[English] 日本語
Yorodumi
- PDB-6r99: Crystal Structure of Human CLN protein 5 (Ceroid Lipofuscinosis N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6r99
TitleCrystal Structure of Human CLN protein 5 (Ceroid Lipofuscinosis Neuronal Protein 5)
ComponentsCeroid-lipofuscinosis neuronal protein 5
KeywordsUNKNOWN FUNCTION / neuronal ceroid lipofiscinosis / CLN5 / circularly-permuted papain-like fold / glycoprotein
Function / homologyCeroid-lipofuscinosis neuronal protein 5 / Ceroid-lipofuscinosis neuronal protein 5 / lysosome / Ceroid-lipofuscinosis, neuronal 5, isoform CRA_a
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsLuebben, A.V. / Sheldrick, G.M.
CitationJournal: Sci Adv / Year: 2022
Title: Cln5 represents a new type of cysteine-based S -depalmitoylase linked to neurodegeneration.
Authors: Luebben, A.V. / Bender, D. / Becker, S. / Crowther, L.M. / Erven, I. / Hofmann, K. / Soding, J. / Klemp, H. / Bellotti, C. / Stauble, A. / Qiu, T. / Kathayat, R.S. / Dickinson, B.C. / ...Authors: Luebben, A.V. / Bender, D. / Becker, S. / Crowther, L.M. / Erven, I. / Hofmann, K. / Soding, J. / Klemp, H. / Bellotti, C. / Stauble, A. / Qiu, T. / Kathayat, R.S. / Dickinson, B.C. / Gartner, J. / Sheldrick, G.M. / Kratzner, R. / Steinfeld, R.
History
DepositionApr 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / 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 / pdbx_struct_special_symmetry / refine / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _refine.pdbx_diffrn_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 2.1Sep 28, 2022Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ceroid-lipofuscinosis neuronal protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3595
Polymers46,9061
Non-polymers1,4534
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint32 kcal/mol
Surface area14650 Å2
Unit cell
Length a, b, c (Å)58.420, 58.420, 179.050
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-634-

HOH

-
Components

#1: Protein Ceroid-lipofuscinosis neuronal protein 5 / Ceroid-lipofuscinosis / neuronal 5 / isoform CRA_a


Mass: 46905.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: protein contains selenomethionine and is glycosylated
Source: (gene. exp.) Homo sapiens (human) / Gene: CLN5, hCG_28176 / Plasmid: pcDNA3 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: A0A024R644
#2: 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
#3: 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
#4: 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.: 2
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, magnesium nitrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.65→44.046 Å / Num. obs: 19772 / % possible obs: 100 % / Redundancy: 27.822 % / Biso Wilson estimate: 63.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.229 / Rrim(I) all: 0.233 / Χ2: 1.034 / Net I/σ(I): 13.53 / Num. measured all: 550105 / Scaling rejects: 1064
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.65-2.7210.1761.2941.5514369141014120.7591.362100
2.72-2.810.0671.181.7514487144014390.7131.24499.9
2.8-2.8814.6770.9382.7620343138613860.8820.972100
2.88-2.9716.4860.7223.8822256135013500.910.745100
2.97-3.0616.3480.5525.0122102135213520.9560.57100
3.06-3.1729.9720.9636.4736746122612260.9670.979100
3.17-3.2935.0940.8377.4843727124612460.9790.849100
3.29-3.4334.8890.6069.7141448118811880.9850.615100
3.43-3.5834.9060.47911.938432110111010.990.486100
3.58-3.7537.8510.38914.5741030108410840.9930.395100
3.75-3.9537.1590.30817.4437419100710070.9960.312100
3.95-4.1937.0270.25620.71365469879870.9960.259100
4.19-4.4834.9750.19124.67316179049040.9970.194100
4.48-4.8435.8680.16427.01303448468460.9980.166100
4.84-5.3138.2310.1529.35301267887880.9990.152100
5.31-5.9337.5830.14329.06259326906900.9990.145100
5.93-6.8534.4450.13428.72208396056050.9980.136100
6.85-8.3937.6610.10833.2203375405400.9990.109100
8.39-11.8636.5270.0843.611475740440410.081100
11.86-44.04633.4010.07846.16724821921710.07999.1

-
Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→44.046 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 28.58 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2471 533 5.15 %
Rwork0.2206 9821 -
obs0.222 10354 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.8 Å2 / Biso mean: 57.0408 Å2 / Biso min: 29.11 Å2
Refinement stepCycle: final / Resolution: 2.7→44.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 95 35 2441
Biso mean--61.21 53.54 -
Num. residues----285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042494
X-RAY DIFFRACTIONf_angle_d0.7273406
X-RAY DIFFRACTIONf_chiral_restr0.044369
X-RAY DIFFRACTIONf_plane_restr0.005429
X-RAY DIFFRACTIONf_dihedral_angle_d3.2431427
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7002-2.97180.37581160.272224222538
2.9718-3.40170.3021350.239523882523
3.4017-4.28520.23171410.204424332574
4.2852-44.05210.21831410.214325782719

+
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://pdbjlc1.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