SAXSdb — 5a4b

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

HUMAN ALPHA-ACTININ-2

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 19–266	Fragment：CALPONIN HOMOLOGY DOMAIN, RESIDUES 19-266 Mutation：YES	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；24% POLYETHYLENE GLYCOL 3350, pH 7.5	Resolution 2.01 Å R-free 0.235
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 19–266	Fragment：CALPONIN HOMOLOGY DOMAIN, RESIDUES 19-266 Mutation：YES	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；24% POLYETHYLENE GLYCOL 3350, pH 7.5	Resolution 2.01 Å R-free 0.235

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 5A4B	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1H8B EF-hands 3,4 from alpha-actinin / Z-repeat 7 from titin Deposited 2001-02-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 822–894（73 aa） Fragment：EF-HANDS 3&4 RESIDUE 822-894	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.6；300 K；Ionic strength (raw mmCIF value) 20；Pressure 1 NMR sample composition 0.7 MM COMPLEX	Resolution not provided
1HCI CRYSTAL STRUCTURE OF THE ROD DOMAIN OF ALPHA-ACTININ Deposited 2001-05-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 274–746（473 aa） Fragment：SPECTRIN-LIKE REPEATS 1,2,3, AND 4 - AMINO ACIDS 274 - 746 Chain B 274–746（473 aa） Fragment：SPECTRIN-LIKE REPEATS 1,2,3, AND 4 - AMINO ACIDS 274 - 746	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.9 M (NH4)2SO4, 0.1 M TRISHCL PH 8.5	Resolution 2.80 Å R-free 0.295
1QUU CRYSTAL STRUCTURE OF TWO CENTRAL SPECTRIN-LIKE REPEATS FROM ALPHA-ACTININ Deposited 1999-07-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 391–637（247 aa） Fragment：SPECTRIN-LIKE REPEATS 2 AND 3 - AMINO ACIDS 391 TO 637	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；26% PEG 400 (FLUKA), 100 MM MGSO4, 100 MM HEPES OR TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.50 Å R-free 0.310
4D1E THE CRYSTAL STRUCTURE OF HUMAN MUSCLE ALPHA-ACTININ-2 Deposited 2014-05-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 19–894（876 aa） Fragment：RESIDUES 19-894	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.2 M MG FORMATE 5% PEG SMEAR, 0.01 M EDTA	Resolution 3.50 Å R-free 0.258
5A36 Mutations in the Calponin homology domain of Alpha-Actinin-2 affect Actin binding and incorporation in muscle. Deposited 2015-05-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–266（248 aa） Fragment：CALPONIN HOMOLOGY DOMAIN, UNP RESIDUES 19-266	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；30% POLYETHYLENE GLYCOL 1500, pH 7.5	Resolution 2.00 Å R-free 0.269
5A36 Mutations in the Calponin homology domain of Alpha-Actinin-2 affect Actin binding and incorporation in muscle. Deposited 2015-05-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 19–266（248 aa） Fragment：CALPONIN HOMOLOGY DOMAIN, UNP RESIDUES 19-266	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；30% POLYETHYLENE GLYCOL 1500, pH 7.5	Resolution 2.00 Å R-free 0.269
5A37 Mutations in the Calponin homology domain of Alpha-Actinin-2 affect Actin binding and incorporation in muscle. Deposited 2015-05-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–266（248 aa） Fragment：CALPONIN HOMOLOGY DOMAIN	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；28% POLYETHYLENE GLYCOL 2000, pH 7.5	Resolution 1.88 Å R-free 0.216
5A37 Mutations in the Calponin homology domain of Alpha-Actinin-2 affect Actin binding and incorporation in muscle. Deposited 2015-05-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 19–266（248 aa） Fragment：CALPONIN HOMOLOGY DOMAIN	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；28% POLYETHYLENE GLYCOL 2000, pH 7.5	Resolution 1.88 Å R-free 0.216
5A38 Mutations in the Calponin homology domain of Alpha-Actinin-2 affect Actin binding and incorporation in muscle. Deposited 2015-05-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–266（248 aa） Fragment：CALPONIN HOMOLOGY DOMAIN, RESIDUES 19 TO 266	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；22% POLYETHYLENE GLYCOL 3350, pH 7.5	Resolution 1.90 Å R-free 0.231
5A38 Mutations in the Calponin homology domain of Alpha-Actinin-2 affect Actin binding and incorporation in muscle. Deposited 2015-05-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 19–266（248 aa） Fragment：CALPONIN HOMOLOGY DOMAIN, RESIDUES 19 TO 266	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；22% POLYETHYLENE GLYCOL 3350, pH 7.5	Resolution 1.90 Å R-free 0.231
6SWT Affimer9 co-crystalised with the CH domains of alpha actinin 2. Deposited 2019-09-23	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 19–270（252 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 3350, 0.2M ammonium tartrate	Resolution 1.20 Å R-free 0.164
6TS3 EF-hands 3 and 4 of alpha-actinin in complex with CaMKII regulatory segment Deposited 2019-12-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 825–894（70 aa）	Not recorded	ACE ACETYL GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350	Resolution 1.28 Å R-free 0.199
6TS3 EF-hands 3 and 4 of alpha-actinin in complex with CaMKII regulatory segment Deposited 2019-12-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 825–894（70 aa）	Not recorded	ACE ACETYL GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350	Resolution 1.28 Å R-free 0.199
7A8T Crystal structure of sarcomeric protein FATZ-1 (mini-FATZ-1 construct) in complex with rod domain of alpha-actinin-2 Deposited 2020-08-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 274–746（473 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；100 mM HEPES (pH 7.0), 16% w/v Jeffamine ED-2003	Resolution 2.69 Å R-free 0.235
7A8U Crystal structure of sarcomeric protein FATZ-1 (d91-FATZ-1 construct) in complex with rod domain of alpha-actinin-2 Deposited 2020-08-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 274–746（473 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；100 mM Tris-HCl (pH 8.5), 200 mM trimethylamine N-oxide, 20% w/v polyethylene glycol 2,000 methyl ether	Resolution 3.80 Å R-free 0.239
7ANK Crystal structure of sarcomeric protein FATZ-1 (d91-FATZ-1 construct) in complex with half dimer of alpha-actinin-2 Deposited 2020-10-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–507（507 aa） Chain B 509–894（386 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；100 mM Bis-Tris propane (pH 7.5), 100 mM sodium citrate, 10 mM zinc chloride, 12% w/w polyethylene glycol 3,350	Resolution 3.20 Å R-free 0.284
7B55 Crystal structure of CaMKII-actinin complex bound to MES Deposited 2020-12-03	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 A 825–894（70 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M MES pH 6.0, 20% w/v PEG4000, 0.2 M Lithium Sulfate	Resolution 1.60 Å R-free 0.214
7B56 Crystal structure of CaMKII-actinin complex bound to AMPPNP Deposited 2020-12-03	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 A 825–894（70 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M MES pH 6.0, 20% w/v PEG4000, 0.2 M Lithium Sulfate	Resolution 1.45 Å R-free 0.215
7B57 Crystal structure of CaMKII-actinin complex bound to ADP Deposited 2020-12-03	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 A 825–894（70 aa）	Not recorded	MG MAGNESIUM ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M MES pH 6.0, 20% w/v PEG4000, 0.2 M Lithium Sulfate	Resolution 1.95 Å R-free 0.247

15 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ACTN2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–248； UniProt 19–266 Author chain B； PDBConstruct 1–248； UniProt 19–266

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	5a4b
Deposition date deposition_date	2015-06-05
Structure title title	Mutations in the Calponin homology domain of Alpha-Actinin-2 affect Actin binding and incorporation in muscle.
Keywords keywords	STRUCTURAL PROTEIN, CALPONIN HOMOLOGY DOMAINS; 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	26.32 Å
Radius of gyration Rg (electron density) rg_electron	25.36 Å
Forward intensity I(0) i0	42267000.00
Molecular weight molecular_weight	51065.0 kDa
Excluded volume excluded_volume	64310 Å³
Envelope volume envelope_volume	78991 Å³
Hydration-shell volume shell_volume	26236 Å³
Envelope diameter envelope_diameter	90.8 Å
Shell Rg shell_rg	32.31 Å
Envelope Rg envelope_rg	25.14 Å
Shape Rg shape_rg	25.37 Å
Total Rg total_rg	26.13 Å
Total atoms total_atoms	3588
Residues n_residues	446
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	84.9 Å
Rg (real space) rg_real	26.29 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	4.2270e+07
I(0) uncertainty (real space) i0_real_error	5.3030e+05
Rg (reciprocal space) rg_reciprocal	26.30 Å
I(0) (reciprocal space) i0_reciprocal	42270000.0000
Solution quality estimate total_estimate	0.7034
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.9 Å
Skewness Skewness skewness	0.261
Kurtosis Kurtosis kurtosis	-0.485
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15990000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 0.981; Smooth: 0.974

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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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5a4ba1
Class class	a — All alpha proteins
Fold Fold fold	a.40 — CH domain-like
Superfamily Superfamily superfamily	a.40.1 — Calponin-homology domain, CH-domain
Family Family family	a.40.1.0 — automated matches

Domain ID domain_id	d5a4ba2
Class class	a — All alpha proteins
Fold Fold fold	a.40 — CH domain-like
Superfamily Superfamily superfamily	a.40.1 — Calponin-homology domain, CH-domain
Family Family family	a.40.1.0 — automated matches

Domain ID domain_id	d5a4bb1
Class class	a — All alpha proteins
Fold Fold fold	a.40 — CH domain-like
Superfamily Superfamily superfamily	a.40.1 — Calponin-homology domain, CH-domain
Family Family family	a.40.1.0 — automated matches

Domain ID domain_id	d5a4bb2
Class class	a — All alpha proteins
Fold Fold fold	a.40 — CH domain-like
Superfamily Superfamily superfamily	a.40.1 — Calponin-homology domain, CH-domain
Family Family family	a.40.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	5a4bA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily	10 — Calponin-like domain

Domain ID domain_id	5a4bA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily	10 — Calponin-like domain

Domain ID domain_id	5a4bB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily	10 — Calponin-like domain

Domain ID domain_id	5a4bB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily	10 — Calponin-like domain

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8. Citations (1)

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Unit-cell length a length_a	38.390 Å
Unit-cell length b length_b	46.630 Å
Unit-cell length c length_c	69.860 Å
Unit-cell angle α angle_alpha	73.80 °
Unit-cell angle β angle_beta	80.02 °
Unit-cell angle γ angle_gamma	75.05 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	66.680 Å
R factor r_factor	0.1994
R_work r_work	0.1976
R_free r_free	0.2346

Description description	HUMAN ALPHA-ACTININ-2
Molecular weight formula_weight	28462.8 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3789

Mutations in the Calponin homology domain of Alpha-Actinin-2 affect Actin binding and incorporation in muscle.

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

HUMAN ALPHA-ACTININ-2

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 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	201

fit	/app/data/saxs_computation/a4/5a4b/5a4b.fit
pddf	/app/data/pr_computation/a4/5a4b/5a4b.pr.out
profile	/app/data/saxs_computation/a4/5a4b/5a4b.dat