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- PDB-1gk4: HUMAN VIMENTIN COIL 2B FRAGMENT (CYS2) -

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Basic information

Entry
Database: PDB / ID: 1gk4
TitleHUMAN VIMENTIN COIL 2B FRAGMENT (CYS2)
ComponentsVIMENTIN
KeywordsVIMENTIN / INTERMEDIATE FILAMENT / DIMER / PARALLEL COILED COIL / HEPTAD REPEAT / STUTTER
Function / homology
Function and homology information


lens fiber cell development / keratin filament binding / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / Striated Muscle Contraction / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / microtubule organizing center ...lens fiber cell development / keratin filament binding / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / Striated Muscle Contraction / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / microtubule organizing center / intermediate filament / cell leading edge / Bergmann glial cell differentiation / positive regulation of collagen biosynthetic process / Caspase-mediated cleavage of cytoskeletal proteins / regulation of mRNA stability / phagocytic vesicle / Late endosomal microautophagy / structural constituent of cytoskeleton / nuclear matrix / cellular response to type II interferon / Aggrephagy / Chaperone Mediated Autophagy / peroxisome / neuron projection development / double-stranded RNA binding / negative regulation of neuron projection development / 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 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...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 - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Vimentin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å
AuthorsStrelkov, S.V. / Herrmann, H. / Geisler, N. / Zimbelmann, R. / Aebi, U. / Burkhard, P.
Citation
Journal: Embo J. / Year: 2002
Title: Conserved Segments 1A and 2B of the Intermediate Filament Dimer: Their Atomic Structures and Role in Filament Assembly.
Authors: Strelkov, S. / Herrmann, H. / Geisler, N. / Wedig, T. / Zimbelmann, R. / Aebi, U. / Burkhard, P.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Divide-and-Conquer Crystallographic Approach Towards an Atomic Structure of Intermediate Filaments
Authors: Strelkov, S.V. / Herrmann, H. / Geisler, N. / Lustig, A. / Ivaninskii, S. / Zimbelmann, R. / Burkhard, P. / Aebi, U.
#2: Journal: J.Mol.Biol. / Year: 2000
Title: The Intermediate Filament Protein Consensus Motif of Helix 2B: Its Atomic Structure and Contribution to Assembly
Authors: Herrmann, H. / Strelkov, S.V. / Feja, B. / Rogers, K.R. / Brettel, M. / Lustig, A. / Haner, M. / Parry, D.A.D. / Steinert, P.M. / Burkhard, P. / Aebi, U.
History
DepositionAug 8, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VIMENTIN
B: VIMENTIN
C: VIMENTIN
D: VIMENTIN
E: VIMENTIN
F: VIMENTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5807
Polymers59,5216
Non-polymers591
Water8,179454
1
A: VIMENTIN
B: VIMENTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8993
Polymers19,8402
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: VIMENTIN
D: VIMENTIN


Theoretical massNumber of molelcules
Total (without water)19,8402
Polymers19,8402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: VIMENTIN
F: VIMENTIN


Theoretical massNumber of molelcules
Total (without water)19,8402
Polymers19,8402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.594, 84.283, 240.785
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2053-

HOH

21A-2054-

HOH

31A-2059-

HOH

41C-2067-

HOH

51D-2076-

HOH

61E-2060-

HOH

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Components

#1: Protein
VIMENTIN


Mass: 9920.125 Da / Num. of mol.: 6 / Fragment: CYS2, RESIDUES 328-411
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-21D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08670
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE NUMBERING USED IN THE LITERATURE FOR VIMENTIN DIFFERS BY +1 FROM THE NUMBERING USED IN ...THE RESIDUE NUMBERING USED IN THE LITERATURE FOR VIMENTIN DIFFERS BY +1 FROM THE NUMBERING USED IN SWISSPROT ENTRY P08670

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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: 3.3 Å3/Da / Density % sol: 63 %
Crystal growpH: 6.5
Details: 0.17M NA ACETATE, 25.5% PEG8000, 0.1M CACODYLATE, PH6.5, pH 6.50
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Strelkov, S.V., (2001) J.Mol.Biol., 306, 773
Components of the solutions
*PLUS
Conc.: 10-15 mg/ml / Common name: protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.9
DetectorDetector: IMAGE PLATE / Date: Sep 15, 1999 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→35 Å / Num. obs: 34937 / % possible obs: 99.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 13.5
Reflection shellResolution: 2.3→2.33 Å / Redundancy: 4 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 1.8 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 35 Å
Reflection shell
*PLUS
% possible obs: 99.7 % / Num. unique obs: 1159

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→34.52 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1095 3.1 %RANDOM
Rwork0.242 ---
obs0.242 34937 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.2273 Å2 / ksol: 0.328614 e/Å3
Displacement parametersBiso mean: 53.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.63 Å20 Å20 Å2
2--15.06 Å20 Å2
3----21.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.3→34.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3711 0 4 454 4169
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.34 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 53 3.1 %
Rwork0.349 1663 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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