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- PDB-5y4e: Crystal Structure of AnkB Ankyrin Repeats R8-14 in complex with a... -

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Basic information

Entry
Database: PDB / ID: 5y4e
TitleCrystal Structure of AnkB Ankyrin Repeats R8-14 in complex with autoinhibition segment AI-b
ComponentsAnkyrin-2,Ankyrin-2
KeywordsPROTEIN BINDING / ANK REPEAT / PROTEIN-PROTEIN INTERACTION / STRUCTURAL PROTEIN / AUTO-INHIBITION
Function / homology
Function and homology information


protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / regulation of calcium ion transmembrane transporter activity / positive regulation of calcium ion transmembrane transporter activity / protein localization to M-band / protein localization to endoplasmic reticulum / positive regulation of potassium ion transmembrane transporter activity / T-tubule organization / SA node cell action potential ...protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / regulation of calcium ion transmembrane transporter activity / positive regulation of calcium ion transmembrane transporter activity / protein localization to M-band / protein localization to endoplasmic reticulum / positive regulation of potassium ion transmembrane transporter activity / T-tubule organization / SA node cell action potential / membrane depolarization during SA node cell action potential / protein localization to organelle / paranodal junction assembly / phosphorylation-dependent protein binding / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / positive regulation of cation channel activity / atrial cardiac muscle cell action potential / sarcoplasmic reticulum calcium ion transport / cytoskeletal anchor activity / atrial septum development / positive regulation of potassium ion transport / ventricular cardiac muscle cell action potential / costamere / positive regulation of calcium ion transport / regulation of cardiac muscle cell contraction / response to methylmercury / regulation of cardiac muscle contraction by calcium ion signaling / regulation of release of sequestered calcium ion into cytosol / regulation of ventricular cardiac muscle cell membrane repolarization / M band / protein localization to cell surface / Interaction between L1 and Ankyrins / A band / spectrin binding / regulation of heart rate by cardiac conduction / regulation of calcium ion transport / intercalated disc / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / COPI-mediated anterograde transport / T-tubule / regulation of heart rate / protein localization to plasma membrane / sarcolemma / regulation of protein stability / protein localization / structural constituent of cytoskeleton / recycling endosome / intracellular calcium ion homeostasis / Z disc / endocytosis / protein-macromolecule adaptor activity / protein transport / ATPase binding / postsynaptic membrane / basolateral plasma membrane / transmembrane transporter binding / lysosome / protein stabilization / cytoskeleton / early endosome / neuron projection / apical plasma membrane / positive regulation of gene expression / protein kinase binding / enzyme binding / mitochondrion / 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. / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain ...Ankyrin, UPA domain / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Ankyrin repeat-containing 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.341 Å
AuthorsChen, K. / Li, J. / Wang, C. / Wei, Z. / Zhang, M.
CitationJournal: Elife / Year: 2017
Title: Autoinhibition of ankyrin-B/G membrane target bindings by intrinsically disordered segments from the tail regions.
Authors: Chen, K. / Li, J. / Wang, C. / Wei, Z. / Zhang, M.
History
DepositionAug 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ankyrin-2,Ankyrin-2
B: Ankyrin-2,Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,05322
Polymers60,1392
Non-polymers1,91320
Water1,13563
1
A: Ankyrin-2,Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,02211
Polymers30,0701
Non-polymers95310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ankyrin-2,Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,03011
Polymers30,0701
Non-polymers96110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.085, 186.085, 75.354
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1504-

SO4

21A-1606-

HOH

31A-1623-

HOH

41A-1626-

HOH

51B-1621-

HOH

61B-1622-

HOH

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Components

#1: Protein Ankyrin-2,Ankyrin-2 / ANK-2 / Ankyrin-B / Brain ankyrin / Non-erythroid ankyrin


Mass: 30069.676 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 857-896,UNP RESIDUES 264-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANK2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01484
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.13 Å3/Da / Density % sol: 60.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES (pH 7.0), 1 M ammonium sulfate, 0.5% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 31971 / % possible obs: 97.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 37.05 Å2 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.063 / Rrim(I) all: 0.126 / Χ2: 1.806 / Net I/σ(I): 7.5 / Num. measured all: 130532
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.35-2.393.80.89315620.7210.5211.41897.9
2.39-2.433.80.7115570.760.4131.37596.50.824
2.43-2.483.80.69415610.7830.4021.37997.90.804
2.48-2.533.90.61315820.8020.3541.35997.10.71
2.53-2.593.90.52515660.8360.3031.41197.10.608
2.59-2.653.90.48915660.8750.2821.41297.40.566
2.65-2.713.90.41815580.9070.2381.37197.10.482
2.71-2.7940.38115750.9270.2171.4796.90.44
2.79-2.8740.34615770.9350.1951.3897.70.398
2.87-2.9640.30515770.9280.1731.5696.70.352
2.96-3.0740.2215680.9630.1241.64596.80.253
3.07-3.194.10.1815750.9770.1011.67696.60.207
3.19-3.3340.14615910.980.0821.80497.20.168
3.33-3.5140.11915780.990.0671.903970.137
3.51-3.733.90.08815950.9940.052.12796.80.101
3.73-4.023.90.07315990.9960.0422.282970.084
4.02-4.424.20.06516460.9960.0362.46898.90.075
4.42-5.064.50.06316630.9970.0332.48298.80.072
5.06-6.3750.07516940.9960.0372.26199.80.084
6.37-504.90.05217810.9970.0262.46597.60.059

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RLV

4rlv


Resolution: 2.341→36.688 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 1540 4.82 %
Rwork0.192 30385 -
obs0.1939 31925 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.53 Å2 / Biso mean: 45.4292 Å2 / Biso min: 19.12 Å2
Refinement stepCycle: final / Resolution: 2.341→36.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 102 63 3571
Biso mean--89.11 38.22 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113553
X-RAY DIFFRACTIONf_angle_d1.1954845
X-RAY DIFFRACTIONf_chiral_restr0.062583
X-RAY DIFFRACTIONf_plane_restr0.008608
X-RAY DIFFRACTIONf_dihedral_angle_d15.9311235
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3411-2.41670.2931270.2422687281496
2.4167-2.50310.27531200.23852717283797
2.5031-2.60320.29531370.2252709284697
2.6032-2.72170.27051370.21912727286498
2.7217-2.86510.27291660.2422685285197
2.8651-3.04460.28311430.21942724286797
3.0446-3.27950.24191290.20762735286496
3.2795-3.60930.24951430.19972740288397
3.6093-4.13090.20841460.1642782292898
4.1309-5.20220.18881340.1512873300799
5.2022-36.69220.19721580.18193006316498
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)
15.8404-7.01553.42758.4089-4.10872.00010.85551.26460.2004-1.2107-1.0449-0.54381.10980.38020.07660.59370.15010.12540.6609-0.03880.592859.4983-45.5362107.4462
23.4512-2.03821.44284.2309-1.4922.7639-0.0101-0.2169-0.41640.39970.1305-0.19740.3274-0.0122-0.10290.36830.0077-0.0660.24440.01410.295761.6451-49.4791123.2321
34.9879-0.14452.80951.22290.47064.3102-0.1804-0.090.0476-0.07960.060.084-0.1253-0.3770.130.2205-0.01080.0220.2897-0.02370.210638.0875-37.7462107.1167
47.5336-2.66382.13283.0562-1.04991.07480.40320.3402-0.3703-0.5284-0.4555-0.06481.02670.25920.2360.52820.13030.00160.341-0.00410.507166.9214-55.338383.1223
55.8629-3.79632.79867.1419-1.64125.490.10980.0743-0.47230.14430.0264-0.28450.0558-0.1055-0.05360.36450.0235-0.01390.25990.09650.480668.312-53.110587.1661
65.6906-1.35791.35862.75820.0312.76650.0181-0.1958-0.49870.04230.0701-0.06480.3064-0.1235-0.07330.31270.00180.00520.22530.05790.345356.7443-44.959384.8241
75.37410.1283.92435.84990.78636.5769-0.17830.0639-0.328-0.35890.14080.27170.2165-0.15180.05730.1976-0.01050.05080.2171-0.02560.256544.4422-40.029478.1223
85.696-2.27552.73558.1871-4.85153.26120.04950.43520.4749-0.10140.7758-0.0981-0.755-0.1817-0.71820.2715-0.07920.00120.4069-0.02760.400442.3642-32.58973.7414
95.74420.20090.61943.77040.22624.3878-0.15010.37740.222-0.21090.09590.0775-0.1231-0.53110.12880.3101-0.0984-0.07350.38660.00320.293634.9799-37.570868.5291
106.7299-1.3329-3.07546.01780.67412.1047-0.63121.32970.1494-1.20790.74230.4609-0.0228-0.2211-0.10740.5505-0.2425-0.09930.67630.0340.390530.7734-41.35561.6774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 883 through 1268 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1269 through 1386 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1387 through 1488 )
4X-RAY DIFFRACTION4chain 'B' and (resid 883 through 1287 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1288 through 1320 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1321 through 1386 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1387 through 1419 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1420 through 1433 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1434 through 1466 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1467 through 1487 )

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