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- PDB-2k3w: NMR structure of VPS4A-MIT-CHMP6 -

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Basic information

Entry
Database: PDB / ID: 2k3w
TitleNMR structure of VPS4A-MIT-CHMP6
Components
  • Charged multivesicular body protein 6
  • Vacuolar protein sorting-associating protein 4A
KeywordsPROTEIN TRANSPORT / ESRCT-III / CHMP6 / MIT / ATP-binding / Membrane / Nucleotide-binding / Transport / Coiled coil / Endosome / Lipoprotein / Myristate
Function / homology
Function and homology information


vesicle uncoating / ESCRT complex disassembly / actomyosin contractile ring contraction / ESCRT III complex assembly / endosomal vesicle fusion / late endosomal microautophagy / mitotic cytokinesis checkpoint signaling / positive regulation of viral budding via host ESCRT complex / negative regulation of cytokinesis / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway ...vesicle uncoating / ESCRT complex disassembly / actomyosin contractile ring contraction / ESCRT III complex assembly / endosomal vesicle fusion / late endosomal microautophagy / mitotic cytokinesis checkpoint signaling / positive regulation of viral budding via host ESCRT complex / negative regulation of cytokinesis / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / negative regulation of epidermal growth factor-activated receptor activity / late endosome to lysosome transport via multivesicular body sorting pathway / intracellular cholesterol transport / multivesicular body-lysosome fusion / amphisome membrane / nuclear envelope organization / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / late endosome to vacuole transport via multivesicular body sorting pathway / cytoskeleton-dependent cytokinesis / mitotic nuclear membrane reassembly / ATP-dependent protein disaggregase activity / nuclear membrane reassembly / multivesicular body sorting pathway / Sealing of the nuclear envelope (NE) by ESCRT-III / vacuole organization / vesicle budding from membrane / positive regulation of exosomal secretion / midbody abscission / protein targeting to lysosome / membrane fission / plasma membrane repair / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body membrane / multivesicular body assembly / regulation of mitotic spindle assembly / Flemming body / Translation of Replicase and Assembly of the Replication Transcription Complex / vesicle-fusing ATPase / vacuolar membrane / endosomal transport / mitotic metaphase chromosome alignment / Macroautophagy / ATPase complex / nucleus organization / viral budding via host ESCRT complex / regulation of protein catabolic process / viral release from host cell / autophagosome membrane / autophagosome maturation / Pyroptosis / nuclear pore / regulation of protein localization to plasma membrane / vesicle-mediated transport / multivesicular body / Endosomal Sorting Complex Required For Transport (ESCRT) / viral budding from plasma membrane / HCMV Late Events / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / kinetochore / autophagy / spindle pole / late endosome membrane / late endosome / protein transport / regulation of protein localization / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / early endosome / lysosome / endosome / endosome membrane / lysosomal membrane / cell division / centrosome / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / extracellular exosome / ATP binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Vacuolar protein sorting-associated protein 4, MIT domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT (microtubule interacting and transport) domain / MIT domain superfamily / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / : / Vps4 C terminal oligomerisation domain / Snf7 family ...Vacuolar protein sorting-associated protein 4, MIT domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT (microtubule interacting and transport) domain / MIT domain superfamily / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / : / Vps4 C terminal oligomerisation domain / Snf7 family / Snf7 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Charged multivesicular body protein 6 / Vacuolar protein sorting-associated protein 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKieffer, C. / Skalicky, J.J. / Morita, E. / De Domini, I. / Ward, D.M. / Kaplan, J. / Sundquist, W.I.
CitationJournal: Dev.Cell / Year: 2008
Title: Two distinct modes of ESCRT-III recognition are required for VPS4 functions in lysosomal protein targeting and HIV-1 budding
Authors: Kieffer, C. / Skalicky, J.J. / Morita, E. / De Domenico, I. / Ward, D.M. / Kaplan, J. / Sundquist, W.I.
History
DepositionMay 19, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar protein sorting-associating protein 4A
B: Charged multivesicular body protein 6


Theoretical massNumber of molelcules
Total (without water)11,7002
Polymers11,7002
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Vacuolar protein sorting-associating protein 4A / Protein SKD2 / hVPS4 / VPS4-1


Mass: 9865.304 Da / Num. of mol.: 1 / Fragment: MIT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS4A, VPS4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UN37
#2: Protein/peptide Charged multivesicular body protein 6 / Chromatin-modifying protein 6 / Vacuolar protein sorting-associated protein 20 / hVps20


Mass: 1835.034 Da / Num. of mol.: 1 / Fragment: residues 166-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHMP6, VPS20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96FZ7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D C(CO)NH
1313D HNCA
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D HN(CO)CA
1713D (H)CCH-COSY
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11223D CBCA(CO)NH
11323D C(CO)NH
11423D HNCA
11523D HN(CA)CB
11623D HBHA(CO)NH
11723D HN(CO)CA
11823D H(CCO)NH
11923D (H)CCH-TOCSY
12023D (H)CCH-COSY
12123D 1H-15N NOESY
12223D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.4 mM [U-99% 13C; U-99% 15N] protein, 1.8 mM peptide, 25 mM sodium phosphate, 50 mM sodium chloride, 1 mM EDTA, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
21.22 mM [U-99% 13C; U-99% 15N] peptide, 1.55 mM protein, 25 mM sodium phosphate, 50 mM sodium chloride, 1 mM EDTA, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.4 mMentity_1[U-99% 13C; U-99% 15N]1
1.8 mMentity_21
25 mMsodium phosphate1
50 mMsodium chloride1
1 mMEDTA1
10 %D2O1
1.22 mMentity_2[U-99% 13C; U-99% 15N]2
1.55 mMentity_12
25 mMsodium phosphate2
50 mMsodium chloride2
1 mMEDTA2
10 %D2O2
Sample conditionsIonic strength: 75 / pH: 5.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorerefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
SparkyGoddarddata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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