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- PDB-3err: Microtubule binding domain from mouse cytoplasmic dynein as a fus... -

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Entry
Database: PDB / ID: 3err
TitleMicrotubule binding domain from mouse cytoplasmic dynein as a fusion with seryl-tRNA synthetase
Componentsfusion protein of microtubule binding domain from mouse cytoplasmic dynein and seryl-tRNA synthetase from Thermus thermophilus
KeywordsLIGASE / dynein / microtubule binding domain / coiled coil / fusion protein
Function / homology
Function and homology information


COPI-independent Golgi-to-ER retrograde traffic / selenocysteine biosynthetic process / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / COPI-mediated anterograde transport / cilium movement / Aggrephagy ...COPI-independent Golgi-to-ER retrograde traffic / selenocysteine biosynthetic process / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / COPI-mediated anterograde transport / cilium movement / Aggrephagy / positive regulation of intracellular transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / serine binding / regulation of metaphase plate congression / establishment of spindle localization / RHO GTPases Activate Formins / positive regulation of spindle assembly / Separation of Sister Chromatids / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / manchette / Regulation of PLK1 Activity at G2/M Transition / P-body assembly / dynein complex / MHC class II antigen presentation / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / retrograde axonal transport / dynein light intermediate chain binding / nuclear migration / dynein intermediate chain binding / cytoplasmic microtubule / stress granule assembly / cytoplasmic microtubule organization / regulation of mitotic spindle organization / axon cytoplasm / Neutrophil degranulation / mitotic spindle organization / filopodium / nuclear envelope / positive regulation of cold-induced thermogenesis / cell cortex / microtubule / tRNA binding / cell division / axon / centrosome / neuronal cell body / ATP hydrolysis activity / protein homodimerization activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Histone Acetyltransferase; Chain A - #60 / Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain, C-terminal domain ...Histone Acetyltransferase; Chain A - #60 / Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, linker, subdomain 3 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, N-terminal region 2 / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Histone Acetyltransferase; Chain A / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Serine--tRNA ligase / Cytoplasmic dynein 1 heavy chain 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Thermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsCarter, A.P.
CitationJournal: Science / Year: 2008
Title: Structure and functional role of dynein's microtubule-binding domain.
Authors: Andrew P Carter / Joan E Garbarino / Elizabeth M Wilson-Kubalek / Wesley E Shipley / Carol Cho / Ronald A Milligan / Ronald D Vale / I R Gibbons /
Abstract: Dynein motors move various cargos along microtubules within the cytoplasm and power the beating of cilia and flagella. An unusual feature of dynein is that its microtubule-binding domain (MTBD) is ...Dynein motors move various cargos along microtubules within the cytoplasm and power the beating of cilia and flagella. An unusual feature of dynein is that its microtubule-binding domain (MTBD) is separated from its ring-shaped AAA+ adenosine triphosphatase (ATPase) domain by a 15-nanometer coiled-coil stalk. We report the crystal structure of the mouse cytoplasmic dynein MTBD and a portion of the coiled coil, which supports a mechanism by which the ATPase domain and MTBD may communicate through a shift in the heptad registry of the coiled coil. Surprisingly, functional data suggest that the MTBD, and not the ATPase domain, is the main determinant of the direction of dynein motility.
History
DepositionOct 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: fusion protein of microtubule binding domain from mouse cytoplasmic dynein and seryl-tRNA synthetase from Thermus thermophilus
B: fusion protein of microtubule binding domain from mouse cytoplasmic dynein and seryl-tRNA synthetase from Thermus thermophilus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,6104
Polymers121,9152
Non-polymers6942
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-26 kcal/mol
Surface area47120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.302, 144.302, 159.946
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein fusion protein of microtubule binding domain from mouse cytoplasmic dynein and seryl-tRNA synthetase from Thermus thermophilus / / Cytoplasmic dynein heavy chain 1 / Dynein heavy chain / cytosolic / Seryl-tRNA(Ser/Sec) synthetase ...Cytoplasmic dynein heavy chain 1 / Dynein heavy chain / cytosolic / Seryl-tRNA(Ser/Sec) synthetase / Serine-tRNA ligase / SerRS


Mass: 60957.734 Da / Num. of mol.: 2 / Mutation: C3323A, C3387A
Source method: isolated from a genetically manipulated source
Details: The coiled coil stalk of cytoplasmic dynein was fused onto the base coiled coil from seryl tRNA synthetase
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Thermus thermophilus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q9JHU4, UniProt: P34945
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: Protein was changed into crystallization buffer (20mM K-HEPES, pH7.5, 10% w/v glycerol, 0.2mM PMSF, 1mM DTT, 4mM Mg-ATP, 0.01% Na-Azide) and concentrated to 18 mg/ml. Crystallization was ...Details: Protein was changed into crystallization buffer (20mM K-HEPES, pH7.5, 10% w/v glycerol, 0.2mM PMSF, 1mM DTT, 4mM Mg-ATP, 0.01% Na-Azide) and concentrated to 18 mg/ml. Crystallization was carried out by setting hanging drops containing 2 ul of protein, (diluted to 13.5mg/ml with 20mM K-Hepes, pH 7.5, 10% glycerol), 0.3 ul 70% glycerol and 1.8 ul of precipitant (20% PEG 4000, 200mM Ammonium sulfate, 100mM Bis-Tris, pH 5.5) over 500ml of the same precipitant solution. Crystals appeared within one day and were of dimensions up to 200 um., VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.5 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2008
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.27→49.27 Å / Num. all: 57296 / Num. obs: 57296 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Net I/σ(I): 18.6
Reflection shellResolution: 2.27→2.35 Å / Mean I/σ(I) obs: 2 / Rsym value: 62 / % possible all: 94.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.4.0067refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1SRY

1sry


Resolution: 2.27→49.27 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 15.276 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.299 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24655 2867 5 %RANDOM
Rwork0.19702 ---
obs0.19954 54226 99.08 %-
all-54226 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.202 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.27→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8420 0 46 123 8589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0228648
X-RAY DIFFRACTIONr_angle_refined_deg1.9231.98511727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61851052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27423.705413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.453151518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8841578
X-RAY DIFFRACTIONr_chiral_restr0.1350.21278
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216596
X-RAY DIFFRACTIONr_mcbond_it0.8451.55276
X-RAY DIFFRACTIONr_mcangle_it1.51528479
X-RAY DIFFRACTIONr_scbond_it2.76733372
X-RAY DIFFRACTIONr_scangle_it4.4094.53248
LS refinement shellResolution: 2.27→2.326 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 181 -
Rwork0.261 3753 -
obs--92.61 %
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)
119.35182.8251-5.67942.89081.16016.6021-0.01040.2345-1.21520.053-0.1539-0.2050.45450.35280.1643-0.0701-0.00970.00380.0042-0.11940.050759.139-28.45320.281
28.22244.7890.35083.60650.39871.4818-0.10850.13360.18770.15530.0706-0.0793-0.5206-0.05830.03790.13060.0064-0.0847-0.12430.16090.0455107.636-4.2920.969
30.98140.12010.13962.47671.82482.49020.0528-0.0702-0.02320.03780.0798-0.210.01440.098-0.1326-0.2923-0.04240.0123-0.1536-0.0159-0.264649.4-0.47649.716
43.8222.98522.85554.3876-5.544931.5371-0.48380.08231.0976-0.03670.22990.3783-2.286-0.16410.25390.4673-0.19210.04150.17930.00320.436362.00938.71546.065
53.8509-0.33462.38032.2141-1.74177.7402-0.0967-0.5153-0.08220.09640.06580.2973-0.531-0.32080.0310.37430.11820.29130.08560.07940.285842.00235.237-3.63
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 34
2X-RAY DIFFRACTION2A35 - 203
3X-RAY DIFFRACTION3A204 - 528
4X-RAY DIFFRACTION3B204 - 528
5X-RAY DIFFRACTION4B3 - 34
6X-RAY DIFFRACTION5B35 - 203

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