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- PDB-9nvk: mjHSP16.5 36mer (+lysozyme, 75C) -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9nvk
TitlemjHSP16.5 36mer (+lysozyme, 75C)
ComponentsSmall heat shock protein HSP16.5
KeywordsCHAPERONE / sHSP / thermophile / holdase
Function / homology
Function and homology information


protein complex oligomerization / response to salt stress / protein folding chaperone / response to hydrogen peroxide / unfolded protein binding / protein folding / response to heat / protein stabilization / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function
Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone
Similarity search - Domain/homology
Small heat shock protein HSP16.5
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsMiller, A.P. / Reichow, S.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI) United States
CitationJournal: To Be Published
Title: Mechanisms of small heat shock protein client sequestration and induced polydispersity
Authors: Miller, A.P. / Reichow, S.L.
History
DepositionMar 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Small heat shock protein HSP16.5
B: Small heat shock protein HSP16.5
D: Small heat shock protein HSP16.5
E: Small heat shock protein HSP16.5
F: Small heat shock protein HSP16.5
G: Small heat shock protein HSP16.5
H: Small heat shock protein HSP16.5
I: Small heat shock protein HSP16.5
J: Small heat shock protein HSP16.5
K: Small heat shock protein HSP16.5
L: Small heat shock protein HSP16.5
M: Small heat shock protein HSP16.5
N: Small heat shock protein HSP16.5
P: Small heat shock protein HSP16.5
Q: Small heat shock protein HSP16.5
R: Small heat shock protein HSP16.5
U: Small heat shock protein HSP16.5
V: Small heat shock protein HSP16.5
W: Small heat shock protein HSP16.5
X: Small heat shock protein HSP16.5
Y: Small heat shock protein HSP16.5
Z: Small heat shock protein HSP16.5
b: Small heat shock protein HSP16.5
c: Small heat shock protein HSP16.5
d: Small heat shock protein HSP16.5
e: Small heat shock protein HSP16.5
f: Small heat shock protein HSP16.5
g: Small heat shock protein HSP16.5
h: Small heat shock protein HSP16.5
i: Small heat shock protein HSP16.5
j: Small heat shock protein HSP16.5
k: Small heat shock protein HSP16.5
l: Small heat shock protein HSP16.5
m: Small heat shock protein HSP16.5
n: Small heat shock protein HSP16.5
o: Small heat shock protein HSP16.5


Theoretical massNumber of molelcules
Total (without water)592,92036
Polymers592,92036
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Small heat shock protein HSP16.5


Mass: 16469.990 Da / Num. of mol.: 36
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0285 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57733
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: mjHSP16.5 36mer (+lysozyme, 75C) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31911 / Details: This map was used for model building / Symmetry type: POINT
RefinementHighest resolution: 4.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00433042
ELECTRON MICROSCOPYf_angle_d0.83244596
ELECTRON MICROSCOPYf_dihedral_angle_d12.4412886
ELECTRON MICROSCOPYf_chiral_restr0.0745291
ELECTRON MICROSCOPYf_plane_restr0.0065687

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