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

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Basic information

Entry
Database: PDB / ID: 4ypc
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 / Striated Muscle Contraction / microtubule organizing center / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton ...keratin filament binding / lens fiber cell development / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / Striated Muscle Contraction / microtubule organizing center / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / intermediate filament / cell leading edge / 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 / cellular response to type II interferon / structural constituent of cytoskeleton / nuclear matrix / Aggrephagy / Chaperone Mediated Autophagy / double-stranded RNA binding / neuron projection development / negative regulation of neuron projection development / peroxisome / scaffold protein binding / cellular response to lipopolysaccharide / 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
Vasodilator-stimulated phosphoprotein / 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 ...Vasodilator-stimulated phosphoprotein / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.44 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 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
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


Theoretical massNumber of molelcules
Total (without water)9,9241
Polymers9,9241
Non-polymers00
Water1,964109
1
A: Vimentin

A: Vimentin

A: Vimentin


Theoretical massNumber of molelcules
Total (without water)29,7723
Polymers29,7723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8740 Å2
ΔGint-77 kcal/mol
Surface area16290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.447, 35.447, 200.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

21A-371-

HOH

31A-372-

HOH

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Components

#1: Protein Vimentin


Mass: 9924.025 Da / Num. of mol.: 1 / Fragment: coil 1B fragment, UNP residues 161-243
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.44 Å3/Da / Density % sol: 49.54 %
Description: twinning -h-k, k, -l with estimated twin fraction 0.453 (Britton analyses), 0468 (H-test), 0.478 (ML method)
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: protein in 10 mM Tris pH 8, 38 mM NaCl mixed in ratio 1:1 with 1M Sodium citrate tribasic dihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 110.97926
SYNCHROTRONSOLEIL PROXIMA 120.8856
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDNov 14, 2010
ADSC QUANTUM 315r2CCDNov 14, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.88561
Reflection twinOperator: -h-k,k,-l / Fraction: 0.51
ReflectionResolution: 1.44→20 Å / Num. all: 16952 / Num. obs: 16952 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.46 % / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.073 / Rsym value: 0.069 / Χ2: 0.959 / Net I/σ(I): 19.94 / Num. measured all: 177342
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
1.44-1.483.620.9420.5672.324624128012760.65899.7
1.48-1.520.9860.3494.386478121212040.38799.3
1.52-1.560.9730.3455.627308120312030.378100
1.56-1.610.9570.5196.7612711116711670.543100
1.61-1.660.9780.3949.0313571109710970.412100
1.66-1.720.9810.32510.7513349107110710.339100
1.72-1.790.9890.25212.6813200106010600.263100
1.79-1.860.9950.17316.1412905103110310.181100
1.86-1.940.9960.12321.42115839329320.128100
1.94-2.040.9970.09826.07114489209200.102100
2.04-2.150.9970.07731.3109598828820.081100
2.15-2.280.9980.06835.08103398318310.071100
2.28-2.430.9970.06437.1696497777770.067100
2.43-2.630.9970.06538.4589837297290.068100
2.63-2.880.9970.06539.6281666696690.068100
2.88-3.220.9980.05940.6875556256250.062100
3.22-3.720.9970.05838.5155295165160.062100
3.72-4.550.9960.05635.8842064524490.0699.3
4.55-6.440.9960.05336.2532513473380.05797.4
6.440.9970.05933.5115281991750.06487.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SWK, 3UF1

3swk

3uf1


Resolution: 1.44→19.39 Å / Cross valid method: FREE R-VALUE / Phase error: 36.94 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2764 853 5.03 %PHENIX selection
Rwork0.2477 16069 --
obs0.2533 16948 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.22 Å2 / Biso mean: 24.0127 Å2 / Biso min: 12.91 Å2
Refinement stepCycle: final / Resolution: 1.44→19.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms694 0 0 109 803
Biso mean---25.4 -
Num. residues----83
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007750
X-RAY DIFFRACTIONf_angle_d0.941013
X-RAY DIFFRACTIONf_chiral_restr0.069113
X-RAY DIFFRACTIONf_plane_restr0.002141
X-RAY DIFFRACTIONf_dihedral_angle_d14.546322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.441-1.53120.44511390.40182708284795
1.5312-1.64930.33111420.34012657279995
1.6493-1.81510.32511440.33612676282095
1.8151-2.07730.37411480.29582686283495
2.0773-2.61560.25881380.25562676281495
2.6156-16.76310.24791420.21142666280894

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