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- PDB-7zty: Structure of Vps39 N-terminal domain from Chaetomium thermophilum -

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Basic information

Entry
Database: PDB / ID: 7zty
TitleStructure of Vps39 N-terminal domain from Chaetomium thermophilum
ComponentsCNH domain-containing protein
KeywordsTRANSPORT PROTEIN / tethering / membrane fusion / GTPase effector / HOPS
Function / homology
Function and homology information


vesicle-mediated transport / intracellular protein transport
Similarity search - Function
Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 1 / Vam6/VPS39/TRAP1 family / Vacuolar sorting protein 39 domain 1 / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / WD40-repeat-containing domain superfamily
Similarity search - Domain/homology
CNH domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsKiontke, S. / Ungermann, C. / Kuemmel, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFP944-P17 Germany
Citation
Journal: Elife / Year: 2022
Title: Structure of the HOPS tethering complex, a lysosomal membrane fusion machinery.
Authors: Dmitry Shvarev / Jannis Schoppe / Caroline König / Angela Perz / Nadia Füllbrunn / Stephan Kiontke / Lars Langemeyer / Dovile Januliene / Kilian Schnelle / Daniel Kümmel / Florian ...Authors: Dmitry Shvarev / Jannis Schoppe / Caroline König / Angela Perz / Nadia Füllbrunn / Stephan Kiontke / Lars Langemeyer / Dovile Januliene / Kilian Schnelle / Daniel Kümmel / Florian Fröhlich / Arne Moeller / Christian Ungermann /
Abstract: Lysosomes are essential for cellular recycling, nutrient signaling, autophagy, and pathogenic bacteria and viruses invasion. Lysosomal fusion is fundamental to cell survival and requires HOPS, a ...Lysosomes are essential for cellular recycling, nutrient signaling, autophagy, and pathogenic bacteria and viruses invasion. Lysosomal fusion is fundamental to cell survival and requires HOPS, a conserved heterohexameric tethering complex. On the membranes to be fused, HOPS binds small membrane-associated GTPases and assembles SNAREs for fusion, but how the complex fulfills its function remained speculative. Here, we used cryo-electron microscopy to reveal the structure of HOPS. Unlike previously reported, significant flexibility of HOPS is confined to its extremities, where GTPase binding occurs. The SNARE-binding module is firmly attached to the core, therefore, ideally positioned between the membranes to catalyze fusion. Our data suggest a model for how HOPS fulfills its dual functionality of tethering and fusion and indicate why it is an essential part of the membrane fusion machinery.
History
DepositionMay 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CNH domain-containing protein


Theoretical massNumber of molelcules
Total (without water)54,9441
Polymers54,9441
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.700, 102.750, 59.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CNH domain-containing protein


Mass: 54944.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0004950 / Production host: Escherichia coli (E. coli) / References: UniProt: G0RY05
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: 20% PEG MME 2000, 0.1 M MES pH 7.25

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97937 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.89→43.82 Å / Num. obs: 17010 / % possible obs: 99.1 % / Redundancy: 6.72 % / CC1/2: 0.993 / Rrim(I) all: 0.231 / Net I/σ(I): 7.7
Reflection shellResolution: 2.89→3.07 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2619 / CC1/2: 0.766 / Rrim(I) all: 1.24

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ALPHAFOLD

Resolution: 2.89→40.23 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.72 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2982 463 5 %
Rwork0.2686 --
obs0.2701 9264 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→40.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 0 10 2691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032726
X-RAY DIFFRACTIONf_angle_d0.5513697
X-RAY DIFFRACTIONf_dihedral_angle_d12.41026
X-RAY DIFFRACTIONf_chiral_restr0.045442
X-RAY DIFFRACTIONf_plane_restr0.005467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-3.310.32451490.29152831X-RAY DIFFRACTION98
3.31-4.170.3161530.26162906X-RAY DIFFRACTION100
4.17-40.230.27951610.26543064X-RAY DIFFRACTION100

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