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- PDB-5i4e: Crystal Structure of Human Nonmuscle Myosin 2C motor domain -

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Basic information

Entry
Database: PDB / ID: 5i4e
TitleCrystal Structure of Human Nonmuscle Myosin 2C motor domain
ComponentsMyosin-14,Alpha-actinin A
KeywordsMOTOR PROTEIN
Function / homology
Function and homology information


contractile vacuole / COPI-mediated anterograde transport / Platelet degranulation / sorocarp development / myosin II filament / Neutrophil degranulation / macropinocytic cup / : / actin filament-based movement / actin crosslink formation ...contractile vacuole / COPI-mediated anterograde transport / Platelet degranulation / sorocarp development / myosin II filament / Neutrophil degranulation / macropinocytic cup / : / actin filament-based movement / actin crosslink formation / vocalization behavior / actomyosin / myosin filament / actomyosin structure organization / myosin II complex / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / hyperosmotic response / Sema4D induced cell migration and growth-cone collapse / microfilament motor activity / cortical actin cytoskeleton / EPHA-mediated growth cone collapse / cell leading edge / RHO GTPases activate PAKs / pseudopodium / actin filament bundle assembly / brush border / neuronal action potential / skeletal muscle contraction / phagocytic vesicle / phagocytosis / skeletal muscle tissue development / stress fiber / RHO GTPases activate PKNs / cellular response to starvation / extracellular matrix / cell projection / cell motility / actin filament / sensory perception of sound / structural constituent of cytoskeleton / actin filament binding / protein-macromolecule adaptor activity / cell junction / cell cortex / regulation of cell shape / growth cone / actin cytoskeleton organization / calmodulin binding / calcium ion binding / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Myosin tail / Myosin tail ...EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Spectrin/alpha-actinin / Spectrin repeats / Myosin S1 fragment, N-terminal / Calponin homology domain / Calponin homology (CH) domain / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / 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 / 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
ADP ORTHOVANADATE / Alpha-actinin A / Myosin-14
Similarity search - Component
Biological speciesHomo sapiens (human)
Dictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsChinthalapudi, K. / Heissler, S.M. / Preller, M. / Sellers, J.R. / Manstein, D.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationMA 1081/21-1 Germany
CitationJournal: Elife / Year: 2017
Title: Mechanistic insights into the active site and allosteric communication pathways in human nonmuscle myosin-2C.
Authors: Chinthalapudi, K. / Heissler, S.M. / Preller, M. / Sellers, J.R. / Manstein, D.J.
History
DepositionFeb 11, 2016Deposition site: RCSB / Processing site: PDBE
SupersessionSep 13, 2017ID: 2YCU
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.3Jan 10, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin-14,Alpha-actinin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1573
Polymers111,5891
Non-polymers5682
Water11,980665
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area49640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.120, 125.610, 153.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Myosin-14,Alpha-actinin A / Myosin heavy chain 14 / Myosin heavy chain / non-muscle IIc / Non-muscle myosin heavy chain IIc / ...Myosin heavy chain 14 / Myosin heavy chain / non-muscle IIc / Non-muscle myosin heavy chain IIc / NMHC II-C / Actin-binding protein A / F-actin cross-linking protein


Mass: 111588.789 Da / Num. of mol.: 1 / Fragment: UNP residues 265-489,UNP residues 265-489
Source method: isolated from a genetically manipulated source
Details: NONMUSCLE MYOSIN 2C MOTOR DOMAIN, RESIDUES 47-799 ALPHA-ACTININ REPEATS, RESIDUES 265-502
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Dictyostelium discoideum (eukaryote)
Gene: MYH14, KIAA2034, FP17425, abpA, actnA, DDB_G0268632 / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7Z406, UniProt: P05095
#2: Chemical ChemComp-AOV / ADP ORTHOVANADATE


Mass: 544.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N5O14P2V / Comment: energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 665 / 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: 3.58 Å3/Da / Density % sol: 65.69 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, hanging drop / Details: TRIS PH 8.2, PEG 5K MME, MPD, NACL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.25→97.33 Å / Num. obs: 75357 / % possible obs: 99.8 % / Redundancy: 14.82 % / Biso Wilson estimate: 42.47 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.6
Reflection shellResolution: 2.25→2.35 Å / Redundancy: 14.97 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.63 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BR2

1br2


Resolution: 2.25→34.77 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.888 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.233 / SU Rfree Blow DPI: 0.184 / SU Rfree Cruickshank DPI: 0.181
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3786 5.03 %RANDOM
Rwork0.22 ---
obs0.221 75245 99.9 %-
Displacement parametersBiso mean: 74.91 Å2
Baniso -1Baniso -2Baniso -3
1-10.7165 Å20 Å20 Å2
2--18.875 Å20 Å2
3----29.5915 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: 1 / Resolution: 2.25→34.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7697 0 33 666 8396
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017878HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1610641HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2886SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes233HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1121HARMONIC5
X-RAY DIFFRACTIONt_it7878HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion18.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion990SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9213SEMIHARMONIC4
LS refinement shellResolution: 2.25→2.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 254 4.65 %
Rwork0.292 5211 -
all0.292 5465 -
obs--99.16 %

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