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- PDB-3edv: Crystal Structure of Repeats 14-16 of Beta2-Spectrin -

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Basic information

Entry
Database: PDB / ID: 3edv
TitleCrystal Structure of Repeats 14-16 of Beta2-Spectrin
ComponentsSpectrin beta chain, brain 1
KeywordsSTRUCTURAL PROTEIN / spectrin repeat / coiled coil / Actin capping / Actin-binding / Alternative splicing / Calmodulin-binding / Cytoplasm / Cytoskeleton / Glycoprotein / Membrane / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


regulation of SMAD protein signal transduction / membrane assembly / central nervous system formation / spectrin / cuticular plate / spectrin-associated cytoskeleton / plasma membrane organization / Golgi to plasma membrane protein transport / actin filament capping / M band ...regulation of SMAD protein signal transduction / membrane assembly / central nervous system formation / spectrin / cuticular plate / spectrin-associated cytoskeleton / plasma membrane organization / Golgi to plasma membrane protein transport / actin filament capping / M band / Nephrin family interactions / Interaction between L1 and Ankyrins / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / ankyrin binding / RHOV GTPase cycle / cortical actin cytoskeleton / RHOU GTPase cycle / mitotic cytokinesis / axolemma / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / Signaling by FLT3 fusion proteins / positive regulation of interleukin-2 production / NCAM signaling for neurite out-growth / cell projection / protein localization to plasma membrane / central nervous system development / positive regulation of protein localization to plasma membrane / structural constituent of cytoskeleton / phospholipid binding / actin filament binding / cell junction / GTPase binding / actin binding / actin cytoskeleton organization / RAF/MAP kinase cascade / postsynaptic density / calmodulin binding / cadherin binding / glutamatergic synapse / nucleolus / RNA binding / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. ...Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / PH domain profile. / Pleckstrin homology domain. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Pleckstrin homology domain / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Spectrin beta chain, non-erythrocytic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.951 Å
AuthorsMichaely, P. / Tomchick, D.R.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Localization and Structure of the Ankyrin-binding Site on beta2-Spectrin
Authors: Davis, L. / Abdi, K. / Machius, M. / Brautigam, C. / Tomchick, D.R. / Bennett, V. / Michaely, P.
History
DepositionSep 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_label_seq_id / _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

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Assembly

Deposited unit
A: Spectrin beta chain, brain 1
B: Spectrin beta chain, brain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,27915
Polymers75,9632
Non-polymers31613
Water12,592699
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Spectrin beta chain, brain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1277
Polymers37,9821
Non-polymers1466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Spectrin beta chain, brain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1528
Polymers37,9821
Non-polymers1707
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.335, 56.415, 261.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Spectrin beta chain, brain 1 / Spectrin / non-erythroid beta chain 1 / Beta-II spectrin / Fodrin beta chain


Mass: 37981.582 Da / Num. of mol.: 2 / Fragment: Spectrin repeats 14-16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPTBN1, SPTB2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q01082
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M TrisHCl, 14% PEG4000, 0.3M Magnesium Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2007
RadiationMonochromator: sagitally focused Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.95→43.6 Å / Num. all: 55069 / Num. obs: 55069 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046
Reflection shellResolution: 1.95→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 1.97 / Rsym value: 0.682 / % possible all: 86.1

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Processing

Software
NameVersionClassification
PHENIX5.2.0019refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.951→28.634 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.919 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 24.55 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2502 2788 5.07 %
Rwork0.1919 --
obs0.195 54958 97.22 %
all-52170 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.631 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso mean: 40.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.4847 Å20 Å20 Å2
2--0.0548 Å20 Å2
3----0.5395 Å2
Refine analyzeLuzzati sigma a obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 1.951→28.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5474 0 13 699 6186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075621
X-RAY DIFFRACTIONf_angle_d0.837587
X-RAY DIFFRACTIONf_dihedral_angle_d15.9532163
X-RAY DIFFRACTIONf_chiral_restr0.056799
X-RAY DIFFRACTIONf_plane_restr0.0031008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.951-1.98470.32851110.24022241X-RAY DIFFRACTION85
1.9847-2.02070.26951150.22612372X-RAY DIFFRACTION89
2.0207-2.05960.27671110.21522463X-RAY DIFFRACTION92
2.0596-2.10160.25051350.20582450X-RAY DIFFRACTION94
2.1016-2.14730.28531240.19312520X-RAY DIFFRACTION95
2.1473-2.19720.24011470.18112561X-RAY DIFFRACTION98
2.1972-2.25220.23241290.18072656X-RAY DIFFRACTION98
2.2522-2.3130.23831460.18172596X-RAY DIFFRACTION99
2.313-2.38110.22571350.18792630X-RAY DIFFRACTION99
2.3811-2.45790.23881360.19352669X-RAY DIFFRACTION99
2.4579-2.54570.27051370.18512632X-RAY DIFFRACTION100
2.5457-2.64750.25421650.18342611X-RAY DIFFRACTION100
2.6475-2.76790.22531300.18212674X-RAY DIFFRACTION100
2.7679-2.91370.29261470.20312687X-RAY DIFFRACTION100
2.9137-3.09610.29041350.20622697X-RAY DIFFRACTION100
3.0961-3.33480.2531480.20972715X-RAY DIFFRACTION100
3.3348-3.66980.25741830.17262680X-RAY DIFFRACTION100
3.6698-4.19940.22671430.1632715X-RAY DIFFRACTION100
4.1994-5.28540.2241530.16382757X-RAY DIFFRACTION100
5.2854-28.63680.24011580.22212844X-RAY DIFFRACTION97
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)
11.29120.69670.26151.49091.01420.89880.06610.30150.02220.05850.2775-0.35110.20010.3389-0.18990.3259-0.0399-0.05950.3279-0.06060.279835.96099.318119.5136
20.8996-0.9015-0.02511.161-0.00510.42640.0970.19530.1353-0.1773-0.29440.22710.0954-0.48290.09020.2866-0.121-0.02270.3529-0.06350.260925.84926.635115.3637
30.764-0.0305-0.26250.86650.61561.77750.20240.2168-0.4480.43540.4467-0.87730.47660.4069-0.67930.18270.0208-0.11260.164-0.11460.356943.294640.196655.2105
41.84350.59631.23620.22261.7451.77510.234-0.0730.01250.1943-0.23540.26270.176-0.1665-0.02850.2435-0.0918-0.01260.2158-0.02140.193234.841739.275853.3738
5-0.7236-1.4711-0.40431.24111.47721.28140.01610.171-0.05040.20480.1181-0.29770.11640.0293-0.05880.094-0.0170.05570.2078-0.05920.18443.099869.146871.4249
61.1527-0.1498-0.05331.94760.96620.9580.00990.05230.0682-0.12780.054-0.2138-0.0187-0.0101-0.05730.1050.00090.03410.06810.00930.073440.353985.88977.0513
70.518-0.00690.75360.86010.59240.8375-0.1049-0.08860.08060.39870.06630.25480.0112-0.18720.04740.1630.01490.03270.1583-0.00340.153939.059691.639784.4033
81.95610.7991.93563.04140.25822.7729-0.1001-0.17840.01351.0663-0.2697-1.74-0.18681.2425-0.07570.4086-0.105-0.24090.34950.00210.250233.395960.421850.1175
90.5521.46840.11720.06930.51451.4363-0.02310.4413-0.282-0.33330.4094-0.4237-0.33480.4119-0.17930.21560.01840.07590.4947-0.14510.251935.265147.299820.6163
101.85530.63570.22180.7692-0.02561.03520.04370.1706-0.25480.0078-0.0224-0.10340.06860.1068-0.00910.07050.05010.01710.1767-0.02160.125828.590649.191836.8998
110.74790.55930.25741.81340.67580.2153-0.0383-0.37020.1466-0.23850.8294-0.8642-0.09250.7181-0.45280.2412-0.00170.04980.2692-0.17680.242834.025120.5578-2.1278
120.590.0758-0.07541.40151.62060.6583-0.0965-0.1246-0.1854-0.37810.03590.3816-0.1250.05170.03680.35080.027-0.02170.2128-0.08290.272327.698514.478-6.17
130.3527-1.0460.50980.37080.0980.5187-0.08980.0172-0.0360.30560.0229-0.54750.2570.12770.08350.3653-0.00140.09460.1832-0.04830.381435.1515-37.4548-28.811
141.5438-0.7811-0.65581.49860.66460.3996-0.08970.2160.0276-0.3203-0.17050.8411-0.1309-0.19210.19640.3484-0.0055-0.05790.148-0.05790.271127.1617-24.0621-30.2461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1695:1750)A1695 - 1750
2X-RAY DIFFRACTION2(chain A and resid 1751:1806)A1751 - 1806
3X-RAY DIFFRACTION3(chain A and resid 1807:1836)A1807 - 1836
4X-RAY DIFFRACTION4(chain A and resid 1837:1897)A1837 - 1897
5X-RAY DIFFRACTION5(chain A and resid 1898:1932)A1898 - 1932
6X-RAY DIFFRACTION6(chain A and resid 1933:1992)A1933 - 1992
7X-RAY DIFFRACTION7(chain A and resid 1993:2015)A1993 - 2015
8X-RAY DIFFRACTION8(chain B and resid 1694:1706)B1694 - 1706
9X-RAY DIFFRACTION9(chain B and resid 1707:1737)B1707 - 1737
10X-RAY DIFFRACTION10(chain B and resid 1738:1794)B1738 - 1794
11X-RAY DIFFRACTION11(chain B and resid 1795:1839)B1795 - 1839
12X-RAY DIFFRACTION12(chain B and resid 1840:1915)B1840 - 1915
13X-RAY DIFFRACTION13(chain B and resid 1916:1958)B1916 - 1958
14X-RAY DIFFRACTION14(chain B and resid 1959:2014)B1959 - 2014

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