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- PDB-3lbx: Crystal Structure of the Erythrocyte Spectrin Tetramerization Dom... -

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Basic information

Entry
Database: PDB / ID: 3lbx
TitleCrystal Structure of the Erythrocyte Spectrin Tetramerization Domain Complex
Components
  • Spectrin alpha chain, erythrocyte
  • Spectrin beta chain, erythrocyte
KeywordsSTRUCTURAL PROTEIN / spectrin / tetramer / complex / three-helix bundle / alpha helix / partial repeat / helical linker / Actin capping / Actin-binding / Cell shape / Cytoskeleton / Disease mutation / Elliptocytosis / Hereditary hemolytic anemia / Pyropoikilocytosis / SH3 domain / Phosphoprotein
Function / homology
Function and homology information


cuticular plate / spectrin / lymphocyte homeostasis / spectrin-associated cytoskeleton / porphyrin-containing compound biosynthetic process / modification of postsynaptic actin cytoskeleton / plasma membrane organization / actin filament capping / Interaction between L1 and Ankyrins / ankyrin binding ...cuticular plate / spectrin / lymphocyte homeostasis / spectrin-associated cytoskeleton / porphyrin-containing compound biosynthetic process / modification of postsynaptic actin cytoskeleton / plasma membrane organization / actin filament capping / Interaction between L1 and Ankyrins / ankyrin binding / 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 / actin binding / regulation of cell shape / actin cytoskeleton organization / RAF/MAP kinase cascade / postsynapse / axon / glutamatergic synapse / calcium ion binding / cell surface / protein-containing complex / plasma membrane / cytosol
Similarity search - Function
Spectrin, beta subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. ...Spectrin, beta subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / SH3 domain / Src homology 3 domains / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / EF-hand domain / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain pair / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Spectrin alpha chain, erythrocytic 1 / Spectrin beta chain, erythrocytic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsIpsaro, J.J. / Harper, S.L. / Messick, T.E. / Marmorstein, R. / Mondragon, A. / Speicher, D.W.
CitationJournal: Blood / Year: 2010
Title: Crystal structure and functional interpretation of the erythrocyte spectrin tetramerization domain complex.
Authors: Ipsaro, J.J. / Harper, S.L. / Messick, T.E. / Marmorstein, R. / Mondragon, A. / Speicher, D.W.
History
DepositionJan 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: 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, erythrocyte
B: Spectrin beta chain, erythrocyte


Theoretical massNumber of molelcules
Total (without water)40,7162
Polymers40,7162
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-14 kcal/mol
Surface area22010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.901, 213.901, 31.461
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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


Mass: 18945.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPTA, SPTA1 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P02549
#2: Protein Spectrin beta chain, erythrocyte / Beta-I spectrin


Mass: 21770.697 Da / Num. of mol.: 1 / Fragment: UNP residues 1902-2084
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPTB, SPTB1 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P11277

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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: 4.42 Å3/Da / Density % sol: 72.17 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 10% PEG-6000, 10% glycerol, 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 5, 2009
RadiationMonochromator: Diamond laue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. all: 18271 / Num. obs: 18015 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.057 / Net I/σ(I): 13.5
Reflection shellResolution: 2.8→2.92 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 2195 / Rsym value: 0.297 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MAR345data collection
SHARPphasing
REFMAC5.5.0088refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.8→35 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.905 / SU B: 32.085 / SU ML: 0.283 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.496 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.29938 922 5.1 %RANDOM
Rwork0.26795 ---
obs0.26943 17085 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.693 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.8→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 0 0 2673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212714
X-RAY DIFFRACTIONr_bond_other_d0.0010.021937
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9513636
X-RAY DIFFRACTIONr_angle_other_deg0.82134686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1796.851042
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.93124.094149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71615545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3421527
X-RAY DIFFRACTIONr_chiral_restr0.0710.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02558
X-RAY DIFFRACTIONr_mcbond_it0.421.51600
X-RAY DIFFRACTIONr_mcbond_other0.0551.5649
X-RAY DIFFRACTIONr_mcangle_it0.80722564
X-RAY DIFFRACTIONr_scbond_it1.15331114
X-RAY DIFFRACTIONr_scangle_it1.9674.51072
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 76 -
Rwork0.409 1251 -
obs--98.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
111.4529.7946-8.462611.344-10.18710.1145-1.23920.8649-0.0152-1.63570.7313-0.94320.7336-0.26090.50790.9384-0.56030.34960.75430.16670.9019-4.824-37.649-12.307
210.47724.7976-3.84588.0184-0.92396.6826-0.0302-0.463-0.14241.1348-0.39770.49120.13090.34660.42790.229-0.0260.13060.0970.1310.345-36.791-64.73318.673
36.24432.6062-6.70665.4779-2.72617.8075-0.69110.3258-0.5239-0.56730.0793-0.55860.3488-0.00110.61190.3946-0.10650.02630.58390.12040.7033-32.654-63.4553.424
42.06714.367-1.211412.0856-2.62261.6511-0.2349-0.0833-0.52040.10260.4119-1.22270.3406-0.6828-0.17710.7334-0.31720.1150.86090.10611.117724.3437.908-24.358
54.8771-0.1874-0.211116.4222-5.9266.4969-0.4205-0.1323-0.412-0.15950.33760.36470.1849-1.23720.08290.2642-0.22190.13950.4849-0.11580.426418.64716.829-28.835
63.30885.7447-3.275411.4962-6.24554.3811-0.2658-0.0949-0.3182-0.3961-0.0175-1.7395-0.50470.10050.28320.8828-0.50.17680.83770.17661.34490.488-26.251-11.239
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 59
2X-RAY DIFFRACTION2A60 - 106
3X-RAY DIFFRACTION3A107 - 158
4X-RAY DIFFRACTION4B1900 - 1943
5X-RAY DIFFRACTION5B1944 - 2000
6X-RAY DIFFRACTION6B2001 - 2084

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