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- PDB-3s4r: Crystal structure of vimentin coil1A/1B fragment with a stabilizi... -

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Basic information

Entry
Database: PDB / ID: 3s4r
TitleCrystal structure of vimentin coil1A/1B fragment with a stabilizing mutation
ComponentsVimentin
KeywordsSTRUCTURAL PROTEIN / alpha-helix / cytoskeleton / intermediate filament
Function / homology
Function and homology information


keratin filament binding / lens fiber cell development / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / intermediate filament cytoskeleton / Striated Muscle Contraction / intermediate filament / RHOBTB1 GTPase cycle ...keratin filament binding / lens fiber cell development / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / intermediate filament cytoskeleton / Striated Muscle Contraction / intermediate filament / RHOBTB1 GTPase cycle / cell leading edge / Bergmann glial cell differentiation / microtubule organizing center / positive regulation of collagen biosynthetic process / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / regulation of mRNA stability / Late endosomal microautophagy / cellular response to type II interferon / structural constituent of cytoskeleton / nuclear matrix / Chaperone Mediated Autophagy / neuron projection development / Aggrephagy / peroxisome / double-stranded RNA binding / negative regulation of neuron projection development / cellular response to lipopolysaccharide / scaffold protein binding / Interleukin-4 and Interleukin-13 signaling / molecular adaptor activity / cytoskeleton / protein domain specific binding / axon / focal adhesion / positive regulation of gene expression / extracellular exosome / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Intermediate filament head, DNA-binding domain / : / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.452 Å
AuthorsChernyatina, A.A. / Strelkov, S.V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Atomic structure of the vimentin central alpha-helical domain and its implications for intermediate filament assembly.
Authors: Chernyatina, A.A. / Nicolet, S. / Aebi, U. / Herrmann, H. / Strelkov, S.V.
History
DepositionMay 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Vimentin
B: Vimentin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3614
Polymers22,1772
Non-polymers1842
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-24 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.329, 65.329, 377.339
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-205-

HOH

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Components

#1: Protein Vimentin


Mass: 11088.521 Da / Num. of mol.: 2 / Fragment: coil 1A/1B fragment (UNP residues 99-189) / Mutation: Y117L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLJ36605, VIM / Plasmid: pPEP-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08670
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.4964.79
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop60.1M Na cacodylate, MPD 20%, Mg acetate 0.45M, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting drop60.1M MES, MPD 35%, 0.35M Li2SO4, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06DA11
SYNCHROTRONSLS X06DA20.9796
SYNCHROTRONSLS X06DA30.9798
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDMay 29, 2009
MARMOSAIC 225 mm CCD2CCDJul 16, 2009
MARMOSAIC 225 mm CCD3CCDJul 16, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97961
30.97981
ReflectionRedundancy: 9.2 % / Av σ(I) over netI: 43.18 / Number: 71320 / Rmerge(I) obs: 0.088 / Χ2: 1.5 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 7749 / % possible obs: 86.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.325099.410.0573.9159
5.817.3210010.0892.05810.2
5.085.8110010.0741.58510.5
4.625.0810010.0641.54210.5
4.294.6210010.0781.67910.7
4.034.2910010.0981.92910.8
3.834.0310010.1051.810.6
3.663.8310010.1421.50310.8
3.523.6610010.1581.20410.6
3.43.5210010.1790.98610.3
3.33.410010.1870.949.8
3.23.310010.2150.859
3.123.299.110.1780.7928.1
3.043.1295.910.170.8136.8
2.973.0486.210.1430.8496.1
2.912.9767.910.130.8466.1
2.852.9151.910.1570.9186.5
2.82.8545.510.1620.8886.7
2.752.842.910.2220.7446.7
2.72.754110.2560.7646.6
ReflectionResolution: 2.45→50 Å / Num. all: 11209 / Num. obs: 11209 / % possible obs: 93.7 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -6 / Redundancy: 10.9 % / Rsym value: 0.071 / Χ2: 1.765 / Net I/σ(I): 14.5
Reflection shell

Diffraction-ID: 1,2,1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.45-2.498.50.421.73251.56355.9
2.49-2.548.30.2953691.4462.2
2.54-2.597.80.3284241.52372.6
2.59-2.647.40.3434961.60185.4
2.64-2.780.4135631.45896.1
2.7-2.769.70.4355901.434100
2.76-2.8311.20.3685921.465100
2.83-2.9120.2825771.52100
2.9-2.9911.90.1845941.542100
2.99-3.0912.20.2065881.561100
3.09-3.2120.1775911.534100
3.2-3.32120.1525861.604100
3.32-3.4812.10.1315921.67100
3.48-3.66120.1066032.015100
3.66-3.8911.90.0855862.356100
3.89-4.1911.60.0626092.665100
4.19-4.6111.70.0526092.528100
4.61-5.2811.60.0386101.702100
5.28-6.6511.50.0426351.644100
6.65-5010.20.0266701.73799.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
beamline - specificdata collection
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.452→48.52 Å / Occupancy max: 1 / Occupancy min: 0.69 / SU ML: 0.38 / σ(F): 0 / Phase error: 43.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3147 532 4.8 %RANDOM
Rwork0.2917 ---
all0.2929 11151 --
obs0.2929 11076 92.57 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.609 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 153.94 Å2 / Biso mean: 78.265 Å2 / Biso min: 39.7 Å2
Baniso -1Baniso -2Baniso -3
1-23.2798 Å20 Å2-0 Å2
2--23.2798 Å20 Å2
3----42.9403 Å2
Refinement stepCycle: LAST / Resolution: 2.452→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 12 4 1521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111519
X-RAY DIFFRACTIONf_angle_d1.2172020
X-RAY DIFFRACTIONf_chiral_restr0.077223
X-RAY DIFFRACTIONf_plane_restr0.003272
X-RAY DIFFRACTIONf_dihedral_angle_d17.074634
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4522-2.6990.46131130.38822041215474
2.699-3.08950.43641300.35082773290399
3.0895-3.89210.35381450.30352780292599
3.8921-48.5290.25381440.25892950309499

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