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- PDB-3ud1: Crystal structure of ZU5A-ZU5B domains of human erythrocyte ankyrin -

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Basic information

Entry
Database: PDB / ID: 3ud1
TitleCrystal structure of ZU5A-ZU5B domains of human erythrocyte ankyrin
ComponentsAnkyrin-1
KeywordsPROTEIN BINDING / Beta sandwich / ZU5 / Adapter protein / Spectrin binding / Cytoskeleton
Function / homology
Function and homology information


spectrin-associated cytoskeleton / positive regulation of organelle organization / maintenance of epithelial cell apical/basal polarity / NrCAM interactions / ankyrin-1 complex / Neurofascin interactions / 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 / ankyrin-1 complex / Neurofascin interactions / 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 / cytoplasmic side of plasma membrane / structural constituent of cytoskeleton / Z disc / ATPase binding / postsynaptic membrane / basolateral plasma membrane / protein phosphatase binding / transmembrane transporter binding / cytoskeleton / neuron projection / structural molecule activity / enzyme binding / signal transduction / plasma membrane / cytosol
Similarity search - Function
Chondroitinase Ac; Chain A, domain 3 - #30 / Ankyrin, UPA domain / UPA domain / Chondroitinase Ac; Chain A, domain 3 / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Ankyrin repeat / Death domain profile. ...Chondroitinase Ac; Chain A, domain 3 - #30 / Ankyrin, UPA domain / UPA domain / Chondroitinase Ac; Chain A, domain 3 / 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 / Death domain / Ankyrin repeats (many copies) / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsYasunaga, M. / Ipsaro, J.J. / Mondragon, A.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structurally Similar but Functionally Diverse ZU5 Domains in Human Erythrocyte Ankyrin.
Authors: Yasunaga, M. / Ipsaro, J.J. / Mondragon, A.
History
DepositionOct 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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-1
B: Ankyrin-1
C: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,80915
Polymers108,2563
Non-polymers55312
Water12,358686
1
A: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3166
Polymers36,0851
Non-polymers2305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3166
Polymers36,0851
Non-polymers2305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1773
Polymers36,0851
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)160.123, 40.491, 178.104
Angle α, β, γ (deg.)90.00, 112.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ankyrin-1 / / ANK-1 / Ankyrin-R / Erythrocyte ankyrin


Mass: 36085.289 Da / Num. of mol.: 3 / Fragment: ZU5A-ZU5B Ankyrin-R, UNP residues 911-1233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANK1, ANK / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16157
#2: Chemical
ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 686 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% ethanol, 0.1 M Tris pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 283.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 9, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→29.68 Å / Num. all: 71819 / Num. obs: 71819 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.18 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 7.3
Reflection shellResolution: 2→2.09 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHARPphasing
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 3F59

3f59


Resolution: 2→29.68 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3623 5.05 %RANDOM
Rwork0.171 ---
obs0.173 71813 --
all-71813 --
Displacement parametersBiso mean: 27.65 Å2
Baniso -1Baniso -2Baniso -3
1--3.1774 Å20 Å2-0.4731 Å2
2--2.4228 Å20 Å2
3---0.7546 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7527 0 36 686 8249
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018055HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0510978HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1218HARMONIC5
X-RAY DIFFRACTIONt_it8055HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion14.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1062SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9501SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2002 257 5.15 %
Rwork0.1906 4737 -
all0.1911 4994 -
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)
11.0354-0.3002-0.05791.50790.06651.7903-0.00110.04070.0080.0404-0.00830.017-0.05460.20.0094-0.0436-0.02710.0104-0.0107-0.008-0.1034-2.053422.8252-69.6267
20.93930.1063-0.44632.56470.19490.71210.03170.00010.0504-0.21620.04750.162-0.0238-0.0497-0.0792-0.0595-0.0180.0096-0.089-0.0164-0.0038-34.224312.648-62.7252
31.3343-0.3778-0.33651.49110.0512.83550.0557-0.03320.0352-0.06520.0224-0.0577-0.2353-0.0063-0.07810.0219-0.0079-0.0184-0.10420.0021-0.13862.06711.6347-15.3732
41.0561-0.4935-0.17435.39190.42920.51280.04110.0174-0.07930.4373-0.12780.1440.107800.0867-0.0241-0.00280.0005-0.1213-0.0142-0.0824-29.4866-6.5021-9.8874
51.00750.1192-0.11241.603-0.19781.5751-0.02920.0106-0.02040.12070.04370.0043-0.0180.0078-0.0144-0.02140.0072-0.0083-0.04510.0022-0.0913-6.37522.0287-39.2093
60.9987-0.1168-0.05862.16160.12910.7326-0.04190.0371-0.0914-0.0712-0.0751-0.080.1164-0.01050.117-0.0452-0.01340.0255-0.07550.0092-0.006125.119814.3438-43.6664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1A 912 A 1072
2X-RAY DIFFRACTION2A 1073 A 1233
3X-RAY DIFFRACTION3B 912 B 1072
4X-RAY DIFFRACTION4B 1073 B 1233
5X-RAY DIFFRACTION5C 912 C 1072
6X-RAY DIFFRACTION6C 1073 C 1233

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