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- PDB-5y4f: Crystal Structure of AnkB Ankyrin Repeats R13-24 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5y4f
TitleCrystal Structure of AnkB Ankyrin Repeats R13-24 in complex with autoinhibition segment AI-c
ComponentsAnkyrin-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 / 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 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 / 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 / protein localization to endoplasmic reticulum / 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 release of sequestered calcium ion into cytosol / response to methylmercury / regulation of ventricular cardiac muscle cell membrane repolarization / M band / regulation of cardiac muscle cell contraction / protein localization to cell surface / Interaction between L1 and Ankyrins / regulation of cardiac muscle contraction by calcium ion signaling / 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 / regulation of protein stability / protein localization / recycling endosome / structural constituent of cytoskeleton / sarcolemma / Z disc / intracellular calcium ion homeostasis / endocytosis / protein transport / protein-macromolecule adaptor activity / ATPase binding / basolateral plasma membrane / postsynaptic membrane / transmembrane transporter binding / lysosome / early endosome / cytoskeleton / protein stabilization / 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
ACETATE ION / Ankyrin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.953 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)94,8134
Polymers94,7132
Non-polymers992
Water4,936274
1
A: Ankyrin-2


Theoretical massNumber of molelcules
Total (without water)47,3571
Polymers47,3571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4563
Polymers47,3571
Non-polymers992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.304, 127.803, 257.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 47356.727 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 430-873
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M CaCl2, 0.1 M HEPES (pH 7.5), 28% v/v PEG 400

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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: Sep 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 68019 / % possible obs: 94.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 27.19 Å2 / Rmerge(I) obs: 0.082 / Χ2: 2.497 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.95-1.983.20.74231631.516192.2
1.98-2.023.20.60732041.582191.7
2.02-2.063.10.50232261.61189.4
2.06-2.13.10.43331631.664188.9
2.1-2.153.10.35832561.668193.2
2.15-2.23.10.3232831.688193
2.2-2.2530.28233261.811190.8
2.25-2.3130.2532761.929194.7
2.31-2.3830.20134061.984195.1
2.38-2.462.90.16934162.107194.4
2.46-2.5430.15633682.345196.1
2.54-2.652.90.13334972.593195.8
2.65-2.772.90.12234112.897196.9
2.77-2.912.90.10835473.198196.7
2.91-3.12.90.08734553.342197.4
3.1-3.332.90.07335693.575197.4
3.33-3.6730.05935843.803197.4
3.67-4.23.30.0535713.671197.1
4.2-5.293.70.04636233.325198
5.29-503.70.04436752.847191.4

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
PHENIXdev_2689refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RLV

4rlv


Resolution: 1.953→38.161 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.04
RfactorNum. reflection% reflection
Rfree0.2198 3357 4.95 %
Rwork0.1838 --
obs0.1856 67875 94.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.23 Å2 / Biso mean: 30.9267 Å2 / Biso min: 12.41 Å2
Refinement stepCycle: final / Resolution: 1.953→38.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6112 0 5 274 6391
Biso mean--50.01 32.74 -
Num. residues----828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016234
X-RAY DIFFRACTIONf_angle_d0.9938505
X-RAY DIFFRACTIONf_chiral_restr0.0581060
X-RAY DIFFRACTIONf_plane_restr0.0071091
X-RAY DIFFRACTIONf_dihedral_angle_d3.5575072
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9531-1.9810.3411860.25452326241284
1.981-2.01060.26361280.23732555268392
2.0106-2.0420.2771490.23882530267991
2.042-2.07550.24881260.22892521264788
2.0755-2.11120.25041440.21942530267490
2.1112-2.14960.29371340.21392598273294
2.1496-2.1910.30771280.2162606273493
2.191-2.23570.25631360.20872643277992
2.2357-2.28430.2441520.20022596274893
2.2843-2.33740.25621340.20822635276994
2.3374-2.39590.24121380.19562682282095
2.3959-2.46060.27721560.19662725288195
2.4606-2.5330.22711370.19132635277296
2.533-2.61480.22281620.19122737289995
2.6148-2.70820.23731350.18922758289396
2.7082-2.81660.23171430.19412725286897
2.8166-2.94470.21421550.18952814296997
2.9447-3.09990.23841440.19092739288397
3.0999-3.2940.22221420.19632853299597
3.294-3.54820.22331460.1732789293598
3.5482-3.9050.17651550.15742787294296
3.905-4.46930.17831480.14572869301798
4.4693-5.62790.18541420.15542956309898
5.6279-38.16820.19441370.1882909304691
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)
12.59981.69491.11565.70052.15221.60450.0671-0.00560.1836-0.0219-0.07340.22510.09380.03340.01230.26480.03880.00820.29050.07030.1939-25.09-29.118-11.114
20.38851.8322-0.07627.3059-0.84930.91850.0476-0.0141-0.03780.1980.00560.02730.01370.0485-0.06450.15190.03960.01650.22560.05460.21-14.228-4.271-4.033
30.71690.3022-0.6041.3218-1.09532.15410.0292-0.02350.04160.1791-0.0013-0.0379-0.17620.0794-0.02070.1182-0.0125-0.01650.2118-0.02670.1511-3.52330.911-18.962
42.3525-0.4493-0.55920.90840.94641.10310.06350.1707-0.0672-0.2474-0.0404-0.00970.1840.1218-0.04040.2122-0.001-0.03130.3226-0.0180.19882.21141.584-43.814
50.452-2.5317-0.2277.12460.5944-0.01380.01780.01970.0109-0.17650.0008-0.07450.0779-0.0009-0.02030.2315-0.0428-0.00860.26050.01250.2563-24.5829.923-58.797
60.79430.2993-0.21721.2751-1.11452.7155-0.0248-0.0755-0.11880.0659-0.0221-0.14980.09760.03770.06270.17070.0401-0.01830.2083-0.02780.173-18.042-37.349-43.647
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 430:492 )A430 - 492
2X-RAY DIFFRACTION2( CHAIN A AND RESID 493:624 )A493 - 624
3X-RAY DIFFRACTION3( CHAIN A AND RESID 625:780 )A625 - 780
4X-RAY DIFFRACTION4( CHAIN A AND RESID 781:819 )A781 - 819
5X-RAY DIFFRACTION5( CHAIN B AND RESID 430:591 )B430 - 591
6X-RAY DIFFRACTION6( CHAIN B AND RESID 592:819 )B592 - 819

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