[English] 日本語
Yorodumi
- PDB-6jvx: Crystal structure of RBM38 in complex with RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jvx
TitleCrystal structure of RBM38 in complex with RNA
Components
  • RNA (5'-R(*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*G)-3')
  • RNA-binding protein 38
KeywordsRNA BINDING PROTEIN/RNA / RBM38 / RNA binding / Translational regulation / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


regulation of myotube differentiation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / 3'-UTR-mediated mRNA stabilization / regulation of RNA splicing / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / RNA splicing / mRNA 3'-UTR binding / mRNA processing / cell differentiation / regulation of cell cycle ...regulation of myotube differentiation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / 3'-UTR-mediated mRNA stabilization / regulation of RNA splicing / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / RNA splicing / mRNA 3'-UTR binding / mRNA processing / cell differentiation / regulation of cell cycle / cell cycle / negative regulation of cell population proliferation / mRNA binding / RNA binding / nucleus / cytosol
Similarity search - Function
RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA-binding protein 38
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsQian, K. / Li, M. / Wang, J. / Zhang, M. / Wang, M.
CitationJournal: Biochem.J. / Year: 2020
Title: Structural basis for mRNA recognition by human RBM38.
Authors: Qian, K. / Li, M. / Wang, J. / Zhang, M. / Wang, M.
History
DepositionApr 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA-binding protein 38
B: RNA (5'-R(*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9094
Polymers17,7172
Non-polymers1922
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-38 kcal/mol
Surface area6080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.809, 78.809, 66.982
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein RNA-binding protein 38 / CLL-associated antigen KW-5 / HSRNASEB / RNA-binding motif protein 38 / RNA-binding region- ...CLL-associated antigen KW-5 / HSRNASEB / RNA-binding motif protein 38 / RNA-binding region-containing protein 1 / ssDNA-binding protein SEB4


Mass: 13853.546 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM38, RNPC1, SEB4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H0Z9
#2: RNA chain RNA (5'-R(*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*G)-3')


Mass: 3863.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.39 Å3/Da / Density % sol: 63.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris-HCl (pH8.0), 2M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 10894 / % possible obs: 98.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.049 / Rrim(I) all: 0.113 / Χ2: 1.049 / Net I/σ(I): 9.8 / Num. measured all: 53598
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3850.94210750.6790.4681.0571.09499.1
2.38-2.484.80.67910640.7240.3420.7651.05698.7
2.48-2.594.80.46610590.8580.2290.5221.08298.7
2.59-2.735.20.36110980.9320.1740.4031.05899.8
2.73-2.95.20.24310730.9680.1160.2711.06399.9
2.9-3.125.10.14410930.9880.0680.161.00899.8
3.12-3.444.90.09910890.9920.0480.111.0299.3
3.44-3.934.70.07510740.9950.0360.0831.02297.1
3.93-4.9550.06111180.9950.0290.0680.988100
4.95-504.60.05811510.9960.0280.0651.10597.1

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2cqd

2cqd


Resolution: 2.301→39.405 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.37
RfactorNum. reflection% reflection
Rfree0.2205 524 4.82 %
Rwork0.1775 --
obs0.1795 10876 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.63 Å2 / Biso mean: 43.1122 Å2 / Biso min: 15.44 Å2
Refinement stepCycle: final / Resolution: 2.301→39.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms670 153 10 127 960
Biso mean--69.6 49.04 -
Num. residues----95
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3014-2.5330.3361340.26562530266499
2.533-2.89950.24021350.206825672702100
2.8995-3.65260.18971200.15952578269899
3.6526-39.41030.19841350.15582677281299
Refinement TLS params.Method: refined / Origin x: -30.1613 Å / Origin y: 25.7511 Å / Origin z: 4.679 Å
111213212223313233
T0.1881 Å2-0.022 Å2-0.0209 Å2-0.1809 Å20.0187 Å2--0.2115 Å2
L4.982 °22.7382 °20.7568 °2-4.394 °21.0372 °2--5.1837 °2
S-0.2635 Å °-0.0755 Å °-0.032 Å °-0.2416 Å °0.1664 Å °0.1162 Å °0.2879 Å °-0.1764 Å °0.1078 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 29 through 115)

+
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