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- PDB-4yv3: Trimeric crystal structure of vimentin coil1B fragment -

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Basic information

Entry
Database: PDB / ID: 4yv3
TitleTrimeric crystal structure of vimentin coil1B fragment
ComponentsVimentin
KeywordsSTRUCTURAL PROTEIN / cytoskeleton / intermediate filament / vimentin / alpha-helical coiled-coil trimer
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 / RHOBTB1 GTPase cycle / intermediate filament ...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 / RHOBTB1 GTPase cycle / intermediate filament / cell leading edge / microtubule organizing center / Bergmann glial cell differentiation / positive regulation of collagen biosynthetic process / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / regulation of mRNA stability / Late endosomal microautophagy / structural constituent of cytoskeleton / cellular response to type II interferon / nuclear matrix / Chaperone Mediated Autophagy / Aggrephagy / neuron projection development / 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 / cytosol / cytoplasm
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 / SAD / Resolution: 2 Å
AuthorsChernyatina, A.A. / Strelkov, S.V.
Funding support Belgium, 1items
OrganizationGrant numberCountry
KU Leuven07/071 Belgium
CitationJournal: Meth. Enzymol. / Year: 2016
Title: How to Study Intermediate Filaments in Atomic Detail.
Authors: Chernyatina, A.A. / Hess, J.F. / Guzenko, D. / Voss, J.C. / Strelkov, S.V.
History
DepositionMar 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Apr 9, 2025Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vimentin
B: Vimentin
C: Vimentin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2995
Polymers28,1683
Non-polymers1322
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-100 kcal/mol
Surface area14290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.060, 60.950, 48.900
Angle α, β, γ (deg.)90.000, 104.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Vimentin


Mass: 9389.188 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VIM / Plasmid: pETHSUL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P08670
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10mg/ml protein in 10mM Tris-HCl pH 8, 38 mM NaCl mixed in v/v ratio 1:1 with ammonium sulphate 2.2M, sodium thiocyanate 0.2 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97895 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 29510 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 36.23 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.098 / Χ2: 0.983 / Net I/σ(I): 11.98 / Num. measured all: 219408
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.170.8380.8952.2528160405740240.96699.2
2.1-2.20.9420.5433.7925393333433260.58299.8
2.2-2.30.9670.3855.1521098276727660.413100
2.3-2.40.9740.36.5417804233023360.322100
2.4-2.50.9880.2238.0914977196819570.23999.4
2.5-2.70.990.17310.2523799312331240.186100
2.7-30.9970.1114.4724917328432830.118100
3-40.9970.07122.1237025503350240.07699.8
4-60.9970.06126.0618707260826060.06699.9
6-90.9980.06125.9854867687650.06699.6
90.9960.05427.420423262990.05991.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→47.379 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 36.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2962 1441 4.89 %
Rwork0.2547 28027 -
obs0.2568 29468 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.63 Å2 / Biso mean: 49.7377 Å2 / Biso min: 22.56 Å2
Refinement stepCycle: final / Resolution: 2→47.379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 6 64 1866
Biso mean--68.81 54.31 -
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041889
X-RAY DIFFRACTIONf_angle_d0.4872534
X-RAY DIFFRACTIONf_chiral_restr0.019280
X-RAY DIFFRACTIONf_plane_restr0.002349
X-RAY DIFFRACTIONf_dihedral_angle_d10.504791
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.07150.41061450.3392803294899
2.0715-2.15440.37771560.318428182974100
2.1544-2.25250.32431600.290827622922100
2.2525-2.37120.38821450.287528202965100
2.3712-2.51980.30471200.286828042924100
2.5198-2.71430.3681470.276828292976100
2.7143-2.98740.29111240.27128182942100
2.9874-3.41960.30661530.269327992952100
3.4196-4.30790.24821490.212328162965100
4.3079-47.39180.26511420.23442758290099

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