[English] 日本語
Yorodumi
- PDB-5gxi: Structure of the Gemin5 WD40 domain in complex with AAUUUUUGAG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gxi
TitleStructure of the Gemin5 WD40 domain in complex with AAUUUUUGAG
Components
  • Gem-associated protein 5
  • RNA (5'-R(*A*AP*UP*UP*UP*UP*UP*GP*AP*G)-3')
KeywordsRNA BINDING PROTEIN/RNA / snRNP assembly / snRNA / Structural Genomics / Structural Genomics Consortium / SGC / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


SMN-Gemin2 complex / Gemini of Cajal bodies / SMN complex / U4atac snRNA binding / snRNA binding / RNA 7-methylguanosine cap binding / SMN-Sm protein complex / U4 snRNA binding / spliceosomal snRNP assembly / U1 snRNA binding ...SMN-Gemin2 complex / Gemini of Cajal bodies / SMN complex / U4atac snRNA binding / snRNA binding / RNA 7-methylguanosine cap binding / SMN-Sm protein complex / U4 snRNA binding / spliceosomal snRNP assembly / U1 snRNA binding / mRNA 3'-UTR binding / mRNA splicing, via spliceosome / regulation of translation / ribosome binding / protein-containing complex assembly / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / nuclear body / translation / RNA binding / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
: / : / : / : / : / RIG first beta-propeller / GEMI5 TPR domain / RIG second beta-propeller / GEMI5 RBS C-terminal domain / Anaphase-promoting complex subunit 4 WD40 domain ...: / : / : / : / : / RIG first beta-propeller / GEMI5 TPR domain / RIG second beta-propeller / GEMI5 RBS C-terminal domain / Anaphase-promoting complex subunit 4 WD40 domain / Quinoprotein alcohol dehydrogenase-like superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
RNA / Gem-associated protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsXu, C. / He, H. / Li, Y. / Dong, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Genes Dev. / Year: 2016
Title: Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly
Authors: Xu, C. / Ishikawa, H. / Izumikawa, K. / Li, L. / He, H. / Nobe, Y. / Yamauchi, Y. / Shahjee, H.M. / Wu, X.-H. / Yu, Y.-T. / Isobe, T. / Takahashi, N. / Min, J.
History
DepositionSep 18, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Oct 17, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line ..._entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector_type
Revision 1.3Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Dec 14, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gem-associated protein 5
B: RNA (5'-R(*A*AP*UP*UP*UP*UP*UP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)87,50124
Polymers87,5012
Non-polymers022
Water6,864381
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.850, 124.520, 60.600
Angle α, β, γ (deg.)90.00, 116.77, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Gem-associated protein 5 / Gemin5


Mass: 84337.359 Da / Num. of mol.: 1 / Fragment: UNP residues 1-739 / Mutation: R682Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN5 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TEQ6
#2: RNA chain RNA (5'-R(*A*AP*UP*UP*UP*UP*UP*GP*AP*G)-3') / U4 (118-127)


Mass: 3163.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 22 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium citrate, 0.2 M ammonium acetate, 15% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→28.92 Å / Num. obs: 65191 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.998 / Net I/σ(I): 14.9
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.8 / CC1/2: 0.592 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OW8,2HES,3DM0

3ow8

2hes

3dm0


Resolution: 1.85→28.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.017 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20738 3294 5.1 %RANDOM
Rwork0.16395 ---
obs0.16614 61867 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.115 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.85→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5150 82 23 381 5636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0195509
X-RAY DIFFRACTIONr_bond_other_d0.0020.025005
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9237556
X-RAY DIFFRACTIONr_angle_other_deg1.062311552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1875690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.10823.728228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91615840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6081525
X-RAY DIFFRACTIONr_chiral_restr0.1190.2845
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216164
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021275
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4072.2942695
X-RAY DIFFRACTIONr_mcbond_other2.4022.2932694
X-RAY DIFFRACTIONr_mcangle_it3.5043.4233366
X-RAY DIFFRACTIONr_mcangle_other3.5043.4233367
X-RAY DIFFRACTIONr_scbond_it2.9432.5522814
X-RAY DIFFRACTIONr_scbond_other2.9422.5532815
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3083.7244174
X-RAY DIFFRACTIONr_long_range_B_refined6.23919.3776333
X-RAY DIFFRACTIONr_long_range_B_other6.16319.1066165
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 255 -
Rwork0.255 4531 -
obs--99.73 %

+
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