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- PDB-1n11: D34 REGION OF HUMAN ANKYRIN-R AND LINKER -

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Basic information

Entry
Database: PDB / ID: 1n11
TitleD34 REGION OF HUMAN ANKYRIN-R AND LINKER
ComponentsAnkyrin
KeywordsSTRUCTURAL PROTEIN / ANKYRIN / CLATHRIN / BAND 3 / ANION EXCHANGER
Function / homology
Function and homology information


spectrin-associated cytoskeleton / positive regulation of organelle organization / maintenance of epithelial cell apical/basal polarity / NrCAM interactions / Neurofascin interactions / ankyrin-1 complex / CHL1 interactions / cytoskeletal anchor activity / M band / Interaction between L1 and Ankyrins ...spectrin-associated cytoskeleton / positive regulation of organelle organization / maintenance of epithelial cell apical/basal polarity / NrCAM interactions / Neurofascin interactions / ankyrin-1 complex / CHL1 interactions / cytoskeletal anchor activity / M band / Interaction between L1 and Ankyrins / spectrin binding / exocytosis / axolemma / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / cytoskeleton organization / sarcoplasmic reticulum / protein localization to plasma membrane / sarcolemma / structural constituent of cytoskeleton / Z disc / cytoplasmic side of plasma membrane / ATPase binding / basolateral plasma membrane / protein phosphatase binding / postsynaptic membrane / transmembrane transporter binding / cytoskeleton / neuron projection / structural molecule activity / enzyme binding / signal transduction / plasma membrane / cytosol
Similarity search - Function
Ankyrin, UPA domain / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Ankyrin repeat / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain ...Ankyrin, UPA domain / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Ankyrin repeat / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Ankyrin repeat-containing domain / Death domain / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / Ankyrin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsMichaely, P. / Tomchick, D.R. / Machius, M. / Anderson, R.G.W.
CitationJournal: Embo J. / Year: 2002
Title: Crystal structure of a 12 ANK repeat stack from human ankyrinR
Authors: Michaely, P. / Tomchick, D.R. / Machius, M. / Anderson, R.G.W.
History
DepositionOct 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ankyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,85911
Polymers46,4601
Non-polymers39910
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.329, 137.329, 197.801
Angle α, β, γ (deg.)90, 90, 120
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Ankyrin


Mass: 46459.898 Da / Num. of mol.: 1 / Fragment: D34 region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ank-1 / Plasmid: pGEX-kg / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P16157
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl

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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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, HEPES, NaBr, CaCl2, acetonitrile, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
220 mMHEPES-Na1droppH7.5
3500 mM1dropNaBr
41 mMEDTA1drop
51 mMdithiothreitol1drop
6100 mMHEPES1reservoirpH7.5
7500 mM1reservoirCaCl2
87-10 %(v/v)PEG4001reservoir
95 %(v/v)acetonitrile1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97925 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jan 31, 2001
RadiationMonochromator: Graphite Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 421780 / Num. obs: 415031 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 67 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 22.6
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 1.3 / % possible all: 93
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 37994 / Num. measured all: 415031
Reflection shell
*PLUS
% possible obs: 93 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
TRUNCATEdata reduction
MLPHAREphasing
CNSrefinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→30 Å / Isotropic thermal model: individual isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.303 1155 random
Rwork0.319 --
all0.318 30300 -
obs0.318 30300 -
Displacement parametersBiso mean: 67 Å2
Baniso -1Baniso -2Baniso -3
1--37.037 Å2-30.296 Å20 Å2
2---37.037 Å20 Å2
3---74.075 Å2
Refine analyzeLuzzati sigma a obs: 1.07 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3073 0 0 0 3073
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.62
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 3.7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.01

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