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- PDB-1gk6: Human vimentin coil 2B fragment linked to GCN4 leucine zipper (Z2B) -

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Basic information

Entry
Database: PDB / ID: 1gk6
TitleHuman vimentin coil 2B fragment linked to GCN4 leucine zipper (Z2B)
ComponentsVIMENTIN
KeywordsSTRUCTURAL PROTEIN / INTERMEDIATE FILAMENT / DIMER / PARALLEL COILED COIL / HEPTAD REPEAT / LEUCINE ZIPPER / FUSION PROTEIN
Function / homology
Function and homology information


keratin filament binding / lens fiber cell development / intermediate filament organization / cellular response to muramyl dipeptide / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / structural constituent of eye lens / negative regulation of ribosomal protein gene transcription by RNA polymerase II ...keratin filament binding / lens fiber cell development / intermediate filament organization / cellular response to muramyl dipeptide / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / structural constituent of eye lens / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / astrocyte development / intermediate filament cytoskeleton / Oxidative Stress Induced Senescence / Striated Muscle Contraction / intermediate filament / RHOBTB1 GTPase cycle / cell leading edge / Bergmann glial cell differentiation / TFIID-class transcription factor complex binding / amino acid biosynthetic process / microtubule organizing center / positive regulation of collagen biosynthetic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Caspase-mediated cleavage of cytoskeletal proteins / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / phagocytic vesicle / regulation of mRNA stability / cellular response to amino acid starvation / Late endosomal microautophagy / cellular response to type II interferon / structural constituent of cytoskeleton / RNA polymerase II transcription regulator complex / nuclear matrix / Chaperone Mediated Autophagy / neuron projection development / Aggrephagy / peroxisome / double-stranded RNA binding / negative regulation of neuron projection development / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / scaffold protein binding / Interleukin-4 and Interleukin-13 signaling / transcription regulator complex / molecular adaptor activity / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cytoskeleton / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / axon / focal adhesion / chromatin binding / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / nucleus / 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 / : ...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 / : / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
General control transcription factor GCN4 / Vimentin
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 Motifof Helix 2B: Its Atomic Structure and Contribution to Assembly
Authors: Herrmann, H. / Strelkov, S.V. / Feja, B. / Rogers, K.R. / Brettel, M. / Lustig, A. / Haener, 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
SupersessionMar 27, 2003ID: 1E7T
Revision 1.1Nov 25, 2015Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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

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Assembly

Deposited unit
A: VIMENTIN
B: VIMENTIN


Theoretical massNumber of molelcules
Total (without water)13,8522
Polymers13,8522
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-32.4 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.801, 98.801, 36.473
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein VIMENTIN


Mass: 6926.064 Da / Num. of mol.: 2
Fragment: Z2B FUSION CONSTRUCT CONTAINING THE GCN4 LEUCINE ZIPPER LINKED TO VIMENTIN RESIDUES 385 - 412
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL HALF OF THE MOLECULE CONTAINS THE GCN4 LEUCINE ZIPPER SEQUENCE WHILE THE C-TERMINAL HALF CONTAINS THE VIMENTIN SEQUENCE
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast), (gene. exp.) HOMO SAPIENS (human)
Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P03069, UniProt: P08670
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 3.72 Å3/Da / Density % sol: 67.5 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: HANGING DROPS WITH 12.5MG/ML PROTEIN AND 0.55M (NH4)2HPO4, PH ADJUSTED TO 9.0 WITH NAOH, AS PRECIPITANT
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: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.2545
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2545 Å / Relative weight: 1
ReflectionResolution: 1.9→33.5 Å / Num. obs: 16241 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 15
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3.3 / % possible all: 99.4
Reflection
*PLUS
Lowest resolution: 35 Å / Num. obs: 15422 / Redundancy: 4 %
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 99.4 % / Redundancy: 3.7 % / Num. unique obs: 1604

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZTA

2zta


Resolution: 1.9→35 Å / SU B: 2.76753 / SU ML: 0.08356 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11921 / ESU R Free: 0.1154
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 819 5 %RANDOM
Rwork0.19927 ---
obs0.20062 15422 99.2 %-
Refinement stepCycle: LAST / Resolution: 1.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 0 194 1064
Refinement
*PLUS
Num. reflection Rfree: 778 / Rfactor Rfree: 0.2267
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.53 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.7

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