[English] 日本語
Yorodumi
- PDB-1vec: Crystal structure of the N-terminal domain of rck/p54, a human DE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vec
TitleCrystal structure of the N-terminal domain of rck/p54, a human DEAD-box protein
ComponentsATP-dependent RNA helicase p54
KeywordsRNA BINDING PROTEIN / RNA HELICASE / DEAD-BOX PROTEIN
Function / homology
Function and homology information


mRNA decay by 5' to 3' exoribonuclease / miRNA-mediated gene silencing by inhibition of translation / viral RNA genome packaging / P-body assembly / RISC complex / stem cell population maintenance / stress granule assembly / negative regulation of neuron differentiation / P-body / neuron differentiation ...mRNA decay by 5' to 3' exoribonuclease / miRNA-mediated gene silencing by inhibition of translation / viral RNA genome packaging / P-body assembly / RISC complex / stem cell population maintenance / stress granule assembly / negative regulation of neuron differentiation / P-body / neuron differentiation / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / helicase activity / negative regulation of translation / RNA helicase activity / RNA helicase / cadherin binding / mRNA binding / protein domain specific binding / ATP hydrolysis activity / RNA binding / ATP binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. ...DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Probable ATP-dependent RNA helicase DDX6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsHogetsu, K. / Matsui, T. / Yukihiro, Y. / Tanaka, M. / Sato, T. / Kumasaka, T. / Tanaka, N.
CitationJournal: Genes Cells / Year: 2006
Title: Structural insight of human DEAD-box protein rck/p54 into its substrate recognition with conformational changes
Authors: Matsui, T. / Hogetsu, K. / Usukura, J. / Sato, T. / Kumasaka, T. / Akao, Y. / Tanaka, N.
History
DepositionMar 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent RNA helicase p54
B: ATP-dependent RNA helicase p54
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4424
Polymers46,2262
Non-polymers2152
Water5,855325
1
A: ATP-dependent RNA helicase p54
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1782
Polymers23,1131
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent RNA helicase p54
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2632
Polymers23,1131
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: ATP-dependent RNA helicase p54
hetero molecules

B: ATP-dependent RNA helicase p54
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4424
Polymers46,2262
Non-polymers2152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1210 Å2
ΔGint-34 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.520, 73.140, 84.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ATP-dependent RNA helicase p54 / RCK / DEAD-box protein 6


Mass: 23113.076 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HUMRCK / Plasmid: PTYB11 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P26196
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: PEG3350, di-sodium tartrate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 15, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→29.9 Å / Num. all: 52406 / Num. obs: 52054 / % possible obs: 99.3 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.4
Reflection shellResolution: 2.01→2.08 Å / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5271 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QDE

1qde


Resolution: 2.01→29.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 116477.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2534 4.9 %RANDOM
Rwork0.198 ---
all0.198 ---
obs0.198 51717 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.4738 Å2 / ksol: 0.335418 e/Å3
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--3.08 Å20 Å2
3----3.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.01→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3232 0 11 325 3568
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 366 4.7 %
Rwork0.284 7477 -
obs-7477 88.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4TAR_XPLOR_PARAMTAR_XPLOR_TOP

+
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://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