SAXSdb — 4bex

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1. Protein Identity and Related Structures Protein Identity & Related Structures

COFILIN-1

HOMO SAPIENS

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain 1； UniProt 1–166	Fragment：COFILIN-LIKE FOLD, RESIDUES 1-166 Mutation：YES	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；2.4 M SODIUM MALONATE PH 7.0 THE CRYSTALS WERE AIR-DRIED BEFORE FREEZING TO DEHYDRATE.	Resolution 2.80 Å R-free 0.236

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 4BEX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Q8G NMR structure of human Cofilin Deposited 2003-08-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–166（166 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 1；Pressure 1 NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 1；Pressure 1 NMR sample composition 0.8 mM cofilin U-15N,13C;10 mM phosphate buffer, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM cofilin U-15N, 10 mM phosphate buffer ,90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
1Q8X NMR structure of human cofilin Deposited 2003-08-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–166（166 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 1；Pressure 1 NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 1；Pressure 1 NMR sample composition 0.8 mM cofilin U-15N,13C; 10mM phosphate buffer; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM cofilin U-15N, 10mM phosphate buffer; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
5HVK Crystal structure of LIMK1 mutant D460N in complex with full-length cofilin-1 Deposited 2016-01-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–166（165 aa）	Mutation：A69T Non-standard monomer：Yes (specific site not provided by mmCIF)	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；1.2-1.4 M tri-Sodium citrate, 0.1 M sodium acetate, pH 5.5. 4 crystals used.	Resolution 3.50 Å R-free 0.310
5HVK Crystal structure of LIMK1 mutant D460N in complex with full-length cofilin-1 Deposited 2016-01-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–166（165 aa）	Mutation：A69T	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；1.2-1.4 M tri-Sodium citrate, 0.1 M sodium acetate, pH 5.5. 4 crystals used.	Resolution 3.50 Å R-free 0.310
5L6W Structure Of the LIMK1-ATPgammaS-CFL1 Complex Deposited 2016-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–166（166 aa）	Mutation：S3C	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；35% pentaerythritol propoxylate 5/4, 0.1 M HEPES pH 7.5, 0.2 M potassium chloride	Resolution 2.53 Å R-free 0.284
6UBY Isolated cofilin bound to an actin filament Deposited 2019-09-13	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 × 9 PDB declaration: nonameric	Chain I 1–166（166 aa）	Not recorded	MG MAGNESIUM ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 6.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.50 Å
6UC0 Isolated S3D-cofilin bound to an actin filament Deposited 2019-09-13	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 I 1–166（166 aa）	Mutation：S3D	MG MAGNESIUM ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.50 Å
6UC4 Barbed end side of a cofilactin cluster Deposited 2019-09-13	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 × 16 PDB declaration: hexadecameric	Chain I 1–166（166 aa） Chain M 1–166（166 aa） Chain N 1–166（166 aa） Chain O 1–166（166 aa） Chain P 1–166（166 aa）	Not recorded	MG MAGNESIUM ION × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 6.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.20 Å
6VAO Human cofilin-1 decorated actin filament Deposited 2019-12-17	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 × 10 PDB declaration: decameric	Chain F 1–166（166 aa） Chain G 1–166（166 aa） Chain H 1–166（166 aa） Chain I 1–166（166 aa） Chain J 1–166（166 aa）	Not recorded	MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 6.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9H1F Cofilin-1 in complex with high-affinity Sybody B12 Deposited 2024-10-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–166（166 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.1 M Citric acid pH 4.0 and 2.4 M Ammonium sulfate	Resolution 1.80 Å R-free 0.226
9QFD Cryo-EM structure of the fully cofilin-1-decorated actin filament (cofilactin) Deposited 2025-03-11	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 × 14 PDB declaration: 14-meric	Chain H 1–166（166 aa） Chain I 1–166（166 aa） Chain J 1–166（166 aa） Chain K 1–166（166 aa） Chain L 1–166（166 aa） Chain M 1–166（166 aa） Chain N 1–166（166 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1；1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.02% Tween20). cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.61 Å
9QFE Cryo-EM structure of the actin filament hetero-decorated by Coronin-1 and Cofilin-1 on separate actin strands Deposited 2025-03-11	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 × 14 PDB declaration: 14-meric	Chain H 1–166（166 aa） Chain I 1–166（166 aa） Chain J 1–166（166 aa） Chain K 1–166（166 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1；1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.02% Tween20). cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.12 Å
9QFG Cryo-EM structure of the actin filament hetero-decorated by Coronin-1 and Cofilin-1, strand boundary Deposited 2025-03-11	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 × 14 PDB declaration: 14-meric	Chain H 1–166（166 aa） Chain I 1–166（166 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1；1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.02% Tween20). cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.49 Å
9QFJ Cryo-EM structure of the cofilactin filament core at 2.3 Angstrom resolution. Deposited 2025-03-11	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 × 10 PDB declaration: decameric	Chain F 1–166（166 aa） Chain G 1–166（166 aa） Chain H 1–166（166 aa） Chain I 1–166（166 aa） Chain J 1–166（166 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1；1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.015% Tween) cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.31 Å
9QFK Cryo-EM structure of the Coronin-1B-decorated actin filament bound by one Cofilin-1 molecule (crosslinked) Deposited 2025-03-11	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 × 14 PDB declaration: 14-meric	Chain J 1–166（166 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1；1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.02% Tween20). cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.99 Å
9QFO Cryo-EM structure of the cofilactin filament pointed end Deposited 2025-03-12	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 × 10 PDB declaration: decameric	Chain G 1–166（166 aa） Chain H 1–166（166 aa） Chain I 1–166（166 aa） Chain J 1–166（166 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1；1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.015% Tween20) cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.96 Å
9QFQ Cryo-EM structure of the cofilactin barbed end bound by AIP1 Deposited 2025-03-12	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: 11-meric	Chain F 1–166（166 aa） Chain G 1–166（166 aa） Chain H 1–166（166 aa） Chain I 1–166（166 aa） Chain J 1–166（166 aa）	Not recorded	MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1；1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.015% Tween20) cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.76 Å
9QFW Cryo-EM structure of the cofilactin barbed end bound by two AIP1 molecules Deposited 2025-03-12	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 × 12 PDB declaration: 12-meric	Chain F 1–166（166 aa） Chain G 1–166（166 aa） Chain H 1–166（166 aa） Chain I 1–166（166 aa） Chain J 1–166（166 aa）	Not recorded	MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1；1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.015% Tween20) cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.16 Å

17 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	COF1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 1； PDBConstruct 16–181； UniProt 1–166

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4bex
Deposition date deposition_date	2013-03-12
Structure title title	Structure of human Cofilin1
Keywords keywords	STRUCTURAL PROTEIN, ACTIN-BINDING, CYTOSKELETON; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	17.23 Å
Radius of gyration Rg (electron density) rg_electron	15.82 Å
Forward intensity I(0) i0	6103680.00
Molecular weight molecular_weight	18455.0 kDa
Excluded volume excluded_volume	23454 Å³
Envelope volume envelope_volume	27247 Å³
Hydration-shell volume shell_volume	14628 Å³
Envelope diameter envelope_diameter	55.6 Å
Shell Rg shell_rg	21.72 Å
Envelope Rg envelope_rg	16.17 Å
Shape Rg shape_rg	15.77 Å
Total Rg total_rg	17.13 Å
Total atoms total_atoms	1294
Residues n_residues	166
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	57.7 Å
Rg (real space) rg_real	17.13 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	6.1040e+06
I(0) uncertainty (real space) i0_real_error	8.3080e+04
Rg (reciprocal space) rg_reciprocal	17.14 Å
I(0) (reciprocal space) i0_reciprocal	6104000.0000
Solution quality estimate total_estimate	0.7944
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.8 Å
Skewness Skewness skewness	0.155
Kurtosis Kurtosis kurtosis	-0.378
Angular range angular_range	— – 0.4600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1437000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.775; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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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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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4bex1_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.109 — Gelsolin-like
Superfamily Superfamily superfamily	d.109.1 — Actin depolymerizing proteins
Family Family family	d.109.1.2 — Cofilin-like

CATH v4.4 (1 domains)

Domain ID domain_id	4bex100
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	10 — Severin

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8. Citations (1)

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Unit-cell length a length_a	85.940 Å
Unit-cell length b length_b	85.940 Å
Unit-cell length c length_c	85.290 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	28.130 Å
R factor r_factor	0.2079
R_work r_work	0.2065
R_free r_free	0.2357

Description description	COFILIN-1
Molecular weight formula_weight	19712.7 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	1
Atom count atom_count	1310

Structure of human Cofilin1

1. Protein Identity and Related Structures Protein Identity & Related Structures

COFILIN-1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	16

fit	/app/data/saxs_computation/be/4bex/4bex.fit
pddf	/app/data/pr_computation/be/4bex/4bex.pr.out
profile	/app/data/saxs_computation/be/4bex/4bex.dat