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- PDB-3f31: Crystal Structure of the N-terminal region of AlphaII-spectrin Te... -

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Basic information

Entry
Database: PDB / ID: 3f31
TitleCrystal Structure of the N-terminal region of AlphaII-spectrin Tetramerization Domain
ComponentsSpectrin alpha chain, brain
KeywordsACTIN BINDING / STRUCTURAL PROTEIN / lone helix followed by a triple helical bundle / Actin capping / Actin-binding / Alternative splicing / Calcium / Calmodulin-binding / Cytoplasm / Cytoskeleton / Phosphoprotein / Polymorphism / SH3 domain / SPECTRIN
Function / homology
Function and homology information


spectrin / actin filament capping / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / Nephrin family interactions / RHOV GTPase cycle / cortical actin cytoskeleton / RHOU GTPase cycle / Caspase-mediated cleavage of cytoskeletal proteins ...spectrin / actin filament capping / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / Nephrin family interactions / RHOV GTPase cycle / cortical actin cytoskeleton / RHOU GTPase cycle / Caspase-mediated cleavage of cytoskeletal proteins / COPI-mediated anterograde transport / NCAM signaling for neurite out-growth / cell projection / structural constituent of cytoskeleton / specific granule lumen / microtubule cytoskeleton / extracellular vesicle / actin filament binding / tertiary granule lumen / cell junction / actin binding / actin cytoskeleton organization / RAF/MAP kinase cascade / calmodulin binding / cadherin binding / intracellular membrane-bounded organelle / calcium ion binding / Neutrophil degranulation / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / SH3 domain / EF-hand domain pair / EF-hand, calcium binding motif / Src homology 3 domains / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.3 Å
AuthorsMehboob, S. / Santarsiero, B.D. / Long, F. / Witek, M. / Fung, L.W.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of the nonerythroid alpha-spectrin tetramerization site reveals differences between erythroid and nonerythroid spectrin tetramer formation.
Authors: Mehboob, S. / Song, Y. / Witek, M. / Long, F. / Santarsiero, B.D. / Johnson, M.E. / Fung, L.W.
History
DepositionOct 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spectrin alpha chain, brain
B: Spectrin alpha chain, brain


Theoretical massNumber of molelcules
Total (without water)35,3822
Polymers35,3822
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-18 kcal/mol
Surface area18830 Å2
MethodPISA
2
A: Spectrin alpha chain, brain


Theoretical massNumber of molelcules
Total (without water)17,6911
Polymers17,6911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Spectrin alpha chain, brain


Theoretical massNumber of molelcules
Total (without water)17,6911
Polymers17,6911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.720, 71.460, 80.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer, as known from light scattering, in solution.

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Components

#1: Protein Spectrin alpha chain, brain / Spectrin / non-erythroid alpha chain / Alpha-II spectrin / Fodrin alpha chain


Mass: 17690.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPTAN1, SPTA2 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13813
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG8000:PEG1000 (1:2), 4% 1,4-butane-diol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 14, 2008 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 22316 / Num. obs: 22316 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.65 % / Biso Wilson estimate: 34.943 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.058
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 4.54 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2.51 / Rsym value: 0.737 / % possible all: 82.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
HYSS/RESOLVEmodel building
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
HYSS/RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→18.984 Å / SU ML: 0.4 / Isotropic thermal model: isotropic / σ(F): 1.99 / Phase error: 27.57 / Stereochemistry target values: ML / Details: phenix least squares
RfactorNum. reflection% reflection
Rfree0.2798 1323 8.98 %
Rwork0.214 --
obs0.22 14733 95.99 %
all-14740 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.713 Å2 / ksol: 0.308 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.0479 Å211.8208 Å2-4.7729 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.3→18.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2322 0 0 206 2528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042401
X-RAY DIFFRACTIONf_angle_d0.6893219
X-RAY DIFFRACTIONf_dihedral_angle_d12.879946
X-RAY DIFFRACTIONf_chiral_restr0.049342
X-RAY DIFFRACTIONf_plane_restr0.002426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.39190.31131410.22031427X-RAY DIFFRACTION95
2.3919-2.50060.31041440.20551451X-RAY DIFFRACTION96
2.5006-2.63210.32981460.22371491X-RAY DIFFRACTION96
2.6321-2.79650.30241440.21181451X-RAY DIFFRACTION96
2.7965-3.01160.27721480.21811501X-RAY DIFFRACTION97
3.0116-3.31330.27691470.22541502X-RAY DIFFRACTION97
3.3133-3.78940.30381420.20891437X-RAY DIFFRACTION92
3.7894-4.76170.23231500.19581522X-RAY DIFFRACTION96
4.7617-18.9850.24961610.19191628X-RAY DIFFRACTION98

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