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- PDB-7zet: Crystal structure of human Clusterin, crystal form I -

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Basic information

Entry
Database: PDB / ID: 7zet
TitleCrystal structure of human Clusterin, crystal form I
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 ...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 / protein carrier chaperone / Terminal pathway of complement / protein targeting to lysosome involved in chaperone-mediated autophagy / chromaffin granule / regulation of amyloid-beta clearance / microglial cell proliferation / misfolded protein binding / apical dendrite / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / reverse cholesterol transport / positive regulation of ubiquitin-dependent protein catabolic process / protein import / negative regulation of amyloid fibril formation / complement activation / neurofibrillary tangle / positive regulation of tau-protein kinase activity / Antimicrobial peptides / positive regulation of amyloid fibril formation / low-density lipoprotein particle receptor binding / positive regulation of amyloid-beta formation / negative regulation of release of cytochrome c from mitochondria / negative regulation of amyloid-beta formation / chaperone-mediated protein complex assembly / negative regulation of protein-containing complex assembly / chaperone-mediated protein folding / positive regulation of intrinsic apoptotic signaling pathway / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / platelet alpha granule lumen / complement activation, classical pathway / Regulation of Complement cascade / microglial cell activation / positive regulation of protein-containing complex assembly / response to virus / tau protein binding / cell morphogenesis / lipid metabolic process / positive regulation of receptor-mediated endocytosis / positive regulation of tumor necrosis factor production / positive regulation of nitric oxide biosynthetic process / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Platelet degranulation / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / regulation of cell population proliferation / protein-folding chaperone binding / regulation of apoptotic process / collagen-containing extracellular matrix / negative regulation of neuron apoptotic process / mitochondrial inner membrane / protein stabilization / blood microparticle / positive regulation of apoptotic process / protein heterodimerization activity / intracellular membrane-bounded organelle / innate immune response / signaling receptor binding / synapse / ubiquitin protein ligase binding / protein-containing complex binding / positive regulation of gene expression / perinuclear region of cytoplasm / Golgi apparatus / cell surface / 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: 2.8 Å
AuthorsYuste-Checa, P. / Bracher, A. / Hartl, F.U.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Crystal structure of human Clusterin, crystal form I
Authors: Yuste-Checa, P. / Bracher, A. / Hartl, F.U.
History
DepositionMar 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Clusterin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9357
Polymers47,0391
Non-polymers1,8966
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint29 kcal/mol
Surface area22220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.742, 43.808, 102.800
Angle α, β, γ (deg.)90.000, 107.290, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 1 / 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.: 1
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: 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-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
#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.: 4 / 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

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.07 % / Mosaicity: 0.25 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 30% PEG-4000, 0.2 M NH4-acetate, 0.1 M Na-citrate pH 5.6

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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: 2.8→49.08 Å / Num. obs: 13861 / % possible obs: 98.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 75.02 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.088 / Rrim(I) all: 0.172 / Net I/σ(I): 5.9 / Num. measured all: 50668 / Scaling rejects: 4
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
2.8-2.953.61.656710819660.41711.9420.796.1
8.85-49.083.20.04114714630.9970.0260.04919.495.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.596
Highest resolutionLowest resolution
Rotation61.53 Å3.14 Å

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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: AlphaFold AF-P10909-F1-model_v1.pdb

Resolution: 2.8→27.61 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.41 / 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, which prevents trimming of mannose moieties, resulting in ...Details: The Clusterin construct is a glyco-protein, which was expressed in the presence of the alpha-mannosidase I inhibitor kifunensine, which 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
Rfree0.2742 701 5.07 %
Rwork0.2322 13113 -
obs0.2346 13814 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.13 Å2 / Biso mean: 80.9892 Å2 / Biso min: 36.33 Å2
Refinement stepCycle: final / Resolution: 2.8→27.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 0 123 0 3130
Biso mean--119.48 --
Num. residues----377
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 (%)
2.8-3.020.40191410.35652539268096
3.02-3.320.39091290.31832627275698
3.32-3.80.31691530.23942593274698
3.8-4.780.23891260.19892664279099
4.78-27.610.23361520.20922690284298

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