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- PDB-3thk: Structure of SH3 chimera with a type II ligand linked to the chai... -

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Basic information

Entry
Database: PDB / ID: 3thk
TitleStructure of SH3 chimera with a type II ligand linked to the chain C-terminal
Components
  • Proline-rich peptide
  • Spectrin alpha chain, brain
KeywordsSTRUCTURAL PROTEIN / SH3 domain / chimera
Function / homology
Function and homology information


Caspase-mediated cleavage of cytoskeletal proteins / Interaction between L1 and Ankyrins / : / COPI-mediated anterograde transport / cuticular plate / spectrin / NCAM signaling for neurite out-growth / paranode region of axon / fascia adherens / actin filament capping ...Caspase-mediated cleavage of cytoskeletal proteins / Interaction between L1 and Ankyrins / : / COPI-mediated anterograde transport / cuticular plate / spectrin / NCAM signaling for neurite out-growth / paranode region of axon / fascia adherens / actin filament capping / RAF/MAP kinase cascade / syntaxin binding / Neutrophil degranulation / spectrin binding / cortical cytoskeleton / lateral plasma membrane / Z disc / actin binding / calmodulin binding / calcium ion binding / protein-containing complex binding / protein-containing complex / membrane / plasma membrane / cytosol
Similarity search - Function
Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / SH3 Domains / SH3 domain / EF-hand domain pair ...Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / SH3 Domains / SH3 domain / EF-hand domain pair / EF-hand, calcium binding motif / SH3 type barrels. / Src homology 3 domains / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair / Roll / Mainly Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGabdulkhakov, A.G. / Gushchina, L.V. / Nikulin, A.D. / Nikonov, S.V. / Filimonov, V.V.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2011
Title: High-Resolution Crystal Structure of Spectrin SH3 Domain Fused with a Proline-Rich Peptide.
Authors: Gushchina, L.V. / Gabdulkhakov, A.G. / Nikonov, S.V. / Filimonov, V.V.
History
DepositionAug 19, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionNov 23, 2011ID: 2PQH
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Sep 13, 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 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _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

Downloads & links

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Assembly

Deposited unit
A: Spectrin alpha chain, brain
B: Spectrin alpha chain, brain
C: Proline-rich peptide
D: Proline-rich peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6377
Polymers18,3854
Non-polymers2523
Water81145
1
A: Spectrin alpha chain, brain
C: Proline-rich peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2713
Polymers9,1922
Non-polymers781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spectrin alpha chain, brain
D: Proline-rich peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3674
Polymers9,1922
Non-polymers1742
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.380, 36.380, 112.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Spectrin alpha chain, brain / Alpha-II spectrin / Fodrin alpha chain / Spectrin / non-erythroid alpha chain


Mass: 8211.320 Da / Num. of mol.: 2 / Fragment: SH3 DOMAIN, UNP residues 967 - 1035
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Sptan1, Spna2, Spta2 / Plasmid: pBAT-4/WT-CIIA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3 / References: UniProt: P16086
#2: Protein/peptide Proline-rich peptide


Mass: 981.101 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence was synthesized
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN WAS EXPRESSED AS ONE CHIMERIC ENTITY WITH THE COMPLETE SEQUENCE OF ...THE PROTEIN WAS EXPRESSED AS ONE CHIMERIC ENTITY WITH THE COMPLETE SEQUENCE OF MGTGKELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVNDRQGFVPAAYVKKLDPAQSASRENLGGPPPVPPYSAG. BUT IT IS REPRESENTED HERE AS TWO ENTITIES FOR EASE OF UNDERSTANDING FOR THE USERS. CHAINS C AND D (THE PEPTIDE PART) ARE THUS THE C-TERMINAL PART OF CHAINS A AND B (THE PROTEIN PART). DUE TO LACK OF DENSITY IN THE LINKER REGION, THE CORRECT ASSOCIATION BETWEEN THE TWO DIFFERENT PROTEIN AND PEPTIDE PARTS ARE UNKNOWN

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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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2M ammonium sulfate, 20 mM sodium acetate trihydrate, 5mM B-mercaptoethanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.072 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 28, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.564
11-H-K, K, -L20.436
ReflectionResolution: 1.7→30 Å / Num. all: 18279 / Num. obs: 17902 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.48 % / Rmerge(I) obs: 0.036 / Rsym value: 0.039 / Net I/σ(I): 23.5
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 5.26 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 3.49 / Num. unique all: 2892 / Rsym value: 0.391 / % possible all: 94.4

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SHG

1shg


Resolution: 1.7→27.47 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.747 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20113 929 5.2 %RANDOM
Rwork0.1796 ---
obs0.18076 16972 97.95 %-
all-18279 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.111 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å20 Å2
2--1.76 Å20 Å2
3----3.52 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 0 13 45 1098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221138
X-RAY DIFFRACTIONr_angle_refined_deg1.0161.9991554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1865137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.826.07851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87415201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.485154
X-RAY DIFFRACTIONr_chiral_restr0.0650.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022854
X-RAY DIFFRACTIONr_mcbond_it0.5181.5682
X-RAY DIFFRACTIONr_mcangle_it0.9521125
X-RAY DIFFRACTIONr_scbond_it1.0953456
X-RAY DIFFRACTIONr_scangle_it1.9034.5425
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 64 -
Rwork0.22 1195 -
obs-1195 92.03 %

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