[English] 日本語
Yorodumi
- PDB-3swk: Crystal structure of vimentin coil1B fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3swk
TitleCrystal structure of vimentin coil1B fragment
ComponentsVimentin
KeywordsSTRUCTURAL PROTEIN / cytoskeleton / intermediate filament / alpha-helix
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
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 ...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 / SAD / Resolution: 1.7 Å
AuthorsChernyatina, A.A. / Strelkov, S.V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Atomic structure of the vimentin central alpha-helical domain and its implications for intermediate filament assembly.
Authors: Chernyatina, A.A. / Nicolet, S. / Aebi, U. / Herrmann, H. / Strelkov, S.V.
History
DepositionJul 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vimentin
B: Vimentin


Theoretical massNumber of molelcules
Total (without water)20,7952
Polymers20,7952
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-48 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.150, 54.460, 44.090
Angle α, β, γ (deg.)90.000, 109.750, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Vimentin


Mass: 10397.688 Da / Num. of mol.: 2 / Fragment: coil 1B fragment (UNP residues 153-238)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLJ36605, VIM / Plasmid: pETHSUL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: P08670
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: protein in 10 mM Tris pH 8, 38 mM NaCl + PEG 3350 25% w/v, 0.2M ammonium acetate, BIS-TRIS 0.1M pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97895 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionNumber: 187035 / Rmerge(I) obs: 0.068 / D res high: 1.7 Å / Num. obs: 38320 / % possible obs: 98.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
5.0634.3142896.310.034
3.295.06384698.910.04
2.943.29212910010.048
2.552.94397499.510.06
2.282.55458599.910.082
2.082.28506899.710.127
1.932.08530299.810.239
1.81.93614899.510.482
1.71.8584096.110.778
ReflectionResolution: 1.7→34.3 Å / Num. all: 38296 / Num. obs: 36328 / % possible obs: 98.9 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 30.574 Å2 / Rsym value: 0.068 / Net I/σ(I): 13.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured obsNum. unique obsRsym value% possible all
1.7-1.84.642.592714458400.77896.1
1.8-1.934.233066561480.48299.5
1.93-2.087.362651453020.23999.8
2.08-2.2811.872535850680.12799.7
2.28-2.5516.12292645850.08299.9
2.55-2.9420.531963339740.0699.5
2.94-3.2924.11020021290.048100
3.29-5.0629.971796038460.0498.9
5.06-34.332.06663514280.03496.3

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→34.299 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.27 / σ(F): 1.99 / Phase error: 30.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2723 1968 5.14 %RANDOM
Rwork0.2315 ---
obs0.2335 36328 99.08 %-
all-38296 --
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.908 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 169.91 Å2 / Biso mean: 38.8169 Å2 / Biso min: 13.16 Å2
Baniso -1Baniso -2Baniso -3
1--4.1576 Å20 Å212.0176 Å2
2---1.816 Å20 Å2
3---5.9737 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1440 0 0 247 1687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041443
X-RAY DIFFRACTIONf_angle_d0.6441923
X-RAY DIFFRACTIONf_chiral_restr0.041215
X-RAY DIFFRACTIONf_plane_restr0.002262
X-RAY DIFFRACTIONf_dihedral_angle_d13.875603
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7002-1.7610.43371910.37063429362094
1.761-1.83150.39732060.317636783884100
1.8315-1.91490.32012070.292336433850100
1.9149-2.01580.3161680.277336873855100
2.0158-2.14210.27912060.248436373843100
2.1421-2.30740.24271880.223536763864100
2.3074-2.53960.27882230.237636283851100
2.5396-2.90690.27312160.229636453861100
2.9069-3.66170.24792060.206336743880100
3.6617-34.30580.23481570.20243631378898
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.07010.10950.0599-0.05050.00010.08270.0939-0.0523-0.1030.0823-0.0805-0.0148-0.12370.069800.1008-0.0032-0.0060.10210.02430.102447.092826.564321.042
20.00470.011-0.00250.00080.01140.0187-0.2060.0443-0.05740.1082-0.0066-0.1202-0.1347-0.077-00.1097-0.03910.0240.1001-0.02590.125-9.60016.275147.891
30.00090.0014-0.01380.0042-0.0076-0.001-0.07770.10030.1210.15550.09130.11610.07210.226300.155-0.04470.09860.1275-0.0310.3261-26.0226.233955.8823
40.0021-0.0138-0.0098-0.01810.0039-0.0106-0.041-0.0304-0.03520.1611-0.0814-0.17080.08350.027100.31830.06580.20770.22590.20970.793973.153228.28338.0838
5-0.07990.1399-0.28290.36240.076-0.1457-0.00070.1833-0.14950.0014-0.0179-0.0346-0.0872-0.122-00.07210.0057-0.02440.15410.0340.110535.202722.219720.9355
6-0.0047-0.0265-0.05230.02620.0407-0.02040.1662-0.03780.198-0.0382-0.088-0.11980.1343-0.0138-00.1309-0.0314-0.00820.0922-0.01650.09220.834715.917147.4238
70.0193-0.0130.0115-0.0076-0.01460.0189-0.03680.03480.06060.0965-0.23030.0548-0.01850.020300.2706-0.12860.08880.1432-0.09730.0401-17.30110.605261.2482
8-0.004-0.00770.00330.01720.00150.0211-0.1416-0.2852-0.2055-0.16010.00810.0951-0.2282-0.058600.1696-0.03830.04730.15320.03420.33379.23775.96541.3922
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 153:204)A153 - 204
2X-RAY DIFFRACTION2(chain A and resid 216:229)A216 - 229
3X-RAY DIFFRACTION3(chain A and resid 230:238)A230 - 238
4X-RAY DIFFRACTION4(chain B and resid 153:165)B153 - 165
5X-RAY DIFFRACTION5(chain B and resid 166:206)B166 - 206
6X-RAY DIFFRACTION6(chain B and resid 207:224)B207 - 224
7X-RAY DIFFRACTION7(chain B and resid 225:237)B225 - 237
8X-RAY DIFFRACTION8(chain A and resid 205:215)A205 - 215

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more