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- PDB-6ixr: Structure of Myo2-GTD in complex with Inp2 -

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Basic information

Entry
Database: PDB / ID: 6ixr
TitleStructure of Myo2-GTD in complex with Inp2
Components
  • Inheritance of peroxisomes protein 2
  • Myosin-2
KeywordsPROTEIN BINDING / Cargo binding domain
Function / homology
Function and homology information


peroxisome inheritance / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex / RHOT2 GTPase cycle / membrane addition at site of cytokinesis / mitochondrion inheritance / RHOU GTPase cycle / meiotic nuclear membrane microtubule tethering complex / myosin V complex / vacuole inheritance ...peroxisome inheritance / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex / RHOT2 GTPase cycle / membrane addition at site of cytokinesis / mitochondrion inheritance / RHOU GTPase cycle / meiotic nuclear membrane microtubule tethering complex / myosin V complex / vacuole inheritance / vesicle transport along actin filament / incipient cellular bud site / cellular bud tip / Golgi inheritance / cellular bud neck / mating projection tip / fungal-type vacuole membrane / vesicle docking involved in exocytosis / peroxisomal membrane / microfilament motor activity / actin filament bundle / filamentous actin / intracellular distribution of mitochondria / establishment of mitotic spindle orientation / transport vesicle / vesicle-mediated transport / protein-membrane adaptor activity / actin filament organization / small GTPase binding / actin filament binding / protein transport / actin cytoskeleton / vesicle / calmodulin binding / ATP binding / membrane / cytoplasm
Similarity search - Function
Inheritance of peroxisomes protein 2 / : / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. ...Inheritance of peroxisomes protein 2 / : / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin-2 / Inheritance of peroxisomes protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.854 Å
AuthorsTang, K. / Wei, Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31770791 China
National Natural Science Foundation of China31570741 China
National Natural Science Foundation of China31600612 China
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural mechanism for versatile cargo recognition by the yeast class V myosin Myo2.
Authors: Tang, K. / Li, Y. / Yu, C. / Wei, Z.
History
DepositionDec 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin-2
B: Inheritance of peroxisomes protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7164
Polymers51,5242
Non-polymers1922
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-34 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.508, 63.508, 225.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Myosin-2 / Cell division control protein 66 / Class V unconventional myosin MYO2 / Type V myosin heavy chain ...Cell division control protein 66 / Class V unconventional myosin MYO2 / Type V myosin heavy chain MYO2 / Myosin V MYO2


Mass: 48900.484 Da / Num. of mol.: 1 / Mutation: Deletions 1342-1347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MYO2, CDC66, YOR326W, O6167 / Plasmid: modified pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19524
#2: Protein/peptide Inheritance of peroxisomes protein 2 / Inp2


Mass: 2623.817 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: INP2, YMR163C, YM8520.12C / Plasmid: modified pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03824
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 8% w/v PEG 4000, 0.2-0.3 M lithium/ammonium sulfate pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.85→55 Å / Num. obs: 13042 / % possible obs: 99.9 % / Redundancy: 19 % / Biso Wilson estimate: 79.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.041 / Rrim(I) all: 0.177 / Net I/σ(I): 14.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.85-3.0120.11.55718540.9630.3551.59899.8
9.03-5514.90.074940.9980.0180.07399.6

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F6H

2f6h


Resolution: 2.854→49.446 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.49
RfactorNum. reflection% reflection
Rfree0.2632 698 5.41 %
Rwork0.2092 --
obs0.2121 12906 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 188.14 Å2 / Biso mean: 93.3167 Å2 / Biso min: 50.5 Å2
Refinement stepCycle: final / Resolution: 2.854→49.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3212 0 10 0 3222
Biso mean--174.69 --
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023286
X-RAY DIFFRACTIONf_angle_d0.5174461
X-RAY DIFFRACTIONf_chiral_restr0.019523
X-RAY DIFFRACTIONf_plane_restr0.002554
X-RAY DIFFRACTIONf_dihedral_angle_d11.7441196
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8543-3.07470.40871590.35292331249099
3.0747-3.3840.33691190.28912387250699
3.384-3.87360.29231460.24062400254699
3.8736-4.87960.27321270.18324862613100
4.8796-49.45320.20581470.178326042751100
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)
10.3172-0.19270.25430.4659-0.34261.88010.08510.422-0.1401-0.2897-0.0574-0.0407-0.10330.5413-0.00130.9073-0.229-0.05690.6538-0.00130.606793.8318-11.0935439.4258
20.3787-0.28510.49620.3991-0.04141.759-0.05320.0151-0.14970.13230.05430.1533-0.08730.346300.7864-0.0410.0450.83430.0650.7994104.9704-21.5338468.7581
30.0332-0.0233-0.0030.0383-0.00810.0596-0.21740.0904-0.33750.25960.81740.2726-0.6057-0.5152-0.00061.1784-0.0483-0.02940.91820.07181.017478.3106-8.7552432.3703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1152 through 1325 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1326 through 1571 )
3X-RAY DIFFRACTION3chain 'B' and (resid 532 through 540 )

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