of protein stability / lysosome / hydrolase activity / Golgi apparatus / protein homodimerization activity / mitochondrion / proteolysis / extracellular space / membrane / cytoplasm
Similarity search - Function
Beta-galactosidase 1-like / : / Beta-galactosidase, first all-beta domain / Serine carboxypeptidase, serine active site / : / Beta-galactosidase second all-beta domain / Beta-galactosidase, galactose-binding domain / Serine carboxypeptidases, serine active site. / Peptidase S10, serine carboxypeptidase / Serine carboxypeptidases, histidine active site ...Beta-galactosidase 1-like / : / Beta-galactosidase, first all-beta domain / Serine carboxypeptidase, serine active site / : / Beta-galactosidase second all-beta domain / Beta-galactosidase, galactose-binding domain / Serine carboxypeptidases, serine active site. / Peptidase S10, serine carboxypeptidase / Serine carboxypeptidases, histidine active site / Serine carboxypeptidase / Serine carboxypeptidases, histidine active site. / Glycoside hydrolase, family 35, conserved site / Glycosyl hydrolases family 35 putative active site. / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / Galactose-binding-like domain superfamily / Alpha/Beta hydrolase fold / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Lysosomal protective protein / Beta-galactosidase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.59 Å
AuthorsGorelik, A. / Illes, K. / Hasan, S.M.N. / Nagar, B. / Mazhab-Jafari, M.T.
Funding support Canada, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MFE-164773 Canada
Canadian Institutes of Health Research (CIHR)MOP-133535 Canada
Canadian Institutes of Health Research (CIHR)419240 Canada
CitationJournal: Sci Adv / Year: 2021
Title: Structure of the murine lysosomal multienzyme complex core.
Authors: Alexei Gorelik / Katalin Illes / S M Naimul Hasan / Bhushan Nagar / Mohammad T Mazhab-Jafari /
Abstract: The enzymes β-galactosidase (GLB1) and neuraminidase 1 (NEU1; sialidase 1) participate in the degradation of glycoproteins and glycolipids in the lysosome. To remain active and stable, they ...The enzymes β-galactosidase (GLB1) and neuraminidase 1 (NEU1; sialidase 1) participate in the degradation of glycoproteins and glycolipids in the lysosome. To remain active and stable, they associate with PPCA [protective protein cathepsin A (CTSA)] into a high-molecular weight lysosomal multienzyme complex (LMC), of which several forms exist. Genetic defects in these three proteins cause the lysosomal storage diseases GM1-gangliosidosis/mucopolysaccharidosis IV type B, sialidosis, and galactosialidosis, respectively. To better understand the interactions between these enzymes, we determined the three-dimensional structure of the murine LMC core. This 0.8-MDa complex is composed of three GLB1 dimers and three CTSA dimers, adopting a triangular architecture maintained through six copies of a unique GLB1-CTSA polar interface. Mutations in this contact surface that occur in GM1-gangliosidosis prevent formation of the LMC in vitro. These findings may facilitate development of therapies for lysosomal storage disorders.
History
DepositionOct 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-22830
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-22830
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-galactosidase
B: Lysosomal protective protein
C: Beta-galactosidase
D: Lysosomal protective protein
E: Beta-galactosidase
F: Lysosomal protective protein
G: Beta-galactosidase
H: Lysosomal protective protein
I: Beta-galactosidase
J: Lysosomal protective protein
K: Beta-galactosidase
L: Lysosomal protective protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)759,89260
Polymers744,64412
Non-polymers15,24848
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, complex observed by gel filtration and dynamic light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area39720 Å2
ΔGint104 kcal/mol
Surface area248350 Å2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "K"
d_2ens_1chain "A"
d_3ens_1chain "E"
d_4ens_1chain "G"
d_5ens_1chain "I"
d_6ens_1chain "C"
d_1ens_2chain "L"
d_2ens_2chain "D"
d_3ens_2chain "F"
d_4ens_2chain "H"
d_5ens_2chain "J"
d_6ens_2chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRSERK1 - 600
d_12ens_1NAGNAGK
d_13ens_1NAGNAGK
d_14ens_1NAGNAGK
d_15ens_1NAGNAGK
d_16ens_1NAGNAGK
d_17ens_1NAGNAGK
d_18ens_1NAGNAGK
d_19ens_1NAGNAGK
d_21ens_1THRSERA1 - 600
d_22ens_1NAGNAGA
d_23ens_1NAGNAGA
d_24ens_1NAGNAGA
d_25ens_1NAGNAGA
d_26ens_1NAGNAGA
d_27ens_1NAGNAGA
d_28ens_1NAGNAGA
d_29ens_1NAGNAGA
d_31ens_1THRSERE1 - 600
d_32ens_1NAGNAGE
d_33ens_1NAGNAGE
d_34ens_1NAGNAGE
d_35ens_1NAGNAGE
d_36ens_1NAGNAGE
d_37ens_1NAGNAGE
d_38ens_1NAGNAGE
d_39ens_1NAGNAGE
d_41ens_1THRSERG1 - 600
d_42ens_1NAGNAGG
d_43ens_1NAGNAGG
d_44ens_1NAGNAGG
d_45ens_1NAGNAGG
d_46ens_1NAGNAGG
d_47ens_1NAGNAGG
d_48ens_1NAGNAGG
d_49ens_1NAGNAGG
d_51ens_1THRSERI1 - 600
d_52ens_1NAGNAGI
d_53ens_1NAGNAGI
d_54ens_1NAGNAGI
d_55ens_1NAGNAGI
d_56ens_1NAGNAGI
d_57ens_1NAGNAGI
d_58ens_1NAGNAGI
d_59ens_1NAGNAGI
d_61ens_1THRSERC1 - 600
d_62ens_1NAGNAGC
d_63ens_1NAGNAGC
d_64ens_1NAGNAGC
d_65ens_1NAGNAGC
d_66ens_1NAGNAGC
d_67ens_1NAGNAGC
d_68ens_1NAGNAGC
d_69ens_1NAGNAGC
d_11ens_2SERTYRL1 - 452
d_12ens_2NAGNAGL
d_13ens_2NAGNAGL
d_14ens_2NAGNAGL
d_15ens_2BMABMAL
d_21ens_2SERTYRD1 - 452
d_22ens_2NAGNAGD
d_23ens_2NAGNAGD
d_24ens_2NAGNAGD
d_25ens_2BMABMAD
d_31ens_2SERTYRF1 - 452
d_32ens_2NAGNAGF
d_33ens_2NAGNAGF
d_34ens_2NAGNAGF
d_35ens_2BMABMAF
d_41ens_2SERTYRH1 - 452
d_42ens_2NAGNAGH
d_43ens_2NAGNAGH
d_44ens_2NAGNAGH
d_45ens_2BMABMAH
d_51ens_2SERTYRJ1 - 452
d_52ens_2NAGNAGJ
d_53ens_2NAGNAGJ
d_54ens_2NAGNAGJ
d_55ens_2BMABMAJ
d_61ens_2SERTYRB1 - 452
d_62ens_2NAGNAGB
d_63ens_2NAGNAGB
d_64ens_2NAGNAGB
d_65ens_2BMABMAB

NCS ensembles :
ID
ens_1
ens_2

-
Components

#1: Protein
Beta-galactosidase / Acid beta-galactosidase / Lactase


Mass: 71450.180 Da / Num. of mol.: 6 / Mutation: R468Q, N517D, E534G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Glb1, Bgl, Glb-1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P23780, beta-galactosidase
#2: Protein
Lysosomal protective protein / Carboxypeptidase C / Carboxypeptidase L / Cathepsin A / Protective protein cathepsin A / PPCA / ...Carboxypeptidase C / Carboxypeptidase L / Cathepsin A / Protective protein cathepsin A / PPCA / Protective protein for beta-galactosidase


Mass: 52657.141 Da / Num. of mol.: 6 / Mutation: C32A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctsa, Ppgb / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P16675, carboxypeptidase C
#3: 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.: 12
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: 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.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#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.: 30 / Source method: obtained synthetically / 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
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: core lysosomal multienzyme complex composed of CTSA and GLB1
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 4.5 / Details: 50 mM sodium acetate pH 4.5, 50 mM NaCl
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid type: Homemade
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: two datasets: untilted and 40 degrees tilted
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 41 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 315

-
Processing

Software
NameVersionClassification
phenix.real_space_refine1.19rc6_4061refinement
PHENIX1.19rc6_4061refinement
EM software
IDNameVersionCategory
4cryoSPARC2CTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10cryoSPARC2initial Euler assignment
11cryoSPARC2final Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionDetails: Patch CTF implemented in cryoSPARC V2 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 4.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17591 / Symmetry type: POINT
Atomic model buildingB value: 116 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13THC

3thc

13THC1PDBexperimental model
21IVY

1ivy

11IVY2PDBexperimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 116.52 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004253184
ELECTRON MICROSCOPYf_angle_d0.838672420
ELECTRON MICROSCOPYf_chiral_restr0.0487902
ELECTRON MICROSCOPYf_plane_restr0.00669312
ELECTRON MICROSCOPYf_dihedral_angle_d12.346219506
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.00070461484779
ens_1d_3EELECTRON MICROSCOPYNCS constraints0.000712040365276
ens_1d_4GELECTRON MICROSCOPYNCS constraints0.000709758902306
ens_1d_5IELECTRON MICROSCOPYNCS constraints0.00070447071257
ens_1d_6CELECTRON MICROSCOPYNCS constraints0.000712657601518
ens_2d_2DELECTRON MICROSCOPYNCS constraints0.000711383251419
ens_2d_3FELECTRON MICROSCOPYNCS constraints0.0007039782168
ens_2d_4HELECTRON MICROSCOPYNCS constraints0.000707792476645
ens_2d_5JELECTRON MICROSCOPYNCS constraints0.000711143676864
ens_2d_6BELECTRON MICROSCOPYNCS constraints0.000712922505645

+
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