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- PDB-3g1e: X-ray crystal structure of coil 1A of human vimentin -

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Basic information

Entry
Database: PDB / ID: 3g1e
TitleX-ray crystal structure of coil 1A of human vimentin
ComponentsVimentin
KeywordsSTRUCTURAL PROTEIN / dimeric parallel coiled coil / Acetylation / Coiled coil / Host-virus interaction / Intermediate filament / Phosphoprotein
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
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
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å
AuthorsMeier, M. / Padilla, G.P. / Herrmann, H. / Wedig, T. / Hergt, M. / Patel, T.R. / Stetefeld, J. / Aebi, U. / Burkhard, P.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: Vimentin coil 1A-A molecular switch involved in the initiation of filament elongation.
Authors: Meier, M. / Padilla, G.P. / Herrmann, H. / Wedig, T. / Hergt, M. / Patel, T.R. / Stetefeld, J. / Aebi, U. / Burkhard, P.
#1: Journal: J.Mol.Biol. / Year: 2009
Title: Near-UV Circular Dichroism Reveals Structural Transitions of Vimentin Subunits during Intermediate Filament Assembly
Authors: Georgakopoulou, S. / Moeller, D. / Sachs, N. / Herrmann, H. / Aebi, U.
History
DepositionJan 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vimentin
B: Vimentin


Theoretical massNumber of molelcules
Total (without water)8,9682
Polymers8,9682
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-21 kcal/mol
Surface area6180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.496, 35.496, 108.022
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein/peptide Vimentin


Mass: 4484.115 Da / Num. of mol.: 2 / Fragment: coil 1A / Mutation: Y117L / Source method: obtained synthetically
Details: residue 102 to 138 from human vimentin chemically synthesized with an N-terminal acetyl and a C-terminal amidyl tag
References: UniProt: P08670
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 1.9 Å3/Da / Density % sol: 36.1 %
Crystal growTemperature: 298 K / pH: 5.6
Details: 20 % PEG, 33 % isopropanol, 0.1 M trisodium citrate, pH 5.6, vapour diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jan 10, 2006 / Details: MULTI-LAYER OPTICS
RadiationMonochromator: ASK OXFORD DIFFRACTION / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→11.65 Å / Num. obs: 6364 / % possible obs: 87.5 % / Observed criterion σ(I): 6 / Redundancy: 9.3 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 7
Reflection shellResolution: 1.77→1.86 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.414 / % possible all: 43.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å11.63 Å
Translation2.5 Å11.63 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
CNS1.2refinement
PDB_EXTRACT3.004data extraction
CrysalisProPRO (OXFORD DIFFRACTION)data reduction
REFMAC5.2.0019/CNS 1.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DIMERIC MODEL BUILT FROM PDB ENTRIES 1GK7 AND 1D7M

1gk7

1d7m


Resolution: 1.83→11.65 Å / Rfactor Rfree error: 0.014 / Occupancy max: 1 / Occupancy min: 0.3
Isotropic thermal model: restrained individual B-factor refinement
Cross valid method: THROUGHOUT / Stereochemistry target values: ENGH & HUBER / Details: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.295 437 7.1 %RANDOM
Rwork0.253 ---
all-6136 --
obs-6136 93 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 74.0181 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 33.19 Å2
Baniso -1Baniso -2Baniso -3
1-3.37 Å20 Å20 Å2
2--3.37 Å20 Å2
3----6.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.83→11.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms663 0 0 24 687
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.461.5
X-RAY DIFFRACTIONc_mcangle_it4.672
X-RAY DIFFRACTIONc_scbond_it5.952
X-RAY DIFFRACTIONc_scangle_it7.712.5
LS refinement shellResolution: 1.83→1.91 Å / Rfactor Rfree error: 0.057
RfactorNum. reflection% reflection
Rfree0.336 35 6.6 %
Rwork0.322 493 -
obs--66.8 %

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