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- PDB-9ihl: Crystal Structure of the Human Nonmuscle Myosin 2A Motor Domain -

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Basic information

Entry
Database: PDB / ID: 9ihl
TitleCrystal Structure of the Human Nonmuscle Myosin 2A Motor Domain
ComponentsMyosin-9,Alpha-actinin A
KeywordsMOTOR PROTEIN / Myosin / NM2A / human / motor / protein
Function / homology
Function and homology information


RHOBTB2 GTPase cycle / RHOU GTPase cycle / RHOV GTPase cycle / negative regulation of actin filament severing / contractile vacuole / uropod organization / regulation of plasma membrane repair / COPI-mediated anterograde transport / Platelet degranulation / establishment of meiotic spindle localization ...RHOBTB2 GTPase cycle / RHOU GTPase cycle / RHOV GTPase cycle / negative regulation of actin filament severing / contractile vacuole / uropod organization / regulation of plasma membrane repair / COPI-mediated anterograde transport / Platelet degranulation / establishment of meiotic spindle localization / sorocarp development / cytokinetic process / myosin II filament / cortical granule exocytosis / macropinocytic cup / Neutrophil degranulation / establishment of T cell polarity / cortical granule / blood vessel endothelial cell migration / actomyosin contractile ring / positive regulation of protein processing in phagocytic vesicle / uropod / actin crosslink formation / regulated exocytosis / actin filament-based movement / meiotic spindle organization / lysosome localization / plasma membrane repair / actomyosin / myosin filament / myoblast fusion / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / Sensory processing of sound by outer hair cells of the cochlea / myosin II complex / hyperosmotic response / Sensory processing of sound by inner hair cells of the cochlea / platelet formation / CD163 mediating an anti-inflammatory response / leukocyte migration / phagocytosis, engulfment / cortical actin cytoskeleton / EPHA-mediated growth cone collapse / microfilament motor activity / pseudopodium / cell leading edge / endodermal cell differentiation / RHO GTPases activate PAKs / brush border / cleavage furrow / monocyte differentiation / cytoskeletal motor activity / membrane protein ectodomain proteolysis / actin filament bundle assembly / immunological synapse / phagocytosis / stress fiber / RHO GTPases activate PKNs / phagocytic vesicle / protein-membrane adaptor activity / ruffle / extracellular matrix / cellular response to starvation / integrin-mediated signaling pathway / cell projection / adherens junction / Translocation of SLC2A4 (GLUT4) to the plasma membrane / FCGR3A-mediated phagocytosis / actin filament / neuromuscular junction / cell motility / ADP binding / Regulation of actin dynamics for phagocytic cup formation / structural constituent of cytoskeleton / platelet aggregation / spindle / cytoplasmic side of plasma membrane / integrin binding / Signaling by ALK fusions and activated point mutants / actin filament binding / protein transport / actin cytoskeleton / regulation of cell shape / actin binding / virus receptor activity / actin cytoskeleton organization / cell cortex / angiogenesis / protein-macromolecule adaptor activity / in utero embryonic development / calmodulin binding / nuclear body / cadherin binding / protein domain specific binding / focal adhesion / calcium ion binding / symbiont entry into host cell / cell surface
Similarity search - Function
EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / RGS domain superfamily / Spectrin repeat / Spectrin repeat / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Actinin-type actin-binding domain signature 1. ...EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / RGS domain superfamily / Spectrin repeat / Spectrin repeat / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin / Spectrin repeats / Myosin S1 fragment, N-terminal / Calponin homology domain / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / 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-9
Similarity search - Component
Biological speciesHomo sapiens (human)
Dictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsHeiringhoff, R.S. / Greve, J.N. / Zahn, M. / Manstein, D.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structure of the Human Non-Muscle Myosin 2A Motor Domain: Insights into Isoform-Specific Mechanochemistry.
Authors: Heiringhoff, R.S. / Greve, J.N. / Zahn, M. / Manstein, D.J.
History
DepositionFeb 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin-9,Alpha-actinin A


Theoretical massNumber of molelcules
Total (without water)117,4191
Polymers117,4191
Non-polymers00
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.994, 120.879, 149.438
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myosin-9,Alpha-actinin A / Cellular myosin heavy chain / type A / Myosin heavy chain 9 / Myosin heavy chain / non-muscle IIa / ...Cellular myosin heavy chain / type A / Myosin heavy chain 9 / Myosin heavy chain / non-muscle IIa / Non-muscle myosin heavy chain A / NMMHC-A / Non-muscle myosin heavy chain IIa / NMMHC II-a / NMMHC-IIA / Actin-binding protein A / F-actin cross-linking protein


Mass: 117418.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimeric protein: residue 1-775 Uniprot: P35579 (Homo sapiens); residue 776-777 Linker; residue 778-1017 Uniprot: P05095 (Dictyostelium discoideum)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Dictyostelium discoideum (eukaryote)
Gene: MYH9, abpA, actnA, DDB_G0268632 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35579, UniProt: P05095
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 16% PEG3350, 240 mM Sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.02→74.72 Å / Num. obs: 34413 / % possible obs: 92.2 % / Redundancy: 13.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.054 / Net I/σ(I): 10.2
Reflection shellResolution: 2.02→2.286 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.702 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1721 / CC1/2: 0.684 / Rpim(I) all: 0.491 / % possible all: 71.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487: ???refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→74.72 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2591 1692 -
Rwork0.205 32721 -
obs0.2078 34413 47.05 %
Refinement stepCycle: LAST / Resolution: 2.02→74.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7668 0 0 385 8053
LS refinement shellResolution: 2.02→2.09 Å
RfactorNum. reflection% reflection
Rfree0.3718 --
Rwork0.2732 --
obs-93 1.3 %
Refinement TLS params.

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)
10.4633-0.0993-0.12390.4885-0.10311.3945-0.07540.1465-0.0304-0.13630.06850.10280.2619-0.39110.01070.2358-0.0937-0.0330.126-0.01960.1316-16.21576.69192.2794
21.32690.0324-0.4460.83650.33262.47830.051-0.2482-0.0210.19640.016-0.10410.34280.2144-0.06210.2240.0041-0.05930.15630.05340.1196-6.43234.483224.5856
30.13540.0134-0.02990.0991-0.3831.76970.01550.12290.0278-0.1044-0.03150.0743-0.26230.26590.01310.5733-0.0343-0.03760.3154-0.04230.24254.018719.6787-60.7842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 351 )
2X-RAY DIFFRACTION2chain 'A' and (resid 352 through 645 )
3X-RAY DIFFRACTION3chain 'A' and (resid 646 through 1016 )

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