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- PDB-2jq9: VPS4A MIT-CHMP1A complex -

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Basic information

Entry
Database: PDB / ID: 2jq9
TitleVPS4A MIT-CHMP1A complex
Components
  • Chromatin-modifying protein 1a
  • Vacuolar protein sorting-associating protein 4AVacuole
KeywordsPROTEIN TRANSPORT / CHMP1A / VPS4A MIT / Complex / Four Helix Bundle
Function / homology
Function and homology information


vesicle uncoating / ESCRT complex disassembly / actomyosin contractile ring contraction / endosomal vesicle fusion / 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 / late endosome to lysosome transport via multivesicular body sorting pathway / intracellular cholesterol transport ...vesicle uncoating / ESCRT complex disassembly / actomyosin contractile ring contraction / endosomal vesicle fusion / 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 / late endosome to lysosome transport via multivesicular body sorting pathway / intracellular cholesterol transport / abscission / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / nuclear envelope organization / ESCRT III complex / late endosomal microautophagy / kinetochore microtubule / cytoskeleton-dependent cytokinesis / endosome transport via multivesicular body sorting pathway / mitotic nuclear membrane reassembly / regulation of centrosome duplication / ATP-dependent protein disaggregase activity / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / protein targeting to lysosome / multivesicular body sorting pathway / vesicle budding from membrane / vacuole organization / membrane fission / plasma membrane repair / multivesicular body membrane / late endosome to vacuole transport / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / regulation of mitotic spindle assembly / mitotic chromosome condensation / vesicle-fusing ATPase / Flemming body / vacuolar membrane / microtubule organizing center / endosomal transport / mitotic metaphase chromosome alignment / ATPase complex / nucleus organization / viral budding via host ESCRT complex / autophagosome membrane / autophagosome maturation / viral release from host cell / endomembrane system / regulation of protein localization to plasma membrane / nuclear pore / vesicle-mediated transport / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / viral budding from plasma membrane / HCMV Late Events / condensed nuclear chromosome / macroautophagy / Budding and maturation of HIV virion / kinetochore / autophagy / nuclear matrix / spindle pole / metallopeptidase activity / regulation of protein localization / late endosome / protein transport / late endosome membrane / midbody / lysosome / early endosome / endosome membrane / endosome / lysosomal membrane / protein domain specific binding / cell division / negative regulation of gene expression / centrosome / protein-containing complex binding / perinuclear region of cytoplasm / protein homodimerization activity / ATP hydrolysis activity / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / nucleus / 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 / Snf7 family / Snf7 / Vps4 C terminal oligomerisation domain ...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 / Snf7 family / Snf7 / Vps4 C terminal oligomerisation domain / 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 1a / Vacuolar protein sorting-associated protein 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsBinary complex of VPS4A MIT domain (residues 1-84) in complex with the C-terminus of CHMP1A (residues 180-196)
AuthorsStuchell-Brereton, M.D. / Skalicky, J.J. / Kieffer, C. / Ghaffarian, S. / Sundquist, W.I.
CitationJournal: Nature / Year: 2007
Title: ESCRT-III recognition by VPS4 ATPases.
Authors: Stuchell-Brereton, M.D. / Skalicky, J.J. / Kieffer, C. / Karren, M.A. / Ghaffarian, S. / Sundquist, W.I.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 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 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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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: Chromatin-modifying protein 1a


Theoretical massNumber of molelcules
Total (without water)11,8822
Polymers11,8822
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 9865.304 Da / Num. of mol.: 1 / Fragment: MIT domain, residues 1-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS4A, VPS4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UN37
#2: Protein/peptide Chromatin-modifying protein 1a / Charged multivesicular body protein 1a / CHMP1a / Vacuolar protein sorting 46-1 / Vps46-1 / hVps46-1


Mass: 2016.268 Da / Num. of mol.: 1 / Fragment: sequence database residues 180-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCOLN3, CHMP1, CHMP1A, KIAA0047, PRSM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HD42

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Binary complex of VPS4A MIT domain (residues 1-84) in complex with the C-terminus of CHMP1A (residues 180-196)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HBHA(CO)NH
1613D HNHA
1713D C(CO)NH
1813D H(CCO)NH
1913D (H)CCH-COSY
11013D (H)CCH-TOCSY
11113D 1H-13C NOESY
11213D 1H-15N NOESY
11322D 1H-15N HSQC
11422D 1H-13C HSQC
11523D HN(CA)CB
11623D CBCA(CO)NH
11723D HBHA(CO)NH
11823D HNHA
11923D C(CO)NH
12023D H(CCO)NH
12123D (H)CCH-COSY
12223D (H)CCH-TOCSY
12323D 1H-13C NOESY
12423D 1H-15N NOESY
NMR detailsText: Half-filtered NOESYs provided the intermolecular NOEs

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] VPS4A MIT, 1.15 mM CHMP1A(180-196), 90% H2O/10% D2O90% H2O/10% D2O
21.15 mM VPS4A MIT, 1.0 mM [U-100% 13C; U-100% 15N] CHMP1A(180-196), 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMVPS4A MIT[U-100% 13C; U-100% 15N]1
1.15 mMCHMP1A(180-196)1
1.15 mMVPS4A MIT2
1.0 mMCHMP1A(180-196)[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 50 / pH: 5.65 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix2004Accelrys Software Inc.processing
Sparky3.112Goddardchemical shift assignment
Sparky3.112Goddardpeak picking
Sparky3.112Goddarddata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Refinement using anneal.inp and using summed NOE constraints with max T of 3000 K for simulated annealing.
NMR constraintsNOE constraints total: 1311 / NOE intraresidue total count: 309 / NOE long range total count: 278 / NOE medium range total count: 391 / NOE sequential total count: 333 / Hydrogen bond constraints total count: 59 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 76 / Protein psi angle constraints total count: 76
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.03 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 0.1 ° / Maximum upper distance constraint violation: 0.017 Å / Torsion angle constraint violation method: CNS
NMR ensemble rmsDistance rms dev: 0.004 Å

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