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

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Basic information

Entry
Database: PDB / ID: 9eyb
TitleA-SPECTRIN SH3 DOMAIN V9L, A11V, V23L, M25C, V46W, V53L and V58L MUTANT
ComponentsSpectrin alpha chain, non-erythrocytic 1
KeywordsSIGNALING PROTEIN / Three-dimensional structure / SH3 domain / Cell signaling / Src-family / Hydrophobic-core mutations
Function / homology
Function and homology information


actin filament capping / costamere / cortical actin cytoskeleton / cell projection / actin filament binding / cell junction / actin cytoskeleton organization / calmodulin binding / calcium ion binding / plasma membrane
Similarity search - Function
Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / SH3 domain / EF-hand domain pair ...Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / SH3 domain / EF-hand domain pair / EF-hand, calcium binding motif / Src homology 3 domains / SH3-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
PHOSPHATE ION / Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.337 Å
AuthorsVizarraga, D. / Fita, I. / Cianferoni, D. / Delgado, J. / Serrano, L.
Funding support Spain, 1items
OrganizationGrant numberCountry
La Caixa FoundationLCF/BQ/D119/11730061 Spain
CitationJournal: Protein Sci. / Year: 2025
Title: Artificial intelligence and first-principle methods in protein redesign: A marriage of convenience?
Authors: Cianferoni, D. / Vizarraga, D. / Delgado, J. / Fita, I. / Serrano, L.
History
DepositionApr 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Spectrin alpha chain, non-erythrocytic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7143
Polymers7,5271
Non-polymers1872
Water1,71195
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-5 kcal/mol
Surface area4550 Å2
MethodPISA
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 number19
Space group name H-MP212121

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Components

#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 interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 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

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: STFC Large Pixel Detector / Detector: PIXEL / Date: Sep 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.337→32.664 Å / Num. obs: 18004 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Net I/σ(I): 16.4
Reflection shellResolution: 1.337→1.36 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 901 / CC1/2: 0.652

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.337→32.664 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflection
Rfree0.1748 909 5.049 %
Rwork0.141 17094 -
all0.143 --
obs-18003 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.816 Å2
Baniso -1Baniso -2Baniso -3
1--1.506 Å2-0 Å2-0 Å2
2---0.251 Å20 Å2
3---1.757 Å2
Refinement stepCycle: LAST / Resolution: 1.337→32.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms530 0 11 95 636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.013592
X-RAY DIFFRACTIONr_bond_other_d0.0010.016559
X-RAY DIFFRACTIONr_angle_refined_deg1.941.652807
X-RAY DIFFRACTIONr_angle_other_deg1.451.61299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.886571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80823.22631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58715110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.222153
X-RAY DIFFRACTIONr_chiral_restr0.1040.269
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02655
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02135
X-RAY DIFFRACTIONr_nbd_refined0.2180.276
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.2491
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2238
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2300
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.264
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1080.27
X-RAY DIFFRACTIONr_nbd_other0.2780.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2020.216
X-RAY DIFFRACTIONr_mcbond_it4.4852.302266
X-RAY DIFFRACTIONr_mcbond_other4.4082.275265
X-RAY DIFFRACTIONr_mcangle_it6.5053.455334
X-RAY DIFFRACTIONr_mcangle_other6.4973.473335
X-RAY DIFFRACTIONr_scbond_it8.1093.056326
X-RAY DIFFRACTIONr_scbond_other8.113.055323
X-RAY DIFFRACTIONr_scangle_it10.1134.273470
X-RAY DIFFRACTIONr_scangle_other10.0854.266465
X-RAY DIFFRACTIONr_lrange_it11.23228.979663
X-RAY DIFFRACTIONr_lrange_other10.62227.521636
X-RAY DIFFRACTIONr_rigid_bond_restr7.61631151
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
1.337-1.3710.268600.27212460.27213060.8970.8940.25
1.371-1.4090.252670.23311930.23412600.9150.9160.206
1.409-1.4490.292700.19511740.212440.8950.9420.166
1.449-1.4940.188500.17911500.17912000.9460.9530.145
1.494-1.5430.195520.15511240.15611760.9470.9610.124
1.543-1.5970.173700.12910770.13211470.9590.9710.106
1.597-1.6570.218530.12710180.13210710.9510.9730.106
1.657-1.7240.198550.10910080.11310630.9660.9770.093
1.724-1.8010.142530.1029490.10410020.9740.9830.089
1.801-1.8890.155480.0919380.0949860.9770.9870.084
1.889-1.990.132470.0998830.1019300.9790.9850.096
1.99-2.1110.143420.118360.1118780.9690.9820.108
2.111-2.2560.112350.1067920.1068270.9860.9830.109
2.256-2.4350.187460.1167440.1197900.9620.9790.124
2.435-2.6660.189430.1316690.1347120.9590.9760.147
2.666-2.9790.158320.1416180.1426500.9730.9720.165
2.979-3.4350.189290.1265640.1295930.9690.9770.155
3.435-4.1950.145280.1344740.1345020.9760.9790.172
4.195-5.8840.254180.1573900.164080.9350.9750.217
5.884-32.6640.171110.3082470.3032580.9530.9270.485

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