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- PDB-1lkx: MOTOR DOMAIN OF MYOE, A CLASS-I MYOSIN -

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Basic information

Entry
Database: PDB / ID: 1lkx
TitleMOTOR DOMAIN OF MYOE, A CLASS-I MYOSIN
ComponentsMYOSIN IE HEAVY CHAIN
KeywordsCONTRACTILE PROTEIN / MYOSIN MOTOR DOMAIN / LEVER ARM / CONVERTER DOMAIN
Function / homology
Function and homology information


macropinocytic cup membrane / pseudopodium membrane / actin wave / macropinocytic cup cytoskeleton / chemotaxis to cAMP / macropinocytic cup / leading edge membrane / vesicle transport along actin filament / early phagosome / myosin complex ...macropinocytic cup membrane / pseudopodium membrane / actin wave / macropinocytic cup cytoskeleton / chemotaxis to cAMP / macropinocytic cup / leading edge membrane / vesicle transport along actin filament / early phagosome / myosin complex / microfilament motor activity / phagocytic cup / phagocytosis, engulfment / pseudopodium / cell leading edge / phosphatidylinositol-3,4,5-trisphosphate binding / phagocytosis / actin filament polymerization / actin filament organization / actin filament binding / actin cytoskeleton / actin binding / vesicle / calmodulin binding / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Arc Repressor Mutant, subunit A - #820 / Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Myosin VI head, motor domain, U50 subdomain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Kinesin motor domain / Kinesin / IQ calmodulin-binding motif ...Arc Repressor Mutant, subunit A - #820 / Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Myosin VI head, motor domain, U50 subdomain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Kinesin motor domain / Kinesin / IQ calmodulin-binding motif / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Arc Repressor Mutant, subunit A / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / VANADATE ION / Myosin IE heavy chain
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKollmar, M. / Durrwang, U. / Kliche, W. / Manstein, D.J. / Kull, F.J.
CitationJournal: EMBO J. / Year: 2002
Title: Crystal structure of the motor domain of a class-I myosin.
Authors: Kollmar, M. / Durrwang, U. / Kliche, W. / Manstein, D.J. / Kull, F.J.
History
DepositionApr 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE AUTHOR STATES THE PUBLISHED SEQUENCE FOR DISTY MYOE IS INCORRECT IN A NUMBER OF PLACES. ...SEQUENCE AUTHOR STATES THE PUBLISHED SEQUENCE FOR DISTY MYOE IS INCORRECT IN A NUMBER OF PLACES. THE AUTHORS BELIEVE THEIR SEQUENCE TO BE MORE ACCURATE. THEY HAVE IDENTIFIED THE FOLLOWING CHANGES IN THEIR SEQUENCE/STRUCTURE FROM THE PUBLISHED ONE. THE DERIVED SEQUENCE OF MYOE WAS DIFFERENT FROM THE PUBLISHED SEQUENCE (URRUTIA ET AL., 1993, ACC. NR. L06805) IN 25 PLACES: WHILE SOME CHANGES CONCERNED NON-CONSERVED RESIDUES, ESPECIALLY IN THE REGIONS WHERE ADDITIONAL RESIDUES OR DELETIONS WERE FOUND, THE DERIVED SEQUENCE WAS IN BETTER AGREEMENT WITH THE AMINO ACID ALIGNMENT OF THE DICTYOSTELIUM MYOSINS. IN ONE REGION, A TEN RESIDUE SURFACE LOOP WAS FOUND TO BE COMPLETELY DIFFERENT. IN DETAIL, THE SEQUENCE CONTAINED THE FOLLOWING MODIFICATIONS COMPARED TO THE PUBLISHED ONE: D26E, R48T, I77M, I137L, R138D, F139 ABSENT, 140 ABSENT, N215D, L371I, S372I, I373N, V374C, H375T, R376T, G378K, T379G, P380 inserted, V427 inserted, R428 INSERTED, K429E, N440 INSERTED, N498I, D604V, I681N, R683T. THE AUTHORS STATE THEIR SEQUENCE COMPLETELY AGREES WITH THE FRAGMENT (AA270-1003) OBTAINED FROM THE DICTY GENOME SEQUENCING PROJECT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYOSIN IE HEAVY CHAIN
B: MYOSIN IE HEAVY CHAIN
C: MYOSIN IE HEAVY CHAIN
D: MYOSIN IE HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,92716
Polymers316,6614
Non-polymers2,26612
Water1,15364
1
A: MYOSIN IE HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7324
Polymers79,1651
Non-polymers5663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MYOSIN IE HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7324
Polymers79,1651
Non-polymers5663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MYOSIN IE HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7324
Polymers79,1651
Non-polymers5663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: MYOSIN IE HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7324
Polymers79,1651
Non-polymers5663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.818, 143.667, 236.050
Angle α, β, γ (deg.)90.0, 94.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
MYOSIN IE HEAVY CHAIN


Mass: 79165.273 Da / Num. of mol.: 4 / Fragment: Motor Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Plasmid: pDXA-3H / Production host: Dictyostelium discoideum (eukaryote) / References: UniProt: Q03479
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: VO4
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 11% PEG 8K, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 or 17 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
111 %(w/v)PEG80001reservoir
2170 mM1reservoirNaCl
350 mMHEPES-NaOH1reservoirpH7.2
45 mM1reservoirMgCl2
55 mMdithiothreitol1reservoir
60.5 mMEGTA1reservoir
72 %MPD1reservoir
80.2 mMADP1drop
90.18 mMvanadate1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1801
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG BW7B10.8424
SYNCHROTRONESRF ID1320.96
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.84241
20.961
ReflectionResolution: 3→50 Å / Num. obs: 54968 / Observed criterion σ(I): -3
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 50 Å / % possible obs: 79.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.195
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.2 Å / % possible obs: 57.4 % / Redundancy: 2 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.87

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Processing

Software
NameClassification
CNSrefinement
MAR345data collection
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å / Cross valid method: THROUGHOUT / σ(F): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.273 5000 RANDOM
Rwork0.228 --
obs-54968 -
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21069 0 132 64 21265
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.376
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d21.22
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 50 Å / Num. reflection obs: 54955 / Num. reflection Rfree: 5579 / % reflection Rfree: 9 % / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.863

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