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- PDB-5whf: Crystal structure of vimentin coil 1B packed in a high-order fila... -

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Basic information

Entry
Database: PDB / ID: 5whf
TitleCrystal structure of vimentin coil 1B packed in a high-order filamentous form
ComponentsVimentin
KeywordsSTRUCTURAL PROTEIN / Intermediate filament / Oligomerization / Coiled coil / Helical domain
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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsObiero, J.M. / Pang, A.H. / Tsodikov, O.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA60872 United States
CitationJournal: FEBS J. / Year: 2018
Title: A crystal structure of coil 1B of vimentin in the filamentous form provides a model of a high-order assembly of a vimentin filament.
Authors: Pang, A.H. / Obiero, J.M. / Kulczyk, A.W. / Sviripa, V.M. / Tsodikov, O.V.
History
DepositionJul 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
G: Vimentin
H: Vimentin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6629
Polymers86,5708
Non-polymers921
Water2,288127
1
A: Vimentin
B: Vimentin
C: Vimentin
D: Vimentin
E: Vimentin
F: Vimentin
G: Vimentin
H: Vimentin
hetero molecules

A: Vimentin
B: Vimentin
C: Vimentin
D: Vimentin
E: Vimentin
F: Vimentin
G: Vimentin
H: Vimentin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,32318
Polymers173,13916
Non-polymers1842
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_456x-1,y,z+11
Unit cell
Length a, b, c (Å)39.990, 77.270, 123.390
Angle α, β, γ (deg.)90.00, 95.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Vimentin


Mass: 10821.196 Da / Num. of mol.: 8 / Fragment: UNP residues 153-238
Source method: isolated from a genetically manipulated source
Details: The N-terminal sequence GPHM is a part of the N-terminal tag that is left after the cleavage of most of the tag
Source: (gene. exp.) Homo sapiens (human) / Gene: VIM / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08670
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 0.2 M magnesium acetate tetrahydrate and 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→65.4 Å / Num. obs: 32009 / % possible obs: 89 % / Observed criterion σ(I): 3.5 / Redundancy: 1.8 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 7.25
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 3.5 / % possible all: 82

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UF1

3uf1


Resolution: 2.25→40.972 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2817 1601 5.02 %
Rwork0.2349 --
obs0.2372 31868 89.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→40.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5334 0 6 127 5467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075348
X-RAY DIFFRACTIONf_angle_d0.837175
X-RAY DIFFRACTIONf_dihedral_angle_d21.352091
X-RAY DIFFRACTIONf_chiral_restr0.044851
X-RAY DIFFRACTIONf_plane_restr0.012966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.32260.29251320.21042507X-RAY DIFFRACTION82
2.3226-2.40560.27141400.22492525X-RAY DIFFRACTION83
2.4056-2.5020.28881380.23512611X-RAY DIFFRACTION84
2.502-2.61580.27311340.22392586X-RAY DIFFRACTION85
2.6158-2.75370.31231810.24882650X-RAY DIFFRACTION88
2.7537-2.92620.27571410.25332654X-RAY DIFFRACTION87
2.9262-3.1520.33281080.25632748X-RAY DIFFRACTION88
3.152-3.46910.30311050.24782879X-RAY DIFFRACTION92
3.4691-3.97070.2611680.21713020X-RAY DIFFRACTION98
3.9707-5.00120.2491550.2053081X-RAY DIFFRACTION99
5.0012-40.97840.2991990.27563006X-RAY DIFFRACTION97

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