[English] 日本語
Yorodumi
- PDB-3iuy: Crystal structure of DDX53 DEAD-box domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3iuy
TitleCrystal structure of DDX53 DEAD-box domain
ComponentsProbable ATP-dependent RNA helicase DDX53
KeywordsHYDROLASE / REC-A-like / DEAD-box / Structural Genomics / Structural Genomics Consortium / SGC / ATP-binding / Helicase / Nucleotide-binding / Nucleus / RNA-binding
Function / homology
Function and homology information


RNA helicase activity / RNA helicase / intracellular membrane-bounded organelle / nucleolus / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / cytosol
Similarity search - Function
KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / K Homology domain, type 1 superfamily / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain ...KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / K Homology domain, type 1 superfamily / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / K Homology domain / K homology RNA-binding 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
ADENOSINE MONOPHOSPHATE / Probable ATP-dependent RNA helicase DDX53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSchutz, P. / Karlberg, T. / Collins, R. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Schutz, P. / Karlberg, T. / Collins, R. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kallas, A. / Kraulis, P. / Kotenyova, T. / Kotzsch, A. / Markova, N. / Moche, M. / Nielsen, T.K. / Nordlund, P. / Nyman, T. / Persson, C. / Roos, A.K. / Siponen, M.I. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Wisniewska, M. / Schuler, H.M. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2010
Title: Comparative Structural Analysis of Human DEAD-Box RNA Helicases.
Authors: Schutz, P. / Karlberg, T. / van den Berg, S. / Collins, R. / Lehtio, L. / Hogbom, M. / Holmberg-Schiavone, L. / Tempel, W. / Park, H.W. / Hammarstrom, M. / Moche, M. / Thorsell, A.G. / Schuler, H.
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Data collection / Structure summary / Category: audit_author / diffrn_radiation_wavelength / Item: _audit_author.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX53
B: Probable ATP-dependent RNA helicase DDX53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2656
Polymers51,5002
Non-polymers7654
Water2,792155
1
A: Probable ATP-dependent RNA helicase DDX53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1333
Polymers25,7501
Non-polymers3832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ATP-dependent RNA helicase DDX53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1333
Polymers25,7501
Non-polymers3832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.442, 61.251, 65.787
Angle α, β, γ (deg.)90.00, 96.36, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Probable ATP-dependent RNA helicase DDX53 / DEAD box protein 53 / DEAD box protein CAGE / Cancer-associated gene protein / Cancer/testis antigen 26 / CT26


Mass: 25750.002 Da / Num. of mol.: 2 / Fragment: UNP residues 204-430, Helicase ATP-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX53, CAGE / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE
References: UniProt: Q86TM3, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 27% PEG6000, 0.1M MES pH 6, 0.2M AmmoniumChloride, 15% Glycerol, 0.2M NaCl , VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→65.382 Å / Num. obs: 17649 / % possible obs: 100 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.187 / Rsym value: 0.187 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.539.50.5781.22440925710.578100
2.53-2.689.50.4521.52312424370.452100
2.68-2.879.50.3222.12134922560.322100
2.87-3.19.50.2422.92005821140.242100
3.1-3.399.50.17341853919500.173100
3.39-3.798.90.1733.51587017880.173100
3.79-4.389.30.12751470715790.127100
4.38-5.379.30.0995.61226613170.099100
5.37-7.599.10.1095.7957010490.109100
7.59-45.138.60.1184.150565880.11899.6

-
Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMAC5.5.0035refinement
PDB_EXTRACT3.005data extraction
DNAdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.13 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.882 / Occupancy max: 1 / Occupancy min: 0 / SU B: 8.703 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.515 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 926 5.3 %RANDOM
Rwork0.201 ---
obs0.204 17613 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.43 Å2 / Biso mean: 23.168 Å2 / Biso min: 4.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 48 155 3387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223299
X-RAY DIFFRACTIONr_angle_refined_deg1.1572.0154496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3135413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89124.464112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41715560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3281515
X-RAY DIFFRACTIONr_chiral_restr0.070.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212369
X-RAY DIFFRACTIONr_mcbond_it0.3861.52095
X-RAY DIFFRACTIONr_mcangle_it0.72523407
X-RAY DIFFRACTIONr_scbond_it0.87631204
X-RAY DIFFRACTIONr_scangle_it1.4984.51089
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 64 -
Rwork0.232 1259 -
all-1323 -
obs--100 %

+
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