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- PDB-4a5z: Structures of MITD1 -

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Basic information

Entry
Database: PDB / ID: 4a5z
TitleStructures of MITD1
ComponentsMIT DOMAIN-CONTAINING PROTEIN 1
KeywordsPROTEIN TRANSPORT / ESCRT / CYTOKINESIS / MIDBODY
Function / homology
Function and homology information


midbody abscission / mitotic cytokinesis / negative regulation of protein binding / phosphatidylinositol binding / late endosome membrane / midbody / protein domain specific binding / intracellular membrane-bounded organelle / extracellular exosome / identical protein binding / membrane
Similarity search - Function
MITD, C-terminal phospholipase D-like domain / MITD1, C-terminal phospholipase D-like domain / MITD1, C-terminal phospholipase D-like domain superfamily / MITD1, N-terminal domain / : / Phospholipase D-like domain at C-terminus of MIT / MIT (microtubule interacting and transport) domain / Endonuclease; Chain A / MIT domain superfamily / MIT domain ...MITD, C-terminal phospholipase D-like domain / MITD1, C-terminal phospholipase D-like domain / MITD1, C-terminal phospholipase D-like domain superfamily / MITD1, N-terminal domain / : / Phospholipase D-like domain at C-terminus of MIT / MIT (microtubule interacting and transport) domain / Endonuclease; Chain A / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MIT domain-containing protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 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 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Data collection / Database references
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: MIT DOMAIN-CONTAINING PROTEIN 1
D: MIT DOMAIN-CONTAINING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,26013
Polymers78,8994
Non-polymers3629
Water3,495194
1
A: MIT DOMAIN-CONTAINING PROTEIN 1
C: MIT DOMAIN-CONTAINING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7058
Polymers39,4492
Non-polymers2556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-59 kcal/mol
Surface area15420 Å2
MethodPISA
2
B: MIT DOMAIN-CONTAINING PROTEIN 1
D: MIT DOMAIN-CONTAINING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5565
Polymers39,4492
Non-polymers1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-46.6 kcal/mol
Surface area15310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.020, 109.410, 74.460
Angle α, β, γ (deg.)90.00, 100.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, 0.004, 0.01), (-0.004, -0.999, 0.032), (0.01, 0.032, 0.999)-13.74559, -16.47846, 0.13176
2given(0.998, -0.056, -0.021), (-0.057, -0.998, -0.026), (-0.02, 0.027, -0.999)-25.29097, -14.2221, 55.96533
3given(-0.997, 0.075, -0.006), (0.075, 0.995, -0.066), (0.001, -0.066, -0.998)12.11552, -0.27307, 54.74832

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Components

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


Mass: 19724.662 Da / Num. of mol.: 4 / Fragment: RESIDUES 90-243 / Mutation: YES
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: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 90 TO ASP ENGINEERED RESIDUE IN CHAIN A, LYS 243 TO ASP ...ENGINEERED RESIDUE IN CHAIN A, LYS 90 TO ASP ENGINEERED RESIDUE IN CHAIN A, LYS 243 TO ASP ENGINEERED RESIDUE IN CHAIN B, LYS 90 TO ASP ENGINEERED RESIDUE IN CHAIN B, LYS 243 TO ASP ENGINEERED RESIDUE IN CHAIN C, LYS 90 TO ASP ENGINEERED RESIDUE IN CHAIN C, LYS 243 TO ASP ENGINEERED RESIDUE IN CHAIN D, LYS 90 TO ASP ENGINEERED RESIDUE IN CHAIN D, LYS 243 TO ASP
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.9 % / Description: NONE
Crystal growpH: 6.5 / Details: 200 MM NACL, 100 MM BISTRIS PH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98050, 0.98070, 0.95000
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98051
20.98071
30.951
ReflectionResolution: 2.3→73.2 Å / Num. obs: 34453 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 12.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3.8 / % possible all: 97.9

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.3→73.2 Å / Cor.coef. Fo:Fc: 0.9207 / Cor.coef. Fo:Fc free: 0.894 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=DMS CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5468. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=4. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=DMS CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5468. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=4. NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 1747 5.07 %RANDOM
Rwork0.1906 ---
obs0.1922 34453 --
Displacement parametersBiso mean: 21.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.0436 Å20 Å2-1.2422 Å2
2---1.9594 Å20 Å2
3---2.0029 Å2
Refine analyzeLuzzati coordinate error obs: 0.258 Å
Refinement stepCycle: LAST / Resolution: 2.3→73.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5252 0 12 194 5458
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015405HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.077287HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1950SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes155HARMONIC2
X-RAY DIFFRACTIONt_gen_planes778HARMONIC5
X-RAY DIFFRACTIONt_it5405HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.39
X-RAY DIFFRACTIONt_other_torsion17.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion681SEMIHARMONIC5
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_contact5731SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.37 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2375 157 5.28 %
Rwork0.1907 2816 -
all0.1933 2973 -
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)
11.26050.30330.33111.48170.0850.96430.0194-0.0222-0.0534-0.02690.0033-0.00330.1097-0.0023-0.0228-0.0496-0.00930.0043-0.07060.0147-0.0352-15.9058-18.149447.5667
20.84480.1118-0.20450.76250.12621.48850.0625-0.0258-0.01890.0207-0.02180.0044-0.15-0.0513-0.0407-0.03610.00690.0062-0.0362-0.006-0.04959.5113.38098.5515
31.12910.1695-0.4520.7906-0.0771.15590.0499-0.0279-0.0079-0.0015-0.00290.034-0.09050.0451-0.0471-0.0177-0.00580.0132-0.06360.0011-0.04692.76613.184447.2926
40.68680.06160.20121.2691-0.47791.2392-0.00450.0238-0.0479-0.0176-0.02180.0160.14290.09080.0262-0.07130.00660.0062-0.0134-0.0216-0.045326.8126-19.57918.7618
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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