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- PDB-3ud2: Crystal structure of Selenomethionine ZU5A-ZU5B protein domains o... -

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Basic information

Entry
Database: PDB / ID: 3ud2
TitleCrystal structure of Selenomethionine ZU5A-ZU5B protein 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: 2.21 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 1.2Dec 25, 2019Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_conn / struct_ref_seq_dif
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Ankyrin-1
B: Ankyrin-1
A: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,56728
Polymers108,8193
Non-polymers74925
Water3,405189
1
C: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4345
Polymers36,2731
Non-polymers1614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,76820
Polymers36,2731
Non-polymers49519
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3653
Polymers36,2731
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)279.480, 40.873, 95.249
Angle α, β, γ (deg.)90.00, 92.01, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A912 - 1233
2114B912 - 1233
1124A912 - 1072
2124C912 - 1072
1134A1073 - 1233
2134C1073 - 1233

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 36272.867 Da / Num. of mol.: 3 / Fragment: SeMet 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.76 %
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-D / Wavelength: 0.97626 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 28, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.2→38.7 Å / Num. all: 55529 / Num. obs: 55529 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 14.2
Reflection shellResolution: 2.2→2.3 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHARPphasing
REFMAC5.5.0088refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.21→24.9 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.914 / SU B: 13.475 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25878 2720 5 %RANDOM
Rwork0.22064 ---
obs0.22258 51530 98.69 %-
all-51531 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.142 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å2-0.3 Å2
2--0.28 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.21→24.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7508 0 39 189 7736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197683
X-RAY DIFFRACTIONr_bond_other_d0.0010.025416
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.98710426
X-RAY DIFFRACTIONr_angle_other_deg0.845313151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6955959
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71722.752327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.652151273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8971578
X-RAY DIFFRACTIONr_chiral_restr0.0750.21189
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218453
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021553
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_it0.4761.54821
X-RAY DIFFRACTIONr_mcbond_other0.1081.51927
X-RAY DIFFRACTIONr_mcangle_it0.91727836
X-RAY DIFFRACTIONr_scbond_it1.58232862
X-RAY DIFFRACTIONr_scangle_it2.6734.52590
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
14276MEDIUM POSITIONAL0.510.5
14276MEDIUM THERMAL2.762
22177MEDIUM POSITIONAL0.470.5
22177MEDIUM THERMAL3.022
32099MEDIUM POSITIONAL0.330.5
32099MEDIUM THERMAL3.522
LS refinement shellResolution: 2.209→2.266 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 155 -
Rwork0.271 3105 -
obs--85.01 %
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)
11.0683-0.1954-0.10361.36590.24582.40990.00670.060.0606-0.1707-0.093-0.0842-0.13090.21540.08630.04180.0252-0.01950.1239-0.00010.0576109.066314.485258.7092
21.6360.4874-0.65280.8102-0.26371.2399-0.06380.0397-0.01880.0142-0.07820.02820.03540.01690.14210.03720.0146-0.00350.0875-0.04030.0419118.4508-5.459396.3803
31.5276-0.0296-1.72590.61290.47642.6545-0.0816-0.1531-0.10190.15740.05460.02450.30530.17930.0270.11270.0252-0.11850.0251-0.00740.283373.315.102665.2292
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C912 - 1233
2X-RAY DIFFRACTION2B913 - 1233
3X-RAY DIFFRACTION3A913 - 1233

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