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9ihl

Crystal Structure of the Human Nonmuscle Myosin 2A Motor Domain

Method: X-RAY DIFFRACTION Dmax: 227.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Myosin-9,Alpha-actinin A

Dictyostelium discoideum

UniProt P05095

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 265–502 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；16% PEG3350, 240 mM Sodium thiocyanate Resolution 2.02 Å R-free 0.259

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9IHL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1G8X STRUCTURE OF A GENETICALLY ENGINEERED MOLECULAR MOTOR Deposited 2000-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 266–503（238 aa） Fragment：MYOSIN II HEAVY CHAIN, MOTOR DOMAIN RESIDUES 1-761, AND ALPHA-ACTININ 3, REPEATS 1 AND 2 RESIDUES 765-1002
Chain B 266–503（238 aa） Fragment：MYOSIN II HEAVY CHAIN, MOTOR DOMAIN RESIDUES 1-761, AND ALPHA-ACTININ 3, REPEATS 1 AND 2 RESIDUES 765-1002
Mutation：ARG238GLU Mutation：ARG238GLU MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；280 K；12% PEGM 5000; 170 mM NaCl; 50 mM HEPES (NaOH) pH 7.2; 5 mM MgCl2; 5 mM DTT; 0.5 mM EGTA; and 2% 2-methyl-1,3-propanediol, at 280 K, VAPOR DIFFUSION, SITTING DROP
Resolution 2.80 Å R-free 0.290
4PD3 Crystal Structure of Rigor-Like Human Nonmuscle Myosin-2B Deposited 2014-04-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 265–502（238 aa） Fragment：UNP P35580 residues 1-782, UNP P05095 residues 265-502
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.5；291.15 K；10% PEG-6000, 0.1 M Tris pH 7.5
Resolution 2.84 Å R-free 0.288
4PD3 Crystal Structure of Rigor-Like Human Nonmuscle Myosin-2B Deposited 2014-04-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 265–502（238 aa） Fragment：UNP P35580 residues 1-782, UNP P05095 residues 265-502
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.5；291.15 K；10% PEG-6000, 0.1 M Tris pH 7.5
Resolution 2.84 Å R-free 0.288
5I4E Crystal Structure of Human Nonmuscle Myosin 2C motor domain Deposited 2016-02-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 265–489（225 aa） Fragment：UNP residues 265-489,UNP residues 265-489
Not recorded AOV ADP ORTHOVANADATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；281.15 K；TRIS PH 8.2, PEG 5K MME, MPD, NACL.
Resolution 2.25 Å R-free 0.241
5JLH Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution Deposited 2016-04-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: undecameric
Chain F 265–502（238 aa）
Chain G 265–502（238 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；5 mM Tris-HCl pH 7.5, 1 mM DTT, 100 mM KCl, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Sample (2 uL of F-actin-tropomyosin solution) was applied to a glow-discharged holey carbon grid, incubated for 20 s and manually blotted from the backside for less than a second with filter paper. Afterwards 1.5 uL of myosin solution (3 uM without nucleotide) were added directly on the grid, incubated for 10 s and then manually blotted for 5 s from the backside with filter paper.
Resolution 3.90 Å

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACTNA_DICDI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 778–1015； UniProt 265–502

Myosin-9,Alpha-actinin A

Dictyostelium discoideum

UniProt P35579

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–775 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；16% PEG3350, 240 mM Sodium thiocyanate Resolution 2.02 Å R-free 0.259

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9IHL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2LNK Solution structure of Ca-bound S100A4 in complex with non-muscle myosin IIA Deposited 2011-12-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1897–1935（39 aa） Fragment：UNP residues 1897-1935
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.1；313 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient
NMR sample composition 0.5 mM protein_1, 1 mM [U-100% 13C; U-100% 15N] protein_2, 5 mM CALCIUM ION, 20 mM MES, 20 mM sodium chloride, 4 mM TCEP, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
3ZWH Ca2+-bound S100A4 C3S, C81S, C86S and F45W mutant complexed with myosin IIA Deposited 2011-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Q 1893–1937（45 aa） Fragment：RESIDUES 1893-1937
Mutation：YES CA CALCIUM ION × 4 ACT ACETATE ION × 2 AZI AZIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；30% PEG 4000, 0.2 M NA-ACETATE PH 5.6, 0.1 M NA-CITRATE.
Resolution 1.94 Å R-free 0.206
4CFQ Ca-bound truncated (delta13C) and C3S, C81S and C86S mutated S100A4 complexed with non-muscle myosin IIA Deposited 2013-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain R 1893–1937（45 aa） Fragment：RESIDUES 1893-1937
Mutation：YES CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；0.1 M MIB, PH 4, 25% W/V PEG 1500
Resolution 1.37 Å R-free 0.193
4CFQ Ca-bound truncated (delta13C) and C3S, C81S and C86S mutated S100A4 complexed with non-muscle myosin IIA Deposited 2013-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Q 1893–1937（45 aa） Fragment：RESIDUES 1893-1937
Mutation：YES CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；0.1 M MIB, PH 4, 25% W/V PEG 1500
Resolution 1.37 Å R-free 0.193
4CFR Ca-bound S100A4 C3S, C81S, C86S and F45W mutant complexed with non- muscle myosin IIA Deposited 2013-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Q 1893–1937（45 aa） Fragment：RESIDUES 1893-1935
Mutation：YES CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；0.2 M AMMONIUM ACETATE, 0.1M SODIUM ACETATE PH4.6, 30% W/V PEG 4000
Resolution 1.40 Å R-free 0.175
4ETO Structure of S100A4 in complex with non-muscle myosin-IIA peptide Deposited 2012-04-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain P 1908–1923（16 aa） Fragment：Coiled coil region residues 1908-1923
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.0, 30% (v/v) Jeffamine ED-2001, Vapor diffusion, Sitting drop, temperature 298K
Resolution 1.54 Å R-free 0.251
9SYU shutdown state non-muscle myosin 2A heads region Deposited 2025-10-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–1960（1960 aa）
Chain B 1–1960（1960 aa）
Chain G 1–1960（1960 aa）
Chain H 1–1960（1960 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 PO4 PHOSPHATE ION × 2 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；140 mM KCl, 10 mM MOPS pH 7.2, 0.1 mM EGTA, 2 mM MgCl2, 1 mM ATP. 1 mM Bissulfosuccinimidyl suberate
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
9SZR shutdown state non-muscle myosin 2A heads region Deposited 2025-10-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–1960（1960 aa）
Chain B 1–1960（1960 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 PO4 PHOSPHATE ION × 2 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；140 mM KCl, 10 mM MOPS pH 7.2, 0.1 mM EGTA, 2 mM MgCl2, 1 mM ATP. 1 mM Bissulfosuccinimidyl suberate
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MYH9_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–775； UniProt 1–775

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9ihl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9ihl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9ihl
Deposition date deposition_date2025-02-21
Structure title titleCrystal Structure of the Human Nonmuscle Myosin 2A Motor Domain
Keywords keywordsMyosin, NM2A, human, motor, protein, MOTOR PROTEIN; MOTOR PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier49.67 Å
Radius of gyration Rg (electron density) rg_electron52.85 Å
Forward intensity I(0) i0176536000.00
Molecular weight molecular_weight108940.0 kDa
Excluded volume excluded_volume136800 ų
Envelope volume envelope_volume195960 ų
Hydration-shell volume shell_volume39482 ų
Envelope diameter envelope_diameter218.5 Å
Shell Rg shell_rg41.87 Å
Envelope Rg envelope_rg55.59 Å
Shape Rg shape_rg52.84 Å
Total Rg total_rg52.30 Å
Total atoms total_atoms7668
Residues n_residues953
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax227.9 Å
Rg (real space) rg_real52.63 Å
Rg uncertainty (real space) rg_real_error4.46 Å
I(0) (real space) i0_real1.7650e+08
I(0) uncertainty (real space) i0_real_error3.7450e+06
Rg (reciprocal space) rg_reciprocal49.69 Å
I(0) (reciprocal space) i0_reciprocal175900000.0000
Solution quality estimate total_estimate0.6138
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.6 Å
Skewness Skewness skewness1.030
Kurtosis Kurtosis kurtosis0.271
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha16650000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.004; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.000; Smooth: 0.964
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)