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- PDB-4pd3: Crystal Structure of Rigor-Like Human Nonmuscle Myosin-2B -

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Basic information

Entry
Database: PDB / ID: 4pd3
TitleCrystal Structure of Rigor-Like Human Nonmuscle Myosin-2B
ComponentsNonmuscle myosin heavy chain B, Alpha-actinin A Chimera Protein
KeywordsCONTRACTILE PROTEIN / myosin / NM-2B / nonmuscle myosin-2B / rigor-like / nucleotide free / MOTOR PROTEIN
Function / homology
Function and homology information


fourth ventricle development / third ventricle development / RHOBTB2 GTPase cycle / RHOU GTPase cycle / RHOV GTPase cycle / contractile vacuole / COPI-mediated anterograde transport / microfilament motor activity => GO:0000146 / Platelet degranulation / sorocarp development ...fourth ventricle development / third ventricle development / RHOBTB2 GTPase cycle / RHOU GTPase cycle / RHOV GTPase cycle / contractile vacuole / COPI-mediated anterograde transport / microfilament motor activity => GO:0000146 / Platelet degranulation / sorocarp development / myosin II filament / : / macropinocytic cup / Neutrophil degranulation / lateral ventricle development / ventricular cardiac muscle cell development / cerebellar Purkinje cell layer development / modification of postsynaptic actin cytoskeleton / cardiac septum development / actin crosslink formation / actin filament-based movement / cardiac myofibril assembly / actomyosin / plasma membrane repair / substrate-dependent cell migration, cell extension / coronary vasculature development / adult heart development / RHO GTPases Activate ROCKs / hyperosmotic response / RHO GTPases activate CIT / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / myosin complex / aorta development / nuclear migration / myosin II complex / cortical actin cytoskeleton / microfilament motor activity / EPHA-mediated growth cone collapse / cell leading edge / exocytosis / pseudopodium / RHO GTPases activate PAKs / brush border / cleavage furrow / actin filament bundle assembly / neuromuscular process controlling balance / mitotic cytokinesis / phagocytosis / stress fiber / RHO GTPases activate PKNs / phagocytic vesicle / cellular response to starvation / extracellular matrix / cell projection / cell motility / positive regulation of protein secretion / actin filament / axon guidance / neuron migration / neuromuscular junction / structural constituent of cytoskeleton / ADP binding / mRNA 5'-UTR binding / spindle / RNA stem-loop binding / actin filament binding / lamellipodium / cell junction / retina development in camera-type eye / protein-macromolecule adaptor activity / actin binding / cell cortex / regulation of cell shape / midbody / growth cone / actin cytoskeleton organization / in utero embryonic development / cell population proliferation / dendritic spine / calmodulin binding / cell adhesion / neuronal cell body / calcium ion binding / ATP hydrolysis activity / extracellular exosome / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Myosin tail / Myosin tail / Spectrin repeat / Spectrin repeat / Myosin N-terminal SH3-like domain / IQ calmodulin-binding motif ...: / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Myosin tail / Myosin tail / Spectrin repeat / Spectrin repeat / Myosin N-terminal SH3-like domain / IQ calmodulin-binding motif / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / Actinin-type actin-binding domain, conserved site / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Calponin homology domain / Calponin homology (CH) domain / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / 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 / 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
Alpha-actinin A / Myosin-10
Similarity search - Component
Biological speciesHomo sapiens (human)
Dictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsMunnich, S. / Pathan-Chhatbar, S. / Manstein, D.J.
CitationJournal: Febs Lett. / Year: 2014
Title: Crystal structure of the rigor-like human non-muscle myosin-2 motor domain.
Authors: Munnich, S. / Pathan-Chhatbar, S. / Manstein, D.J.
History
DepositionApr 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations
Revision 1.4Mar 7, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 2.0Aug 19, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / entity_name_com ...atom_site / entity_name_com / entity_src_gen / pdbx_nonpoly_scheme / refine_hist
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Nonmuscle myosin heavy chain B, Alpha-actinin A Chimera Protein
B: Nonmuscle myosin heavy chain B, Alpha-actinin A Chimera Protein


Theoretical massNumber of molelcules
Total (without water)237,4342
Polymers237,4342
Non-polymers00
Water59433
1
A: Nonmuscle myosin heavy chain B, Alpha-actinin A Chimera Protein


Theoretical massNumber of molelcules
Total (without water)118,7171
Polymers118,7171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nonmuscle myosin heavy chain B, Alpha-actinin A Chimera Protein


Theoretical massNumber of molelcules
Total (without water)118,7171
Polymers118,7171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.850, 157.870, 143.480
Angle α, β, γ (deg.)90.00, 94.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nonmuscle myosin heavy chain B, Alpha-actinin A Chimera Protein / Cellular myosin heavy chain / type B / Myosin heavy chain 10 / Myosin heavy chain / non-muscle IIb ...Cellular myosin heavy chain / type B / Myosin heavy chain 10 / Myosin heavy chain / non-muscle IIb / Non-muscle myosin heavy chain B / NMMHC-B / Non-muscle myosin heavy chain IIb / NMMHC-IIB / Actin-binding protein A / F-actin cross-linking protein


Mass: 118717.047 Da / Num. of mol.: 2
Fragment: UNP P35580 residues 1-782, UNP P05095 residues 265-502
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Dictyostelium discoideum (eukaryote)
Gene: MYH10, abpA, actnA, DDB_G0268632 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35580, UniProt: P05095
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.13 Å3/Da / Density % sol: 60.74 %
Crystal growTemperature: 291.15 K / Method: evaporation / pH: 7.5 / Details: 10% PEG-6000, 0.1 M Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.84→30 Å / Num. obs: 65526 / % possible obs: 95.1 % / Redundancy: 2.2 % / Net I/σ(I): 7.21

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→29.998 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2882 1993 3.05 %
Rwork0.2532 --
obs0.2543 65450 95.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.84→29.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14795 0 0 33 14828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215066
X-RAY DIFFRACTIONf_angle_d0.7120308
X-RAY DIFFRACTIONf_dihedral_angle_d11.3665692
X-RAY DIFFRACTIONf_chiral_restr0.0262229
X-RAY DIFFRACTIONf_plane_restr0.0032647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.91090.43681510.38324466X-RAY DIFFRACTION95
2.9109-2.98960.3911440.38584624X-RAY DIFFRACTION97
2.9896-3.07740.3671350.35734578X-RAY DIFFRACTION97
3.0774-3.17670.40991330.33744584X-RAY DIFFRACTION96
3.1767-3.29010.41591410.31914618X-RAY DIFFRACTION96
3.2901-3.42160.35041490.29594565X-RAY DIFFRACTION96
3.4216-3.57710.32961440.28584510X-RAY DIFFRACTION95
3.5771-3.76540.31431450.25794559X-RAY DIFFRACTION96
3.7654-4.00080.28971440.24254557X-RAY DIFFRACTION96
4.0008-4.30880.28321400.23334518X-RAY DIFFRACTION95
4.3088-4.74090.2441500.20444516X-RAY DIFFRACTION94
4.7409-5.42340.25761390.22274510X-RAY DIFFRACTION94
5.4234-6.81970.27681360.24984484X-RAY DIFFRACTION93
6.8197-29.99980.2041420.20444368X-RAY DIFFRACTION90

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