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- PDB-1aa2: CALPONIN HOMOLOGY (CH) DOMAIN FROM HUMAN BETA-SPECTRIN -

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Basic information

Entry
Database: PDB / ID: 1aa2
TitleCALPONIN HOMOLOGY (CH) DOMAIN FROM HUMAN BETA-SPECTRIN
ComponentsBETA-SPECTRIN
KeywordsCYTOSKELETON / SPECTRIN / F-ACTIN CROSS-LINKING
Function / homology
Function and homology information


regulation of SMAD protein signal transduction / membrane assembly / central nervous system formation / cuticular plate / spectrin / spectrin-associated cytoskeleton / plasma membrane organization / Golgi to plasma membrane protein transport / actin filament capping / M band ...regulation of SMAD protein signal transduction / membrane assembly / central nervous system formation / cuticular plate / spectrin / spectrin-associated cytoskeleton / plasma membrane organization / Golgi to plasma membrane protein transport / actin filament capping / M band / 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 / ankyrin binding / RHOV GTPase cycle / cortical actin cytoskeleton / mitotic cytokinesis / RHOU GTPase cycle / axolemma / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / Signaling by FLT3 fusion proteins / positive regulation of interleukin-2 production / NCAM signaling for neurite out-growth / central nervous system development / cell projection / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / phospholipid binding / structural constituent of cytoskeleton / actin filament binding / cell junction / GTPase binding / actin binding / actin cytoskeleton organization / RAF/MAP kinase cascade / postsynaptic density / calmodulin binding / cadherin binding / glutamatergic synapse / nucleolus / RNA binding / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. ...Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / 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. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Spectrin beta chain, non-erythrocytic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsDjinovic Carugo, K. / Banuelos, S. / Saraste, M.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of a calponin homology domain.
Authors: Djinovic Carugo, K. / Banuelos, S. / Saraste, M.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Identification of a Phosphatidylinositol 4,5-Bisphosphate-Binding Site in Chicken Skeletal Muscle Alpha-Actinin
Authors: Fukami, K. / Sawada, N. / Endo, T. / Takenawa, T.
#2: Journal: FEBS Lett. / Year: 1995
Title: Does Vav Bind to F-Actin Through a Ch Domain?
Authors: Castresana, J. / Saraste, M.
#3: Journal: Protein Profile / Year: 1994
Title: Actin-Binding Proteins 1: Spectrin Superfamily
Authors: Hartwig, J.H.
History
DepositionJan 21, 1997Processing site: BNL
Revision 1.0Feb 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: BETA-SPECTRIN


Theoretical massNumber of molelcules
Total (without water)12,5861
Polymers12,5861
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.471, 53.685, 32.197
Angle α, β, γ (deg.)90.00, 106.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BETA-SPECTRIN / CALPONIN HOMOLOGY (CH) DOMAIN


Mass: 12586.320 Da / Num. of mol.: 1 / Fragment: F-ACTIN BINDING DOMAIN RESIDUES 173 - 281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organelle: NON-ERYTHROCYTE / Plasmid: PBAT4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q01082
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal growpH: 6.6
Details: PROTEIN WAS CRYSTALLIZED FROM 30% PEG 8000, 100 MM SODIUM CACODYLATE, PH 6.6
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlCH domain1drop
220 mMsodium phosphate1drop
325 mM1dropNaCl
41 mMdithiothreitol1drop
51 mM1dropNaN3
60.1 Msodium cacodylate1reservoir
70.2 Msodium acetate1reservoir
830 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1996 / Details: NO OPTICS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→14 Å / Num. obs: 6859 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 2.01→2.04 Å / Redundancy: 3 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 3 / Rsym value: 0.311 / % possible all: 97.2
Reflection
*PLUS
Num. measured all: 27400

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Processing

Software
NameVersionClassification
PHASESphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2→14 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: A POSTERIORI / σ(F): 0 / Stereochemistry target values: TNT PROTGEO / Details: THE REPORTED RMS VALUES ARE UNWEIGHTED
RfactorNum. reflection% reflectionSelection details
Rfree0.21 506 7.5 %RANDOM
all0.16 6831 --
obs0.16 6831 99.1 %-
Solvent computationSolvent model: MOEWS & KRETSINGER (1975) J. MOL. BIOL. 91, 201-228.
Bsol: 83.74 Å2 / ksol: 0.754 e/Å3
Refinement stepCycle: LAST / Resolution: 2→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms887 0 0 130 1017
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01918242.4
X-RAY DIFFRACTIONt_angle_deg2.05924642.3
X-RAY DIFFRACTIONt_dihedral_angle_d24.11410500
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.009466
X-RAY DIFFRACTIONt_gen_planes0.0162588
X-RAY DIFFRACTIONt_it7.6099124
X-RAY DIFFRACTIONt_nbd0.0452820
Software
*PLUS
Name: TNT / Version: 5EA / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.16 / Rfactor Rfree: 0.213 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0096
X-RAY DIFFRACTIONt_plane_restr0.0168

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