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- PDB-2ymb: Structures of MITD1 -

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Basic information

Entry
Database: PDB / ID: 2ymb
TitleStructures of MITD1
Components
  • CHARGED MULTIVESICULAR BODY PROTEIN 1A
  • MIT DOMAIN-CONTAINING PROTEIN 1
KeywordsPROTEIN TRANSPORT / MEMBRANE / PLD
Function / homology
Function and homology information


amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / regulation of centrosome duplication / nuclear membrane reassembly ...amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / regulation of centrosome duplication / nuclear membrane reassembly / midbody abscission / multivesicular body sorting pathway / membrane fission / plasma membrane repair / late endosome to vacuole transport / multivesicular body membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / regulation of mitotic spindle assembly / mitotic chromosome condensation / microtubule organizing center / nucleus organization / mitotic metaphase chromosome alignment / viral budding via host ESCRT complex / autophagosome maturation / autophagosome membrane / mitotic cytokinesis / endomembrane system / nuclear pore / vesicle-mediated transport / phosphatidylinositol binding / multivesicular body / viral budding from plasma membrane / HCMV Late Events / negative regulation of protein binding / condensed nuclear chromosome / kinetochore / nuclear matrix / autophagy / metallopeptidase activity / protein transport / late endosome membrane / midbody / early endosome / cell division / lysosomal membrane / protein domain specific binding / negative regulation of gene expression / intracellular membrane-bounded organelle / protein homodimerization activity / extracellular exosome / zinc ion binding / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
MITD, C-terminal phospholipase D-like domain / MITD1, N-terminal domain / MITD1, C-terminal phospholipase D-like domain / MITD1, C-terminal phospholipase D-like domain superfamily / Phospholipase D-like domain at C-terminus of MIT / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT (microtubule interacting and transport) domain / Endonuclease; Chain A / MIT domain superfamily / Snf7 family ...MITD, C-terminal phospholipase D-like domain / MITD1, N-terminal domain / MITD1, C-terminal phospholipase D-like domain / MITD1, C-terminal phospholipase D-like domain superfamily / Phospholipase D-like domain at C-terminus of MIT / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT (microtubule interacting and transport) domain / Endonuclease; Chain A / MIT domain superfamily / Snf7 family / Snf7 / MIT domain / Microtubule Interacting and Trafficking molecule domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
MIT domain-containing protein 1 / Charged multivesicular body protein 1a
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.404 Å
AuthorsHadders, M.A. / Agromayor, M. / Obita, T. / Perisic, O. / Caballe, A. / Kloc, M. / Lamers, M.H. / Williams, R.L. / Martin-Serrano, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Escrt-III Binding Protein Mitd1 is Involved in Cytokinesis and Has an Unanticipated Pld Fold that Binds Membranes.
Authors: Hadders, M.A. / Agromayor, M. / Obita, T. / Perisic, O. / Caballe, A. / Kloc, M. / Lamers, M.H. / Williams, R.L. / Martin-Serrano, J.
History
DepositionOct 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MIT DOMAIN-CONTAINING PROTEIN 1
B: MIT DOMAIN-CONTAINING PROTEIN 1
C: MIT DOMAIN-CONTAINING PROTEIN 1
D: MIT DOMAIN-CONTAINING PROTEIN 1
F: CHARGED MULTIVESICULAR BODY PROTEIN 1A
H: CHARGED MULTIVESICULAR BODY PROTEIN 1A


Theoretical massNumber of molelcules
Total (without water)124,9266
Polymers124,9266
Non-polymers00
Water0
1
B: MIT DOMAIN-CONTAINING PROTEIN 1
D: MIT DOMAIN-CONTAINING PROTEIN 1
H: CHARGED MULTIVESICULAR BODY PROTEIN 1A


Theoretical massNumber of molelcules
Total (without water)62,4633
Polymers62,4633
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-24.4 kcal/mol
Surface area20250 Å2
MethodPISA
2
A: MIT DOMAIN-CONTAINING PROTEIN 1
C: MIT DOMAIN-CONTAINING PROTEIN 1
F: CHARGED MULTIVESICULAR BODY PROTEIN 1A


Theoretical massNumber of molelcules
Total (without water)62,4633
Polymers62,4633
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-24 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.046, 222.046, 222.046
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein
MIT DOMAIN-CONTAINING PROTEIN 1 / MITD1


Mass: 30393.641 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q8WV92
#2: Protein/peptide CHARGED MULTIVESICULAR BODY PROTEIN 1A / CHMP1A / CHROMATIN-MODIFYING PROTEIN 1A / CHMP1A / VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 46-1 ...CHMP1A / CHROMATIN-MODIFYING PROTEIN 1A / CHMP1A / VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 46-1 / VPS46-1 / HVPS46-1


Mass: 1675.932 Da / Num. of mol.: 2 / Fragment: MIM1, RESIDUES 56-68
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q9HD42

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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: 3.56 Å3/Da / Density % sol: 65.5 % / Description: NONE
Crystal growpH: 8
Details: 8.8% PEG 20000, 8.8% PEG 550 MME, 0.25 M MGCL2 AND 0.1 M TRIS ACETATE PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.4→60 Å / Num. obs: 25007 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 72.81 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 8.3
Reflection shellResolution: 3.4→3.59 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.9 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4A5Z AND 4A5X

4a5z

4a5x


Resolution: 3.404→59.344 Å / SU ML: 0.86 / σ(F): 1.06 / Phase error: 25.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2561 1000 2.1 %
Rwork0.2296 --
obs0.2301 25007 98.53 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.795 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso mean: 96.849 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.404→59.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6629 0 0 0 6629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026756
X-RAY DIFFRACTIONf_angle_d0.5159071
X-RAY DIFFRACTIONf_dihedral_angle_d14.5182582
X-RAY DIFFRACTIONf_chiral_restr0.04973
X-RAY DIFFRACTIONf_plane_restr0.0021161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4036-3.58310.35821400.32736521X-RAY DIFFRACTION96
3.5831-3.80750.27591460.29166668X-RAY DIFFRACTION99
3.8075-4.10140.30081540.26266746X-RAY DIFFRACTION99
4.1014-4.5140.23391570.21216684X-RAY DIFFRACTION99
4.514-5.16690.22441460.19636738X-RAY DIFFRACTION99
5.1669-6.50840.26141180.2366751X-RAY DIFFRACTION99
6.5084-59.35330.21221390.18286697X-RAY DIFFRACTION99

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