[English] 日本語
Yorodumi
- PDB-7zeu: Crystal structure of human Clusterin, crystal form II -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zeu
TitleCrystal structure of human Clusterin, crystal form II
ComponentsClusterin
KeywordsCHAPERONE / molecular chaperone / complement system / Alzheimer's disease
Function / homology
Function and homology information


immune complex clearance / perinuclear endoplasmic reticulum lumen / regulation of neuronal signal transduction / positive regulation of neurofibrillary tangle assembly / central nervous system myelin maintenance / response to misfolded protein / negative regulation of response to endoplasmic reticulum stress / spherical high-density lipoprotein particle / Terminal pathway of complement / protein targeting to lysosome involved in chaperone-mediated autophagy ...immune complex clearance / perinuclear endoplasmic reticulum lumen / regulation of neuronal signal transduction / positive regulation of neurofibrillary tangle assembly / central nervous system myelin maintenance / response to misfolded protein / negative regulation of response to endoplasmic reticulum stress / spherical high-density lipoprotein particle / Terminal pathway of complement / protein targeting to lysosome involved in chaperone-mediated autophagy / protein carrier chaperone / chromaffin granule / regulation of amyloid-beta clearance / microglial cell proliferation / reverse cholesterol transport / misfolded protein binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / apical dendrite / protein import / complement activation / positive regulation of ubiquitin-dependent protein catabolic process / negative regulation of amyloid fibril formation / Antimicrobial peptides / neurofibrillary tangle / low-density lipoprotein particle receptor binding / positive regulation of amyloid fibril formation / positive regulation of amyloid-beta formation / negative regulation of release of cytochrome c from mitochondria / amyloid-beta clearance / negative regulation of amyloid-beta formation / complement activation, classical pathway / chaperone-mediated protein complex assembly / negative regulation of protein-containing complex assembly / positive regulation of intrinsic apoptotic signaling pathway / : / intrinsic apoptotic signaling pathway / platelet alpha granule lumen / Regulation of Complement cascade / release of cytochrome c from mitochondria / positive regulation of protein-containing complex assembly / microglial cell activation / positive regulation of NF-kappaB transcription factor activity / positive regulation of receptor-mediated endocytosis / lipid metabolic process / response to virus / tau protein binding / cell morphogenesis / positive regulation of nitric oxide biosynthetic process / positive regulation of tumor necrosis factor production / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Platelet degranulation / regulation of cell population proliferation / protein-folding chaperone binding / : / amyloid-beta binding / regulation of apoptotic process / blood microparticle / negative regulation of neuron apoptotic process / mitochondrial inner membrane / protein stabilization / positive regulation of apoptotic process / receptor ligand activity / signaling receptor binding / innate immune response / intracellular membrane-bounded organelle / synapse / ubiquitin protein ligase binding / positive regulation of gene expression / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / Golgi apparatus / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / nucleus / cytoplasm / cytosol
Similarity search - Function
Clusterin-like / Clusterin, N-terminal / Clusterin, C-terminal / Clusterin / Clusterin, conserved site / Clusterin / Clusterin signature 1. / Clusterin signature 2. / CLUSTERIN Beta chain / CLUSTERIN alpha chain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsYuste-Checa, P. / Bracher, A. / Hartl, F.U.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2025
Title: Structural analyses define the molecular basis of clusterin chaperone function.
Authors: Yuste-Checa, P. / Carvajal, A.I. / Mi, C. / Paatz, S. / Hartl, F.U. / Bracher, A.
#1: Journal: Biorxiv / Year: 2024
Title: Hydrophobic tails enable diverse functions of the extracellular chaperone clusterin
Authors: Yuste-Checa, P. / Carvajal, A.I. / Mi, C. / Paatz, S. / Ulrich Hartl, F. / Bracher, A.
History
DepositionMar 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Apr 23, 2025Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Sep 17, 2025Group: Database references / Category: citation / citation_author

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Clusterin
D: Clusterin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,74814
Polymers94,0782
Non-polymers3,67012
Water00
1
A: Clusterin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5697
Polymers47,0391
Non-polymers1,5306
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Clusterin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1797
Polymers47,0391
Non-polymers2,1406
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)194.440, 46.438, 155.173
Angle α, β, γ (deg.)90.000, 127.200, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Clusterin / Aging-associated gene 4 protein / Apolipoprotein J / Apo-J / Complement cytolysis inhibitor / CLI / ...Aging-associated gene 4 protein / Apolipoprotein J / Apo-J / Complement cytolysis inhibitor / CLI / Complement-associated protein SP-40 / 40 / Ku70-binding protein 1 / NA1/NA2 / Sulfated glycoprotein 2 / SGP-2 / Testosterone-repressed prostate message 2 / TRPM-2


Mass: 47038.852 Da / Num. of mol.: 2 / Fragment: Clu-delta(214-238) / Mutation: deletion(214-238)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLU, APOJ, CLI, KUB1, AAG4 / Plasmid: pB-T-PAF / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P10909
#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.: 5
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
#3: 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.: 7 / 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: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.53 % / Mosaicity: 0.29 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 24% PEG-1500, 20% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 3.5→48.59 Å / Num. obs: 14413 / % possible obs: 99.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 108.57 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.085 / Rrim(I) all: 0.229 / Net I/σ(I): 6.1 / Num. measured all: 103733 / Scaling rejects: 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.5-3.835.71.5171944934080.6190.6721.6641.499.6
8.57-48.596.80.077713010530.9950.0310.08319.399.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.582
Highest resolutionLowest resolution
Rotation77.69 Å3.5 Å

-
Processing

Software
NameVersionClassification
XDSVERSION Feb 5, 2021data reduction
Aimless0.7.4data scaling
MOLREP11.4.06phasing
PHENIX1.19.2-4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZET

7zet


Resolution: 3.5→29.77 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.05 / Stereochemistry target values: ML
Details: The Clusterin construct is a glyco-protein, which was expressed in the presence of the alpha-mannosidase I inhibitor kifunensine. Kifunensine prevents trimming of mannose moieties, resulting ...Details: The Clusterin construct is a glyco-protein, which was expressed in the presence of the alpha-mannosidase I inhibitor kifunensine. Kifunensine prevents trimming of mannose moieties, resulting in oligo-mannose N-glycans, and thereby prevents processing to mature complex N-glycans (Chang et al., Structure 15, 267(2007), Fig. 1B). Asn residues 86, 103, 145, 291, 354 and 374 are expected to carry predominantly NAG-NAG-BMA-(3->1)MAN-MAN-MAN (6->1)-MAN (3->1)MAN-MAN (6->1)MAN-MAN N-glycan trees (Chang et al., Structure 15, 267(2007), Fig. 1B).
RfactorNum. reflection% reflection
Rfree0.2836 692 4.83 %
Rwork0.2352 13639 -
obs0.2375 14331 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 264.62 Å2 / Biso mean: 137.2869 Å2 / Biso min: 53.43 Å2
Refinement stepCycle: final / Resolution: 3.5→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5726 0 238 0 5964
Biso mean--182.16 --
Num. residues----724
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.770.37951560.32032665282199
3.77-4.150.3371560.259526832839100
4.15-4.750.29871310.21762710284199
4.75-5.970.26711360.246227322868100
5.97-29.770.23321130.210428492962100

+
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