PDB-9eyb: A-SPECTRIN SH3 DOMAIN V9L, A11V, V23L, M25C, V46W, V53L and V58L ...

ID or keywords:

Entry

Database: PDB / ID: 9eyb

Title

A-SPECTRIN SH3 DOMAIN V9L, A11V, V23L, M25C, V46W, V53L and V58L MUTANT

Components

Spectrin alpha chain, non-erythrocytic 1

Keywords

SIGNALING PROTEIN / Three-dimensional structure / SH3 domain / Cell signaling / Src-family / Hydrophobic-core mutations

Function / homology

Function and homology information

costamere / actin filament capping / cortical actin cytoskeleton / cell projection / actin filament binding / cell junction / actin cytoskeleton organization / calmodulin binding / calcium ion binding / plasma membrane
Similarity search - Function

Biological species

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.337 Å

Authors

Vizarraga, D. / Fita, I. / Cianferoni, D. / Delgado, J. / Serrano, L.

Funding support

Spain, 1items

Citation

Journal: Protein Sci. / Year: 2025
Title: Artificial intelligence and first-principle methods in protein redesign: A marriage of convenience?
Authors: Cianferoni, D. / Vizarraga, D. / Fernandez-Escamilla, A.M. / Fita, I. / Hamdani, R. / Reche, R. / Delgado, J. / Serrano, L.

History

Deposition	Apr 9, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 6, 2025	Provider: repository / Type: Initial release
Revision 1.1	Aug 13, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9eyb.cif.gz	47.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9eyb.ent.gz		Display	PDB format
PDBx/mmJSON format	9eyb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9eyb_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	9eyb_full_validation.pdf.gz	1 MB	Display
Data in XML	9eyb_validation.xml.gz	7.1 KB	Display
Data in CIF	9eyb_validation.cif.gz	9.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ey/9eyb ftp://data.pdbj.org/pub/pdb/validation_reports/ey/9eyb	HTTPS FTP

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Related structure data

Related structure data	9eycC 9eyeC 9eyfC 9ih6C 9ih7C 9ihaC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: Spectrin alpha chain, non-erythrocytic 1

hetero molecules

7.71 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	31.694, 36.949, 65.327
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Spectrin alpha chain, non-erythrocytic 1 / Alpha-II spectrin / Fodrin alpha chain Mass: 7526.597 Da / Num. of mol.: 1 / Mutation: V9L, A11V, V23L, M25C, V46W, V53L, V58L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: SPTAN1, SPTA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07751
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.54 Å³/Da / Density % sol: 51.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.8M Ammonium Sulfate and 0.1M HEPES pH: 7.0

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
Detector	Type: STFC Large Pixel Detector / Detector: PIXEL / Date: Sep 21, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97926 Å / Relative weight: 1
Reflection	Resolution: 1.337→32.664 Å / Num. obs: 18004 / % possible obs: 100 % / Redundancy: 12.7 % / CC_1/2: 0.998 / R_merge(I) obs: 0.072 / Net I/σ(I): 16.4
Reflection shell	Resolution: 1.337→1.36 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 901 / CC_1/2: 0.652

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.337→32.664 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.971 / SU B: 1.985 / SU ML: 0.035 / Cross valid method: FREE R-VALUE / ESU R: 0.047 / ESU R Free: 0.047
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1748	909	5.049 %
R_work	0.141	17094	-
all	0.143	-	-
obs	-	18003	100 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 28.816 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.506 Å²	-0 Å²	-0 Å²
2-	-	-0.251 Å²	0 Å²
3-	-	-	1.757 Å²

Refinement step

Cycle: LAST / Resolution: 1.337→32.664 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	530	0	11	95	636

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	592
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	559
X-RAY DIFFRACTION	r_angle_refined_deg	1.94	1.652	807
X-RAY DIFFRACTION	r_angle_other_deg	1.45	1.6	1299
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.886	5	71
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.808	23.226	31
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.587	15	110
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.222	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	69
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	655
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	135
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	76
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	491
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	238
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	300
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.24	0.2	64
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.108	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.278	0.2	32
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.202	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	4.485	2.302	266
X-RAY DIFFRACTION	r_mcbond_other	4.408	2.275	265
X-RAY DIFFRACTION	r_mcangle_it	6.505	3.455	334
X-RAY DIFFRACTION	r_mcangle_other	6.497	3.473	335
X-RAY DIFFRACTION	r_scbond_it	8.109	3.056	326
X-RAY DIFFRACTION	r_scbond_other	8.11	3.055	323
X-RAY DIFFRACTION	r_scangle_it	10.113	4.273	470
X-RAY DIFFRACTION	r_scangle_other	10.085	4.266	465
X-RAY DIFFRACTION	r_lrange_it	11.232	28.979	663
X-RAY DIFFRACTION	r_lrange_other	10.622	27.521	636
X-RAY DIFFRACTION	r_rigid_bond_restr	7.616	3	1151

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	WR_factor R_work
1.337-1.371	0.268	60	0.272	1246	0.272	1306	0.897	0.894	0.25
1.371-1.409	0.252	67	0.233	1193	0.234	1260	0.915	0.916	0.206
1.409-1.449	0.292	70	0.195	1174	0.2	1244	0.895	0.942	0.166
1.449-1.494	0.188	50	0.179	1150	0.179	1200	0.946	0.953	0.145
1.494-1.543	0.195	52	0.155	1124	0.156	1176	0.947	0.961	0.124
1.543-1.597	0.173	70	0.129	1077	0.132	1147	0.959	0.971	0.106
1.597-1.657	0.218	53	0.127	1018	0.132	1071	0.951	0.973	0.106
1.657-1.724	0.198	55	0.109	1008	0.113	1063	0.966	0.977	0.093
1.724-1.801	0.142	53	0.102	949	0.104	1002	0.974	0.983	0.089
1.801-1.889	0.155	48	0.091	938	0.094	986	0.977	0.987	0.084
1.889-1.99	0.132	47	0.099	883	0.101	930	0.979	0.985	0.096
1.99-2.111	0.143	42	0.11	836	0.111	878	0.969	0.982	0.108
2.111-2.256	0.112	35	0.106	792	0.106	827	0.986	0.983	0.109
2.256-2.435	0.187	46	0.116	744	0.119	790	0.962	0.979	0.124
2.435-2.666	0.189	43	0.131	669	0.134	712	0.959	0.976	0.147
2.666-2.979	0.158	32	0.141	618	0.142	650	0.973	0.972	0.165
2.979-3.435	0.189	29	0.126	564	0.129	593	0.969	0.977	0.155
3.435-4.195	0.145	28	0.134	474	0.134	502	0.976	0.979	0.172
4.195-5.884	0.254	18	0.157	390	0.16	408	0.935	0.975	0.217
5.884-32.664	0.171	11	0.308	247	0.303	258	0.953	0.927	0.485

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