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5i4e

Crystal Structure of Human Nonmuscle Myosin 2C motor domain

Method: X-RAY DIFFRACTION Dmax: 207.4 Å Quality: SUSPICIOUS
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Myosin-14,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 265–489 Fragment：UNP residues 265-489,UNP residues 265-489 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

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 5I4E 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 ligand/ion 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 ligand/ion 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
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 ligand/ion 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 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 756–980； UniProt 265–489

Myosin-14,Alpha-actinin A

Dictyostelium discoideum

UniProt Q7Z406

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 47–784 Fragment：UNP residues 265-489,UNP residues 265-489 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

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 5I4E Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 1–799（799 aa）
Chain G 1–799（799 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

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MYH14_HUMAN
Isoform Q7Z406-5
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–738； UniProt 47–784

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 5i4e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5i4e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5i4e
Deposition date deposition_date2016-02-11
Structure title titleCrystal Structure of Human Nonmuscle Myosin 2C motor domain
Keywords keywordsMotor 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_guinier47.50 Å
Radius of gyration Rg (electron density) rg_electron49.89 Å
Forward intensity I(0) i0186680000.00
Molecular weight molecular_weight109840.0 kDa
Excluded volume excluded_volume137140 ų
Envelope volume envelope_volume200300 ų
Hydration-shell volume shell_volume41251 ų
Envelope diameter envelope_diameter209.7 Å
Shell Rg shell_rg42.09 Å
Envelope Rg envelope_rg52.86 Å
Shape Rg shape_rg49.90 Å
Total Rg total_rg49.44 Å
Total atoms total_atoms7730
Residues n_residues959
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 dmax207.4 Å
Rg (real space) rg_real49.76 Å
Rg uncertainty (real space) rg_real_error4.08 Å
I(0) (real space) i0_real1.8670e+08
I(0) uncertainty (real space) i0_real_error4.5150e+06
Rg (reciprocal space) rg_reciprocal47.51 Å
I(0) (reciprocal space) i0_reciprocal186200000.0000
Solution quality estimate total_estimate0.3960
Solution quality rating solution_quality SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.7 Å
Skewness Skewness skewness1.035
Kurtosis Kurtosis kurtosis0.360
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0003
Highest regularization parameter α highest_alpha18680000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.026; Stabil: 1.000; Sysdev: 0.044; Positv: 1.000; Valcen: 0.010; Smooth: 0.925
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id5i4eA01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily360 — Myosin S1 fragment, N-terminal
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8. Citations (1)

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9. Files and Curves (10)