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- PDB-5j4o: Structure of human erythrocytic Spectrin alpha chain repeats 16-17 -

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Basic information

Entry
Database: PDB / ID: 5j4o
TitleStructure of human erythrocytic Spectrin alpha chain repeats 16-17
ComponentsSpectrin alpha chain, erythrocytic 1
KeywordsSTRUCTURAL PROTEIN / erythrocyte / spectrin / helical bundle / domains
Function / homology
Function and homology information


cuticular plate / spectrin / lymphocyte homeostasis / spectrin-associated cytoskeleton / porphyrin-containing compound biosynthetic process / plasma membrane organization / actin filament capping / Interaction between L1 and Ankyrins / cortical actin cytoskeleton / hemopoiesis ...cuticular plate / spectrin / lymphocyte homeostasis / spectrin-associated cytoskeleton / porphyrin-containing compound biosynthetic process / plasma membrane organization / actin filament capping / Interaction between L1 and Ankyrins / cortical actin cytoskeleton / hemopoiesis / COPI-mediated anterograde transport / positive regulation of T cell proliferation / NCAM signaling for neurite out-growth / actin filament organization / cell projection / cytoplasmic side of plasma membrane / structural constituent of cytoskeleton / actin filament binding / actin cytoskeleton / cell junction / regulation of cell shape / actin cytoskeleton organization / RAF/MAP kinase cascade / axon / calcium ion binding / plasma membrane / cytosol
Similarity search - Function
EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / SH3 domain / Src homology 3 domains / EF-hand calcium-binding domain profile. ...EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / SH3 domain / Src homology 3 domains / 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
Similarity search - Domain/homology
Spectrin alpha chain, erythrocytic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsCutts, E.E. / Vakonakis, I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust088497/Z/09/Z United Kingdom
CitationJournal: To Be Published
Title: Interactions of Plasmodium falciparum KAHRP and PfEMP1 with the host cytoskeleton suggest a model for cytoadherent protrusions on the infected erythrocyte surface
Authors: Cutts, E.E. / Laasch, N. / Reiter, D.M. / Trenker, R. / Slater, L.M. / Stansfeld, P.J. / Vakonakis, I.
History
DepositionApr 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spectrin alpha chain, erythrocytic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3947
Polymers26,7571
Non-polymers6376
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint13 kcal/mol
Surface area14720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.640, 43.670, 154.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Spectrin alpha chain, erythrocytic 1 / Erythroid alpha-spectrin


Mass: 26757.439 Da / Num. of mol.: 1 / Fragment: UNP residues 1599-1826
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Cell: Erythrocytes / Gene: SPTA1, SPTA / Plasmid: pET16c
Details (production host): Modified to include 3C protease site
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: P02549
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Molecular Dimensions Morpheus crystallisation screen, condition A2: 0.03M MgCl2, 0.03M CaCl2, 0.1M MES/Imidazole pH 6.5, 20% v/v Ethylene glycol, 10% v/v PEG 8000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 1.54→38.57 Å / Num. obs: 38551 / % possible obs: 99.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 23.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.1
Reflection shellResolution: 1.54→1.58 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.926 / Mean I/σ(I) obs: 1.7 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U5P

1u5p


Resolution: 1.54→30.18 Å / Cor.coef. Fo:Fc: 0.9362 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.089 / SU Rfree Blow DPI: 0.085 / SU Rfree Cruickshank DPI: 0.084
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1880 4.89 %RANDOM
Rwork0.209 ---
obs0.2099 38481 99.48 %-
Displacement parametersBiso mean: 35.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.5392 Å20 Å20 Å2
2---0.3611 Å20 Å2
3----3.1781 Å2
Refine analyzeLuzzati coordinate error obs: 0.207 Å
Refinement stepCycle: 1 / Resolution: 1.54→30.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 28 250 4077
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013855HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.96980HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d923SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes75HARMONIC2
X-RAY DIFFRACTIONt_gen_planes574HARMONIC5
X-RAY DIFFRACTIONt_it3855HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion15.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion238SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4284SEMIHARMONIC4
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2138 144 4.88 %
Rwork0.217 2805 -
all0.2168 2949 -
obs--99.48 %
Refinement TLS params.Method: refined / Origin x: -3.0795 Å / Origin y: 5.4751 Å / Origin z: -23.0408 Å
111213212223313233
T-0.0074 Å20.012 Å20.0547 Å2-0.0087 Å2-0.0131 Å2---0.0212 Å2
L0.9612 °2-0.5139 °2-0.8408 °2-0.3002 °20.5393 °2--0.8356 °2
S-0.0348 Å °0.0658 Å °0.0225 Å °-0.0335 Å °0.0089 Å °-0.0368 Å °-0.0117 Å °0.0683 Å °0.0259 Å °
Refinement TLS groupSelection details: { A|* }

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