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- PDB-3f57: Crystal structure of human erythroid beta spectrin repeats 14 and... -

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Basic information

Entry
Database: PDB / ID: 3f57
TitleCrystal structure of human erythroid beta spectrin repeats 14 and 15 (ankyrin binding domain)
ComponentsSpectrin beta chain, erythrocyte
KeywordsSTRUCTURAL PROTEIN / spectrin / spectrin repeat / three-helix-bundle / ankyrin binding / Actin capping / Actin-binding / Cytoskeleton / Disease mutation / Elliptocytosis / Hereditary hemolytic anemia / Phosphoprotein
Function / homology
Function and homology information


spectrin / spectrin-associated cytoskeleton / modification of postsynaptic actin cytoskeleton / actin filament capping / Interaction between L1 and Ankyrins / ankyrin binding / cortical actin cytoskeleton / COPI-mediated anterograde transport / NCAM signaling for neurite out-growth / cell projection ...spectrin / spectrin-associated cytoskeleton / modification of postsynaptic actin cytoskeleton / actin filament capping / Interaction between L1 and Ankyrins / ankyrin binding / cortical actin cytoskeleton / COPI-mediated anterograde transport / NCAM signaling for neurite out-growth / cell projection / cytoplasmic side of plasma membrane / structural constituent of cytoskeleton / actin filament binding / actin cytoskeleton / cell junction / actin binding / actin cytoskeleton organization / RAF/MAP kinase cascade / postsynapse / glutamatergic synapse / cell surface / protein-containing complex / plasma membrane / cytosol
Similarity search - Function
Spectrin, beta subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / Actinin-type actin-binding domain, conserved site / Calponin homology domain ...Spectrin, beta subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / 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. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Spectrin beta chain, erythrocytic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsIpsaro, J.J. / 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spectrin beta chain, erythrocyte
B: Spectrin beta chain, erythrocyte


Theoretical massNumber of molelcules
Total (without water)51,3992
Polymers51,3992
Non-polymers00
Water00
1
A: Spectrin beta chain, erythrocyte


Theoretical massNumber of molelcules
Total (without water)25,7001
Polymers25,7001
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Spectrin beta chain, erythrocyte


Theoretical massNumber of molelcules
Total (without water)25,7001
Polymers25,7001
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.330, 65.330, 288.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein Spectrin beta chain, erythrocyte / Beta-I spectrin


Mass: 25699.514 Da / Num. of mol.: 2
Fragment: HUMAN ERYTHROID BETA SPECTRIN REPEATS 14 AND 15 (ANKYRIN BINDING DOMAIN): UNP RESIDUES 1686-1907
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPTB, SPTB1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11277

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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 Å3/Da / Density % sol: 58.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG 3350, 0.2 M NaCl, 100 mM Tris-HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2008
RadiationMonochromator: DIAMOND LAUE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.9→19.84 Å / Num. all: 14779 / Num. obs: 14779 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 %
Reflection shellResolution: 2.9→3.03 Å / Redundancy: 7.6 % / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
SHARPphasing
REFMAC5.5.0056refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→19.84 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.874 / SU B: 43.539 / SU ML: 0.359 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1 / ESU R Free: 0.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32165 740 5 %RANDOM
Rwork0.2619 ---
all0.26468 13968 --
obs0.26468 13968 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.677 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20 Å2
2---1.64 Å20 Å2
3---3.29 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 0 0 3038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213090
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0561.9344173
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9515372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82324.944178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.25915539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8241522
X-RAY DIFFRACTIONr_chiral_restr0.0810.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022390
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.2811.51859
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.5822951
X-RAY DIFFRACTIONr_scbond_it0.98531231
X-RAY DIFFRACTIONr_scangle_it1.7314.51222
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Number: 1498 / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDTypeRms dev position (Å)Weight position
11Atight positional0.480.2
22Btight thermal1.410
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 69 -
Rwork0.36 990 -
obs--100 %
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)
15.9372-4.84390.34918.46690.28921.1140.2139-0.01120.6574-0.5921-0.0928-0.7503-0.00790.2996-0.12120.2320.02510.09810.1203-0.03880.11925.34530.1260.13
21.9231-0.2661.4828.2266-1.64135.1253-0.0953-0.4452-0.39830.40960.2585-0.44350.8264-0.1517-0.16310.47420.08910.09730.3528-0.0410.3542.118-10.82453.24
32.8068-2.89511.023610.0295-3.05952.63820.141-0.0165-0.3113-0.35810.14730.55560.1789-0.1434-0.28820.1385-0.0059-0.03830.03340.00710.051314.37510.75460.775
42.8167-1.3181-0.38077.4157-0.33273.8305-0.0976-0.0950.63510.14960.36190.1966-0.5888-0.1182-0.26440.41890.0712-0.02770.38450.07820.36430.0947.11241.037
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1684 - 1799
2X-RAY DIFFRACTION2A1800 - 1896
3X-RAY DIFFRACTION3B1684 - 1799
4X-RAY DIFFRACTION4B1800 - 1891

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