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- PDB-4a5x: Structures of MITD1 -

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Basic information

Entry
Database: PDB / ID: 4a5x
TitleStructures of MITD1
Components
  • CHARGED MULTIVESICULAR BODY PROTEIN 1A
  • MIT DOMAIN-CONTAINING PROTEIN 1
KeywordsPROTEIN TRANSPORT / ESCRT / CYTOKINESIS / MIDBODY
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 / multivesicular body membrane / late endosome to vacuole transport / 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 / multivesicular body / phosphatidylinositol binding / viral budding from plasma membrane / HCMV Late Events / negative regulation of protein binding / condensed nuclear chromosome / kinetochore / autophagy / nuclear matrix / metallopeptidase activity / protein transport / late endosome membrane / midbody / early endosome / lysosomal membrane / protein domain specific binding / cell division / 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
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 / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule domain / Snf7 family ...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 / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule domain / Snf7 family / Snf7 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
2,5,8,11,14,17-HEXAOXANONADECAN-19-OL / MIT domain-containing protein 1 / Charged multivesicular body protein 1a
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsHadders, M.A. / Agromayor, M. / Caballe, A. / Obita, T. / Perisic, O. / 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 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references / Structure summary
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: CHARGED MULTIVESICULAR BODY PROTEIN 1A
D: CHARGED MULTIVESICULAR BODY PROTEIN 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3907
Polymers23,9094
Non-polymers4813
Water1,35175
1
A: MIT DOMAIN-CONTAINING PROTEIN 1
C: CHARGED MULTIVESICULAR BODY PROTEIN 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1394
Polymers11,9552
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-6.9 kcal/mol
Surface area5580 Å2
MethodPISA
2
B: MIT DOMAIN-CONTAINING PROTEIN 1
D: CHARGED MULTIVESICULAR BODY PROTEIN 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2513
Polymers11,9552
Non-polymers2961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-3.3 kcal/mol
Surface area5730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.070, 74.160, 89.785
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.02599, 0.97508, 0.22033), (0.98754, -0.05926, 0.14575), (0.15518, 0.2138, -0.96447)-32.42354, 30.12221, 17.40723
2given(0.06655, 0.95198, 0.29885), (0.98175, -0.11595, 0.15074), (0.17815, 0.28337, -0.94232)-32.04975, 31.69856, 15.42861

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Components

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


Mass: 10053.435 Da / Num. of mol.: 2 / Fragment: MIT, RESIDUES 9-85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): C41 / References: UniProt: Q8WV92
#2: Protein/peptide CHARGED MULTIVESICULAR BODY PROTEIN 1A / CHROMATIN-MODIFYING PROTEIN 1A / CHMP1A / VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 46-1 / VPS46- ...CHROMATIN-MODIFYING PROTEIN 1A / CHMP1A / VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 46-1 / VPS46-1 / HVPS46-1


Mass: 1901.157 Da / Num. of mol.: 2 / Fragment: RESIDUES 184-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): C41 / References: UniProt: Q9HD42
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-P15 / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL


Mass: 296.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H28O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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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: 2 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growDetails: 29% PEG2000MME, 160 MM KSCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.91→30 Å / Num. obs: 17144 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 31.13 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.5
Reflection shellResolution: 1.91→2.02 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.2 / % possible all: 94.6

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WFD

1wfd


Resolution: 1.91→18.34 Å / Cor.coef. Fo:Fc: 0.9364 / Cor.coef. Fo:Fc free: 0.9288 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 875 5.1 %RANDOM
Rwork0.2011 ---
obs0.2024 17144 --
Displacement parametersBiso mean: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.6019 Å20 Å20 Å2
2---6.0606 Å20 Å2
3---1.4586 Å2
Refine analyzeLuzzati coordinate error obs: 0.274 Å
Refinement stepCycle: LAST / Resolution: 1.91→18.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 32 75 1526
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081467HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.91954HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d567SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes48HARMONIC2
X-RAY DIFFRACTIONt_gen_planes201HARMONIC5
X-RAY DIFFRACTIONt_it1448HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.16
X-RAY DIFFRACTIONt_other_torsion16.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion188SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1729SEMIHARMONIC4
LS refinement shellResolution: 1.91→2.03 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.248 133 5.16 %
Rwork0.213 2444 -
all0.2149 2577 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.7086-2.0756-0.41558.07561.35332.00630.07250.56530.5749-0.52710.0421-0.4898-0.14130.1602-0.1146-0.02650.03790.0129-0.03490.0875-0.0609-6.450929.11135.0379
23.7311-0.58491.01584.6734-0.89481.7043-0.1577-0.02560.62910.34080.124-0.2355-0.1819-0.2040.0337-0.0690.0782-0.0591-0.05960.01260.0232-10.933736.927213.8162
31.94631.2132.28498.3632-0.70073.7569-0.0141-0.10690.2567-0.35950.14290.71550.113-0.7862-0.1288-0.13780.0356-0.05910.03250.0247-0.0116-21.375327.93616.9366
44.475-0.4203-2.61494.5503-1.06735.55940.0641-0.08390.4315-0.06040.0209-0.1321-0.21550.0646-0.0849-0.09540.0223-0.0213-0.1187-0.0218-0.1214-1.544423.589917.1845
55.66430.3172-2.04792.0145-0.36232.5334-0.0224-0.00150.11-0.198-0.0723-0.22970.10330.19470.0947-0.00050.03680.0224-0.0160.0182-0.05565.227517.853311.4759
62.28880.9339-0.07198.2547-2.25925.1206-0.1070.0572-0.9802-0.3822-0.02320.35110.3773-0.20860.13020.0708-0.03860.01360.0142-0.05640.1214-7.83976.298111.8957
70.0020.49632.02760.69420.44030.84-0.0326-0.1030.2688-0.0036-0.10470.024-0.0037-0.05350.1373-0.05180.1920.09220.0563-0.04330.0413-18.260539.890120.6593
86.1051-0.8682-0.16270.0023.44660-0.0196-0.2582-0.13680.6345-0.01070.6651-0.2236-0.66810.0303-0.07860.09730.03590.0190.01730.0155-19.396829.605618.2445
98.2302-5.20190.482502.18751.4996-0.10080.2728-0.169-0.0402-0.0939-0.49970.30960.39420.19470.07110.05870.1125-0.00120.03330.007311.114310.84635.3689
101.2371.742-1.02533.8545.37347.7414-0.16160.6315-0.3788-0.6457-0.14180.07050.2288-0.25110.3034-0.01260.01520.0043-0.0254-0.0602-0.07030.158512.01423.1974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 10:30
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 31:65
3X-RAY DIFFRACTION3CHAIN A AND RESSEQ 66:82
4X-RAY DIFFRACTION4CHAIN B AND RESSEQ 9:29
5X-RAY DIFFRACTION5CHAIN B AND RESSEQ 30:72
6X-RAY DIFFRACTION6CHAIN B AND RESSEQ 73:81)
7X-RAY DIFFRACTION7CHAIN C AND RESSEQ 183:187
8X-RAY DIFFRACTION8CHAIN C AND RESSEQ 188:196
9X-RAY DIFFRACTION9CHAIN D AND RESSEQ 181:187
10X-RAY DIFFRACTION10CHAIN D AND RESSEQ 188:196

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