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- PDB-3f59: Crystal structure of ZU5-ANK, the spectrin binding region of huma... -

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Basic information

Entry
Database: PDB / ID: 3f59
TitleCrystal structure of ZU5-ANK, the spectrin binding region of human erythroid ankyrin
ComponentsAnkyrin-1
KeywordsSTRUCTURAL PROTEIN / beta sandwich / ZU5 / ankyrin / spectrin binding / Alternative promoter usage / ANK repeat / Cytoskeleton / Disease mutation / Elliptocytosis / Hereditary hemolytic anemia / Lipoprotein / Membrane / Phosphoprotein / Sarcoplasmic reticulum
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 / cytoplasmic side of plasma membrane / Z disc / ATPase binding / protein phosphatase binding / basolateral plasma membrane / transmembrane transporter binding / postsynaptic membrane / 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 ...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 / 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
BROMIDE ION / Ankyrin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsIpsaro, J.J. / Huang, L. / Mondragon, A.
CitationJournal: Blood / Year: 2009
Title: Structures of the spectrin-ankyrin interaction binding domains.
Authors: Ipsaro, J.J. / Huang, L. / Mondragon, A.
History
DepositionNov 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 27, 2023Group: 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-1
B: Ankyrin-1
C: Ankyrin-1
D: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,98122
Polymers71,5424
Non-polymers1,43818
Water3,423190
1
A: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3657
Polymers17,8861
Non-polymers4796
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1254
Polymers17,8861
Non-polymers2403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2055
Polymers17,8861
Non-polymers3204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2856
Polymers17,8861
Non-polymers4005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.040, 204.110, 43.070
Angle α, β, γ (deg.)90.00, 113.14, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
13C
23D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A912 - 927
2114B912 - 927
3114C912 - 927
4114D907 - 927
1214A935 - 951
2214B935 - 951
3214C935 - 951
4214D935 - 951
1314A961 - 965
2314B961 - 965
3314C961 - 965
4314D961 - 965
1414A970 - 996
2414B970 - 996
3414C970 - 996
4414D970 - 996
1514A1004 - 1020
2514B1004 - 1020
3514C1004 - 1020
4514D1004 - 1020
1614A1025 - 1068
2614B1025 - 1068
3614C1025 - 1068
4614D1025 - 1068
1125A928 - 934
2125B928 - 934
1224A966 - 969
2224B966 - 969
1324A1021 - 1024
2324B1021 - 1024
1135C928 - 934
2135D928 - 934
1234C952 - 960
2234D952 - 960
1335C966 - 969
2335D966 - 969
1434C997 - 999
2434D997 - 999

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 17885.594 Da / Num. of mol.: 4
Fragment: ZU5-ANK, spectrin binding region of human erythroid ankyrin: UNP residues 911-1068
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANK1, ANK / Plasmid: pICANTE / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P16157
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 4000, 0.25 M KBr, 10 mM DTT, 0.1 M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 8, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2→40.8 Å / Num. all: 40191 / Num. obs: 40191 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 %
Reflection shellResolution: 2→2.09 Å / Redundancy: 4.4 % / % possible all: 97.9

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
SHARPphasing
REFMAC5.5.0056refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→36.91 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU B: 13.02 / SU ML: 0.164 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26428 2013 5 %RANDOM
Rwork0.21554 ---
all0.21799 38127 --
obs0.21799 38127 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.427 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å20 Å21.79 Å2
2---1.22 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2→36.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4729 0 18 190 4937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224871
X-RAY DIFFRACTIONr_bond_other_d0.0010.023520
X-RAY DIFFRACTIONr_angle_refined_deg1.2051.9896586
X-RAY DIFFRACTIONr_angle_other_deg0.77438526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0085609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.63721.707205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76315875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2471559
X-RAY DIFFRACTIONr_chiral_restr0.0680.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215297
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021002
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.06723034
X-RAY DIFFRACTIONr_mcbond_other0.15121218
X-RAY DIFFRACTIONr_mcangle_it1.93964931
X-RAY DIFFRACTIONr_scbond_it1.80541837
X-RAY DIFFRACTIONr_scangle_it2.72861647
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1610medium positional0.440.5
11B1610medium positional0.430.5
11C1610medium positional0.40.5
11D1610medium positional0.470.5
22A170medium positional0.440.5
33A219medium positional0.30.5
22A49loose positional0.545
33A77loose positional0.985
11A1610medium thermal1.75
11B1610medium thermal1.775
11C1610medium thermal1.555
11D1610medium thermal1.655
22A170medium thermal0.565
33A219medium thermal0.975
22A49loose thermal0.5710
33A77loose thermal0.9310
LS refinement shellResolution: 2→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 134 -
Rwork0.27 2743 -
obs--96.51 %
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)
12.72331.1327-0.88425.96641.0214.1256-0.07120.00780.0461-0.0101-0.1728-0.0213-0.26490.02590.24390.0265-0.0069-0.0240.00720.00710.021920.008108.8517.686
22.7336-1.0589-0.51387.6886-1.13883.5016-0.0133-0.0178-0.3260.1736-0.3777-0.21960.07260.05050.3910.0072-0.00960.00220.02080.01850.07750.965185.09755.33
31.3241-0.3161-0.22245.7916-0.12992.35410.06690.04-0.0205-0.2662-0.0518-0.1713-0.07710.0965-0.01510.0487-0.03940.02140.0569-0.02020.020613.332133.16326.116
41.95220.5521-0.91555.3458-0.71672.20510.0498-0.04260.06830.2726-0.01160.0304-0.11210.0428-0.03820.06710.02060.01640.040.00520.00639.088161.25237.266
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A908 - 1068
2X-RAY DIFFRACTION2B908 - 1068
3X-RAY DIFFRACTION3C908 - 1068
4X-RAY DIFFRACTION4D908 - 1068

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