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- PDB-1bkr: CALPONIN HOMOLOGY (CH) DOMAIN FROM HUMAN BETA-SPECTRIN AT 1.1 ANG... -

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Basic information

Entry
Database: PDB / ID: 1bkr
TitleCALPONIN HOMOLOGY (CH) DOMAIN FROM HUMAN BETA-SPECTRIN AT 1.1 ANGSTROM RESOLUTION
ComponentsSPECTRIN BETA CHAIN
KeywordsACTIN-BINDING / FILAMENTOUS ACTIN-BINDING DOMAIN / CYTOSKELETON
Function / homology
Function and homology information


regulation of SMAD protein signal transduction / membrane assembly / central nervous system formation / spectrin / spectrin-associated cytoskeleton / cuticular plate / plasma membrane organization / actin filament capping / Golgi to plasma membrane protein transport / Nephrin family interactions ...regulation of SMAD protein signal transduction / membrane assembly / central nervous system formation / spectrin / spectrin-associated cytoskeleton / cuticular plate / plasma membrane organization / actin filament capping / Golgi to plasma membrane protein transport / Nephrin family interactions / M band / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / ankyrin binding / Sensory processing of sound by inner hair cells of the cochlea / RHOV GTPase cycle / cortical actin cytoskeleton / RHOU GTPase cycle / mitotic cytokinesis / 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 / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / cell projection / phospholipid binding / structural constituent of cytoskeleton / actin filament binding / cell junction / actin binding / GTPase binding / RAF/MAP kinase cascade / actin cytoskeleton organization / calmodulin binding / postsynaptic density / cadherin binding / nucleolus / glutamatergic synapse / RNA binding / extracellular exosome / plasma membrane / cytoplasm / cytosol
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 / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. ...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 / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin / Spectrin repeats / 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 / SYNCHROTRON / AB INITIO / Resolution: 1.1 Å
AuthorsDjinovic Carugo, K. / Banuelos, S. / Saraste, M.
Citation
Journal: Structure / Year: 1998
Title: Structural comparisons of calponin homology domains: implications for actin binding.
Authors: Banuelos, S. / Saraste, M. / Carugo, K.D.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal Structure of a Calponin Homology Domain
Authors: Carugo, K.D. / Banuelos, S. / Saraste, M.
#2: Journal: Nat.Struct.Biol. / Year: 1997
Title: The Structure of an Actin-Crosslinking Domain from Human Fimbrin
Authors: Goldsmith, S.C. / Pokala, N. / Shen, W. / Fedorov, A.A. / Matsudaira, P. / Almo, S.C.
History
DepositionJul 10, 1998Processing site: BNL
Revision 1.0Jul 15, 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 / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPECTRIN BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)12,7151
Polymers12,7151
Non-polymers00
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.650, 53.953, 32.354
Angle α, β, γ (deg.)90.00, 105.48, 90.00
Int Tables number4
Space group name H-MP1211
DetailsSPECTRIN IS A HETEROTETRAMER CONSISTING OF 2 ALPHA AND 2 BETA CHAINS. CALPONIN HOMOLOGY DOMAIN IS AT THE N-TERMINAL PART OF THE BETA CHAIN.

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Components

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


Mass: 12715.499 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) / Cell: NON-ERYTHROCYTE / Cellular location: CYTOSKELETAL PROTEIN / 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


Mass: 18.015 Da / Num. of mol.: 208 / 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 0.2 M SODIUM ACETATE 0.1 M SODIUM CACODYLATE PH 6.6 PEG8K 30% (W/V)
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion / Details: Djinovic, C., (1997) Nat. Struct. Biol., 4, 175.
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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8883
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8883 Å / Relative weight: 1
ReflectionResolution: 1.1→55 Å / Num. obs: 42236 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 12
Reflection shellResolution: 1.1→1.11 Å / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 199306

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Processing

Software
NameClassification
SHELXmodel building
SHELXrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1.1→10 Å / Num. parameters: 9858 / Num. restraintsaints: 11588 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) FROM 0.225 TO 0.187. ESTIMATED OVERALL COORDINATE ERROR (FROM LUZZATTI PLOT): 0.05 (ASSUMING PERFECT DATA).
RfactorNum. reflection% reflectionSelection details
Rfree0.187 3092 7 %RANDOM
obs0.141 -99.2 %-
all-42149 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1081.5
Refinement stepCycle: LAST / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms887 0 0 208 1095
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.024
X-RAY DIFFRACTIONs_zero_chiral_vol0.071
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.137
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.01
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.135
X-RAY DIFFRACTIONs_approx_iso_adps0.1
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.141
Solvent computation
*PLUS
Displacement parameters
*PLUS

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