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- PDB-2fot: Crystal structure of the complex between calmodulin and alphaII-s... -

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Basic information

Entry
Database: PDB / ID: 2fot
TitleCrystal structure of the complex between calmodulin and alphaII-spectrin
Components
  • Calmodulin
  • alpha-II spectrin Spectrin
KeywordsMETAL BINDING / STRUCTURAL PROTEIN / calmodulin / calmodulin binding 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 / positive regulation of ryanodine-sensitive calcium-release channel activity / RHOU GTPase cycle ...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 / positive regulation of ryanodine-sensitive calcium-release channel activity / RHOU GTPase cycle / negative regulation of ryanodine-sensitive calcium-release channel activity / Caspase-mediated cleavage of cytoskeletal proteins / COPI-mediated anterograde transport / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / NCAM signaling for neurite out-growth / cell projection / structural constituent of cytoskeleton / spindle pole / specific granule lumen / extracellular vesicle / microtubule cytoskeleton / actin filament binding / tertiary granule lumen / cell junction / actin binding / actin cytoskeleton organization / RAF/MAP kinase cascade / calmodulin binding / cadherin binding / protein domain specific binding / intracellular membrane-bounded organelle / calcium ion binding / Neutrophil degranulation / protein-containing complex / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol / cytoplasm
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 / EF-hand / Recoverin; domain 1 ...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 / EF-hand / Recoverin; 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin / Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSimonovic, M. / Zhang, Z. / Cianci, C.D. / Steitz, T.A. / Morrow, J.S.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure of the calmodulin alphaII-spectrin complex provides insight into the regulation of cell plasticity.
Authors: Simonovic, M. / Zhang, Z. / Cianci, C.D. / Steitz, T.A. / Morrow, J.S.
History
DepositionJan 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
C: alpha-II spectrin Spectrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6746
Polymers21,5142
Non-polymers1604
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-82 kcal/mol
Surface area8300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.288, 57.737, 69.753
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.

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Components

#1: Protein Calmodulin / / CaM


Mass: 16721.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P62157
#2: Protein/peptide alpha-II spectrin Spectrin / Spectrin / non-erythroid alpha chain / Spectrin alpha chain / Fodrin alpha chain


Mass: 4792.410 Da / Num. of mol.: 1 / Fragment: Calmodulin binding domain / Mutation: L1211R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPTAN1, SPTA2 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q13813
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50mM Tris,pH 8.00, 30% PEG 8000, 0.1M ammonium-sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDate
RIGAKU RAXIS II1IMAGE PLATENov 24, 2005
RIGAKU RAXIS II2IMAGE PLATENov 24, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1YALE MIRRORSSINGLE WAVELENGTHMx-ray1
2YALE MIRRORSSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→45 Å / Num. all: 7933 / Num. obs: 7933 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.245 / Net I/σ(I): 4.55
Reflection shellResolution: 2.45→2.6 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.2 / Num. unique all: 986 / % possible all: 87.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1cdm

1cdm


Resolution: 2.45→44.48 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 551349.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 665 10.6 %RANDOM
Rwork0.245 ---
all0.245 6253 --
obs0.245 6253 89.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.4525 Å2 / ksol: 0.355356 e/Å3
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1-19.36 Å20 Å20 Å2
2---9.56 Å20 Å2
3----9.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.45→44.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1177 0 4 58 1239
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0077
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_dihedral_angle_d20.84
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 110 11.2 %
Rwork0.364 876 -
obs-876 87.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramwater.top
X-RAY DIFFRACTION3water_rep.paramion.top

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