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- PDB-4anj: MYOSIN VI (MDinsert2-GFP fusion) PRE-POWERSTROKE STATE (MG.ADP.AlF4) -

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Basic information

Entry
Database: PDB / ID: 4anj
TitleMYOSIN VI (MDinsert2-GFP fusion) PRE-POWERSTROKE STATE (MG.ADP.AlF4)
Components
  • CALMODULIN
  • UNCONVENTIONAL MYOSIN-VI, GREEN FLUORESCENT PROTEIN
KeywordsMOTOR PROTEIN/METAL-BINDNG PROTEIN / MOTOR PROTEIN-METAL-BINDNG PROTEIN COMPLEX / MOLECULAR MOTOR / METAL-BINDING PROTEIN / TRANSITION STATE / PRE-POWERSTROKE STATE / GFP FUSION
Function / homology
Function and homology information


negative regulation of phospholipase C-activating phototransduction signaling pathway / 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 / : ...negative regulation of phospholipase C-activating phototransduction signaling pathway / 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 / G protein-coupled opsin 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 / inner ear morphogenesis / muscle cell cellular homeostasis / 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 / ruffle / centriole / bioluminescence / filopodium / generation of precursor metabolites and energy / 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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4820 / Myosin VI head, motor domain, U50 subdomain / : / Myosin VI, lever arm / Myosin VI, cargo binding domain / Class VI myosin, motor domain / Myosin VI cargo binding domain / Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Kinesin motor domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4820 / Myosin VI head, motor domain, U50 subdomain / : / Myosin VI, lever arm / Myosin VI, cargo binding domain / Class VI myosin, motor domain / Myosin VI cargo binding domain / Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Kinesin motor domain / Kinesin / 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. / Green Fluorescent Protein / Green fluorescent protein / Kinesin motor domain superfamily / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Four Helix Bundle (Hemerythrin (Met), subunit A) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand domain pair / EF-hand, calcium binding motif / SH3 type barrels. / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Roll / Up-down Bundle / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / Green fluorescent protein / Calmodulin / Unconventional myosin-VI
Similarity search - Component
Biological speciesSUS SCROFA (pig)
AEQUOREA VICTORIA (jellyfish)
DROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMenetrey, J. / Isabet, T. / Ropars, V. / Mukherjea, M. / Pylypenko, O. / Liu, X. / Perez, J. / Vachette, P. / Sweeney, H.L. / Houdusse, A.M.
CitationJournal: Mol.Cell / Year: 2012
Title: Processive Steps in the Reverse Direction Require Uncoupling of the Lead Head Lever Arm of Myosin Vi.
Authors: Menetrey, J. / Isabet, T. / Ropars, V. / Mukherjea, M. / Pylypenko, O. / Liu, X. / Perez, J. / Vachette, P. / Sweeney, H.L. / Houdusse, A.M.
History
DepositionMar 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Nov 28, 2012Group: Database references / Other
Revision 1.3Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_struct_special_symmetry ...pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct_conn / struct_conn_type
Revision 1.4Oct 23, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
Revision 1.5Dec 20, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AH" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AH" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UNCONVENTIONAL MYOSIN-VI, GREEN FLUORESCENT PROTEIN
B: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,6328
Polymers136,9572
Non-polymers6756
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-88.8 kcal/mol
Surface area49130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.093, 62.657, 156.040
Angle α, β, γ (deg.)90.00, 117.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2002-

HOH

21A-2003-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein UNCONVENTIONAL MYOSIN-VI, GREEN FLUORESCENT PROTEIN / UNCONVENTIONAL MYOSIN-6


Mass: 120131.617 Da / Num. of mol.: 1 / Fragment: MYOSIN-6 RESIDUES 1-817, GFP RESIDUES 2-238
Source method: isolated from a genetically manipulated source
Details: CHIMERIC PROTEIN, MYOSIN-6 RESIDUES 1-816 (AUTHOR NUMBERING) AND COMPLETE GFP (AFTER INITIATION METHIONINE REMOVAL)
Source: (gene. exp.) SUS SCROFA (pig), (gene. exp.) AEQUOREA VICTORIA (jellyfish)
Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q29122, UniProt: P42212
#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) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P62152

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Non-polymers , 5 types, 97 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsGFP FUSED TO MYOSIN VI, THE AUTHORS STATE THAT THE ORIGINAL SEQUENCE (UNIPROT Q29122) OF MYOSIN VI ...GFP FUSED TO MYOSIN VI, THE AUTHORS STATE THAT THE ORIGINAL SEQUENCE (UNIPROT Q29122) OF MYOSIN VI FROM PIG WAS MOST LIKELY INCORRECT BECAUSE THE CHANGES THAT ARE IN THEIR CLONE (LYS DELETION AND THE 6 MUTATIONS) ARE CONSERVED ACROSS THE MYOSIN VI FAMILY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.54 % / Description: NONE
Crystal growDetails: 5% PEG 8000, 50 MM MES PH 5.5, 100 MM NH4SO4, 20 MM MGCL2, 20 MM NACL AND 3 % PROPAN-2-OL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.6→48.8 Å / Num. obs: 51178 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.2
Reflection shellResolution: 2.6→48.8 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2V26, 3DQA

2v26

3dqa


Resolution: 2.6→137.36 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.84 / SU B: 11.08 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.517 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS SIDE-CHAINS. THAT HAVE NO DEFINED ELECTRON DENSITY WERE OMITTED FROM THE MODEL. REGIONS 35-38, 175-177, 355-361, 395-407 AND 623-638, FROM ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS SIDE-CHAINS. THAT HAVE NO DEFINED ELECTRON DENSITY WERE OMITTED FROM THE MODEL. REGIONS 35-38, 175-177, 355-361, 395-407 AND 623-638, FROM THE MYOSIN VI (CHAIN A) AND REGIONS 27-30, 76- 79 AND 111- 116 FROM THE CALMODULIN (CHAIN B) HAVE NO DEFINED ELECTRON DENSITY AND WERE OMITTED FROM THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.28754 2595 5.1 %RANDOM
Rwork0.23874 ---
obs0.24126 48581 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.874 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å2-0.66 Å2
2--1.98 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.6→137.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8718 0 36 91 8845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228927
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0381.95912071
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.98351111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69524.418421
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.262151465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8921545
X-RAY DIFFRACTIONr_chiral_restr0.070.21330
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026804
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.24029
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.26155
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2307
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0540.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3230.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3261.55720
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.58528874
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.72133602
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2014.53197
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 176 -
Rwork0.298 3547 -
obs--100 %

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