[English] 日本語
Yorodumi
- PDB-2j0u: The crystal structure of eIF4AIII-Barentsz complex at 3.0 A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2j0u
TitleThe crystal structure of eIF4AIII-Barentsz complex at 3.0 A resolution
Components
  • (ATP-DEPENDENT RNA HELICASE DDX48) x 2
  • PROTEIN CASC3
KeywordsHYDROLASE / ATP-BINDING / DNA-BINDING / NUCLEAR PROTEIN / RRNA PROCESSING / DEAD-BOX HELICASE / NUCLEOTIDE-BINDING / EJC / HELICASE / RNA-BINDING / ACETYLATION
Function / homology
Function and homology information


negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / regulation of translation at postsynapse, modulating synaptic transmission / intracellular mRNA localization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / negative regulation of excitatory postsynaptic potential / Deadenylation of mRNA ...negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / regulation of translation at postsynapse, modulating synaptic transmission / intracellular mRNA localization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / negative regulation of excitatory postsynaptic potential / Deadenylation of mRNA / embryonic cranial skeleton morphogenesis / poly(A) binding / mRNA 3'-end processing / M-decay: degradation of maternal mRNAs by maternally stored factors / U2-type catalytic step 1 spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / exploration behavior / associative learning / ribonucleoprotein complex binding / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cellular response to brain-derived neurotrophic factor stimulus / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / positive regulation of translation / mRNA splicing, via spliceosome / ISG15 antiviral mechanism / Regulation of expression of SLITs and ROBOs / RNA stem-loop binding / cytoplasmic stress granule / rRNA processing / regulation of translation / nuclear membrane / RNA helicase activity / postsynapse / negative regulation of translation / nuclear speck / RNA helicase / neuronal cell body / mRNA binding / dendrite / ubiquitin protein ligase binding / nucleolus / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Protein CASC3 / CASC3/Barentsz eIF4AIII binding / CASC3/Barentsz eIF4AIII binding / Btz domain / 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 domain / DEAD/DEAH box helicase ...Protein CASC3 / CASC3/Barentsz eIF4AIII binding / CASC3/Barentsz eIF4AIII binding / Btz domain / 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 domain / DEAD/DEAH box helicase / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein CASC3 / Eukaryotic initiation factor 4A-III
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBono, F. / Ebert, J. / Lorentzen, E. / Conti, E.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: The Crystal Structure of the Exon Junction Complex Reveals How It Mantains a Stable Grip on Mrna
Authors: Bono, F. / Ebert, J. / Lorentzen, E. / Conti, E.
History
DepositionAug 4, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-DEPENDENT RNA HELICASE DDX48
B: ATP-DEPENDENT RNA HELICASE DDX48
T: PROTEIN CASC3


Theoretical massNumber of molelcules
Total (without water)98,9133
Polymers98,9133
Non-polymers00
Water00
1
A: ATP-DEPENDENT RNA HELICASE DDX48
T: PROTEIN CASC3


Theoretical massNumber of molelcules
Total (without water)56,1502
Polymers56,1502
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ATP-DEPENDENT RNA HELICASE DDX48


Theoretical massNumber of molelcules
Total (without water)42,7631
Polymers42,7631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.760, 107.190, 243.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B
17A
27B

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROHISHISAA38 - 1381 - 101
21PROPROHISHISBB38 - 1381 - 101
12ILEILELYSLYSAA150 - 195113 - 158
22ILEILELYSLYSBB150 - 195113 - 158
13ALAALAGLUGLUAA280 - 295243 - 258
23ALAALAGLUGLUBB280 - 295243 - 258
14ARGARGLEULEUAA316 - 331279 - 294
24ARGARGLEULEUBB316 - 331279 - 294
15VALVALILEILEAA346 - 365309 - 328
25VALVALILEILEBB346 - 365309 - 328
16GLUGLUASPASPAA199 - 270162 - 233
26GLUGLUASPASPBB199 - 270162 - 233
17VALVALMETMETAA378 - 405341 - 368
27VALVALMETMETBB378 - 405341 - 368

NCS ensembles :
ID
1
2
3
4
5
6
7

NCS oper: (Code: given
Matrix: (-0.03527, -0.96627, -0.25511), (-0.99798, 0.02056, 0.06011), (-0.05284, 0.25672, -0.96504)
Vector: 0.46485, -9.18389, 61.89357)

-
Components

#1: Protein ATP-DEPENDENT RNA HELICASE DDX48 / EIF4AIII RNA-HELICASE / DEAD BOX PROTEIN 48 / EUKARYOTIC INITIATION FACTOR 4A-LIKE NUK-34 / NUCLEAR ...EIF4AIII RNA-HELICASE / DEAD BOX PROTEIN 48 / EUKARYOTIC INITIATION FACTOR 4A-LIKE NUK-34 / NUCLEAR MATRIX PROTEIN 265 / HNMP 265 / EUKARYOTIC TRANSLATION INITIATION FACTOR 4A ISOFORM 3


Mass: 42793.316 Da / Num. of mol.: 1 / Fragment: RESIDUES 37-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38919
#2: Protein ATP-DEPENDENT RNA HELICASE DDX48 / EIF4AIII RNA-HELICASE / DEAD BOX PROTEIN 48 / EUKARYOTIC INITIATION FACTOR 4A-LIKE NUK-34 / NUCLEAR ...EIF4AIII RNA-HELICASE / DEAD BOX PROTEIN 48 / EUKARYOTIC INITIATION FACTOR 4A-LIKE NUK-34 / NUCLEAR MATRIX PROTEIN 265 / HNMP 265 / EUKARYOTIC TRANSLATION INITIATION FACTOR 4A ISOFORM 3


Mass: 42763.223 Da / Num. of mol.: 1 / Fragment: RESIDUES 37-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38919
#3: Protein PROTEIN CASC3 / BARENTSZ / CANCER SUSCEPTIBILITY CANDIDATE GENE 3 PROTEIN / METASTATIC LYMPH NODE PROTEIN 51 / MLN ...BARENTSZ / CANCER SUSCEPTIBILITY CANDIDATE GENE 3 PROTEIN / METASTATIC LYMPH NODE PROTEIN 51 / MLN 51 PROTEIN / BARENTSZ PROTEIN / BTZ


Mass: 13356.604 Da / Num. of mol.: 1 / Fragment: RESIDUES 137-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15234

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growDetails: 700 MM DI AMMONIUM TARTRATE, 100 MM NA ACETATE PH 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→15 Å / Num. obs: 18221 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 4.3
Reflection shellResolution: 3→3.2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2 / % possible all: 86.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FUU, 1FUK, 1P27

1fuu

1fuk

1p27


Resolution: 3→15 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.814 / SU B: 62.301 / SU ML: 0.523 / Cross valid method: THROUGHOUT / ESU R Free: 0.548 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.328 903 5 %RANDOM
Rwork0.273 ---
obs0.276 17157 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20 Å2
2--1.18 Å20 Å2
3----1.98 Å2
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5139 0 0 0 5139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225219
X-RAY DIFFRACTIONr_bond_other_d0.0030.024975
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9417128
X-RAY DIFFRACTIONr_angle_other_deg0.959311376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8865713
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06723.676185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.87915719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6331528
X-RAY DIFFRACTIONr_chiral_restr0.1350.2876
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025992
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021055
X-RAY DIFFRACTIONr_nbd_refined0.2580.21460
X-RAY DIFFRACTIONr_nbd_other0.1960.25331
X-RAY DIFFRACTIONr_nbtor_refined0.1960.22658
X-RAY DIFFRACTIONr_nbtor_other0.0910.23207
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2169
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4571.54525
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.53325615
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.71631877
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.114.51513
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11292tight positional0.030.05
2523tight positional0.060.05
3212tight positional0.030.05
4119tight positional0.030.05
5340tight positional0.030.05
6914tight positional0.060.05
7356tight positional0.030.05
11292tight thermal0.060.5
2523tight thermal0.050.5
3212tight thermal0.040.5
4119tight thermal0.050.5
5340tight thermal0.060.5
6914tight thermal0.070.5
7356tight thermal0.050.5
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.434 58
Rwork0.357 1118

+
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