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4pd3

Crystal Structure of Rigor-Like Human Nonmuscle Myosin-2B

Method: X-RAY DIFFRACTION Dmax: 229.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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

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 Fragment：UNP P35580 residues 1-782, UNP P05095 residues 265-502 No other associated polymer 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
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 265–502 Fragment：UNP P35580 residues 1-782, UNP P05095 residues 265-502 No other associated polymer 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

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 4PD3 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
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
9IHL Crystal Structure of the Human Nonmuscle Myosin 2A Motor Domain Deposited 2025-02-21 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）
Not recorded No recorded non-water small molecule 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

4 other PDB entries and 4 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 785–1022； UniProt 265–502 Author chain B； PDBConstruct 785–1022； UniProt 265–502

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

Dictyostelium discoideum

UniProt P35580

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 1–782 Fragment：UNP P35580 residues 1-782, UNP P05095 residues 265-502 No other associated polymer 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
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–782 Fragment：UNP P35580 residues 1-782, UNP P05095 residues 265-502 No other associated polymer 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name MYH10_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–782； UniProt 1–782 Author chain B； PDBConstruct 1–782； UniProt 1–782

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 4pd3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4pd3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4pd3
Deposition date deposition_date2014-04-17
Structure title titleCrystal Structure of Rigor-Like Human Nonmuscle Myosin-2B
Keywords keywordsmyosin, NM-2B, nonmuscle myosin-2B, rigor-like, nucleotide free, MOTOR PROTEIN, CONTRACTILE PROTEIN; CONTRACTILE 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_guinier59.59 Å
Radius of gyration Rg (electron density) rg_electron61.35 Å
Forward intensity I(0) i0644159000.00
Molecular weight molecular_weight210170.0 kDa
Excluded volume excluded_volume263150 ų
Envelope volume envelope_volume412140 ų
Hydration-shell volume shell_volume65744 ų
Envelope diameter envelope_diameter266.7 Å
Shell Rg shell_rg49.45 Å
Envelope Rg envelope_rg64.42 Å
Shape Rg shape_rg61.35 Å
Total Rg total_rg60.95 Å
Total atoms total_atoms14795
Residues n_residues1852
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 dmax229.5 Å
Rg (real space) rg_real60.91 Å
Rg uncertainty (real space) rg_real_error2.99 Å
I(0) (real space) i0_real6.4330e+08
I(0) uncertainty (real space) i0_real_error1.4020e+07
Rg (reciprocal space) rg_reciprocal58.21 Å
I(0) (reciprocal space) i0_reciprocal641000000.0000
Solution quality estimate total_estimate0.7232
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary44.1 Å
Skewness Skewness skewness0.873
Kurtosis Kurtosis kurtosis0.408
Angular range angular_range— – 0.1300 Å−1
Current regularization parameter α current_alpha0.0093
Highest regularization parameter α highest_alpha44310000.0000
Real-space data points n_real_points27
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.327; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.565; Smooth: 0.852
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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)