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- PDB-4dbp: Myosin VI nucleotide-free (MDINSERT2) D179Y crystal structure -

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Basic information

Entry
Database: PDB / ID: 4dbp
TitleMyosin VI nucleotide-free (MDINSERT2) D179Y crystal structure
Components
  • Calmodulin
  • Myosin-VI
Keywordsmotor protein/Calcium binding protein / motor protein / motor protein-Calcium binding protein complex
Function / homology
Function and homology information


metarhodopsin inactivation / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere / rhabdomere development / myosin V complex / : ...metarhodopsin inactivation / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere / rhabdomere development / myosin V complex / : / regulation of secretion / kinetochore organization / : / actin filament-based movement / rhodopsin mediated signaling pathway / Neutrophil degranulation / inner ear auditory receptor cell differentiation / myosin V binding / channel regulator activity / vesicle transport along actin filament / cellular response to ethanol / myosin complex / clathrin-coated vesicle / microfilament motor activity / muscle cell cellular homeostasis / inner ear morphogenesis / myosin heavy chain binding / mitotic spindle pole / filamentous actin / microvillus / centriole replication / cytoskeletal motor activity / DNA damage response, signal transduction by p53 class mediator / enzyme regulator activity / clathrin-coated pit / ruffle / centriole / filopodium / actin filament organization / actin filament / ADP binding / sensory perception of sound / intracellular protein transport / mitotic spindle / spindle / ruffle membrane / endocytosis / actin filament binding / sensory perception of smell / actin cytoskeleton / cell cortex / midbody / cytoplasmic vesicle / nuclear membrane / vesicle / calmodulin binding / protein phosphorylation / centrosome / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Myosin VI, lever arm / Myosin VI, cargo binding domain / Class VI myosin, motor domain / Myosin VI cargo binding domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) ...: / Myosin VI, lever arm / Myosin VI, cargo binding domain / Class VI myosin, motor domain / Myosin VI cargo binding domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / TERTIARY-BUTYL ALCOHOL / Unconventional myosin-VI / Calmodulin / Unconventional myosin-VI
Similarity search - Component
Biological speciesSus scrofa (pig)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPylypenko, O. / Sweeney, H.L. / Houdusse, A.
CitationJournal: To be Published
Title: Mutations in myosin VI that cause a loss of coordination between heads provide insights into the structural changes underlying force generation and the importance of gating
Authors: Song, L. / Pylypenko, O. / Yang, Z. / Houdusse, A. / Sweeney, L.H.
History
DepositionJan 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: Myosin-VI
C: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,39327
Polymers109,9072
Non-polymers1,48625
Water14,070781
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-23 kcal/mol
Surface area41020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.600, 104.390, 90.020
Angle α, β, γ (deg.)90.00, 91.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AC

#1: Protein Myosin-VI /


Mass: 93081.164 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN-INSERT2, UNP residues 2-815 / Mutation: D179Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: MYO6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F1RQI7, UniProt: Q29122*PLUS
#2: Protein Calmodulin / / CaM


Mass: 16825.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Cam, CG8472 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62152

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Non-polymers , 5 types, 806 molecules

#3: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL / Tert-Butyl alcohol


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 781 / 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: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4.5% P8K, 50 mM MOPS pH7,3% I-prop, 3% tert-but,1mM TCEP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.2→19.9 Å / Num. all: 64374 / Num. obs: 63904 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.2→2.25 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BKH

2bkh


Resolution: 2.2→19.885 Å / SU ML: 0.65 / σ(F): 0 / Phase error: 21.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3196 5 %RANDOM
Rwork0.1626 ---
obs0.1653 63899 99.41 %-
all-64374 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.641 Å2 / ksol: 0.314 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→19.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7403 0 90 781 8274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077684
X-RAY DIFFRACTIONf_angle_d0.99910341
X-RAY DIFFRACTIONf_dihedral_angle_d13.5962882
X-RAY DIFFRACTIONf_chiral_restr0.0711130
X-RAY DIFFRACTIONf_plane_restr0.0041348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27850.27493160.20785989X-RAY DIFFRACTION99
2.2785-2.36960.2673180.20196050X-RAY DIFFRACTION99
2.3696-2.47720.25623160.19316010X-RAY DIFFRACTION99
2.4772-2.60760.25263190.18366057X-RAY DIFFRACTION99
2.6076-2.77050.24813190.17086063X-RAY DIFFRACTION99
2.7705-2.98380.23433200.16136084X-RAY DIFFRACTION100
2.9838-3.28280.22673200.16296071X-RAY DIFFRACTION100
3.2828-3.75510.20563210.16286094X-RAY DIFFRACTION100
3.7551-4.72060.17253210.13076108X-RAY DIFFRACTION100
4.7206-19.8850.20683260.15846177X-RAY DIFFRACTION99
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)
10.07810.14330.08360.33230.35530.5973-0.1727-0.20460.10330.36140.1749-0.1527-0.08590.1291-0.01481.11410.4537-0.37910.5758-0.24730.047114.9308-7.241952.0317
21.2775-0.8742-0.49941.76771.1552.6989-0.1191-0.16170.01560.27320.15560.1842-0.3118-0.3365-0.00040.67740.31750.03050.3827-0.04230.1835-1.02343.295140.2895
31.0554-0.1687-0.40420.61810.58412.12780.0268-0.22880.19390.17940.1078-0.0251-0.2726-0.14730.07560.68690.2693-0.18850.3575-0.21370.09748.58390.490945.3747
40.6435-0.07380.19151.0705-0.40870.6271-0.05530.02850.0841-0.03120.13020.17230.0196-0.0723-0.0209-0.0279-0.00570.0317-0.0014-0.0220.0426-17.79260.092-0.6475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 80:147 )C80 - 147
2X-RAY DIFFRACTION2( CHAIN C AND RESID 3:72 )C3 - 72
3X-RAY DIFFRACTION3( CHAIN A AND RESID 784:815 )A784 - 815
4X-RAY DIFFRACTION4( CHAIN A AND RESID 3:783 )A3 - 783

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