[English] 日本語
Yorodumi
- PDB-3v53: Crystal structure of human RBM25 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3v53
TitleCrystal structure of human RBM25
ComponentsRNA-binding protein 25
KeywordsRNA BINDING PROTEIN / PWI / RNA-binding domain
Function / homology
Function and homology information


regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Major Pathway / RNA splicing / mRNA processing / regulation of apoptotic process / nuclear speck / mRNA binding / RNA binding / nucleoplasm / cytoplasm
Similarity search - Function
RBM25, RNA recognition motif / : / PWI domain / PWI domain / PWI domain superfamily / PWI domain / PWI domain profile. / PWI domain / PWI, domain in splicing factors / RNA recognition motif ...RBM25, RNA recognition motif / : / PWI domain / PWI domain / PWI domain superfamily / PWI domain / PWI domain profile. / PWI domain / PWI, domain in splicing factors / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA-binding protein 25
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsGong, D.S.
CitationJournal: Biochem.J. / Year: 2013
Title: Crystal structure and functional characterization of the human RBM25 PWI domain and its flanking basic region
Authors: Gong, D.S. / Yang, F. / Li, F. / Qian, D. / Wu, M. / Shao, Z. / Wu, M. / Wu, J. / Shi, Y.
History
DepositionDec 16, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA-binding protein 25
B: RNA-binding protein 25
C: RNA-binding protein 25
D: RNA-binding protein 25
E: RNA-binding protein 25


Theoretical massNumber of molelcules
Total (without water)69,9835
Polymers69,9835
Non-polymers00
Water00
1
A: RNA-binding protein 25


Theoretical massNumber of molelcules
Total (without water)13,9971
Polymers13,9971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-binding protein 25


Theoretical massNumber of molelcules
Total (without water)13,9971
Polymers13,9971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA-binding protein 25


Theoretical massNumber of molelcules
Total (without water)13,9971
Polymers13,9971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RNA-binding protein 25


Theoretical massNumber of molelcules
Total (without water)13,9971
Polymers13,9971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: RNA-binding protein 25


Theoretical massNumber of molelcules
Total (without water)13,9971
Polymers13,9971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.577, 86.172, 197.174
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
RNA-binding protein 25 / Arg/Glu/Asp-rich protein of 120 kDa / RED120 / Protein S164 / RNA-binding motif protein 25 / RNA- ...Arg/Glu/Asp-rich protein of 120 kDa / RED120 / Protein S164 / RNA-binding motif protein 25 / RNA-binding region-containing protein 7


Mass: 13996.522 Da / Num. of mol.: 5 / Fragment: UNP residues 734-843
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM25 / Plasmid: p28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49756

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5.65
Details: pH 5.65, VAPOR DIFFUSION, HANGING DROP, temperature 281K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorDate: Jun 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 15818 / Num. obs: 15818

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→49.29 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.87 / SU B: 43.911 / SU ML: 0.383 / Cross valid method: THROUGHOUT / ESU R Free: 0.47 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29835 765 4.9 %RANDOM
Rwork0.26376 ---
obs0.26537 14732 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.653 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4150 0 0 0 4150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224233
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9731.9685747
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0035530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45124.286154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.02415736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6061517
X-RAY DIFFRACTIONr_chiral_restr0.0570.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213066
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3131.52697
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.57724336
X-RAY DIFFRACTIONr_scbond_it0.55531536
X-RAY DIFFRACTIONr_scangle_it0.9624.51411
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 55 -
Rwork0.315 1062 -
obs--96.13 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.67032.54623.18127.49544.20986.6566-0.1020.11280.14680.36580.1010.25610.60451.00030.00090.23140.20130.01130.56150.1420.248630.35719.52323.728
26.3323-0.50292.67852.1413-1.23634.35850.08120.0286-0.2175-0.273-0.05290.01730.1991-0.6368-0.02830.2568-0.14760.11550.2767-0.09730.072117.73450.74718.33
34.8074-0.1864-0.36862.18241.28053.924-0.0709-0.32850.3197-0.2044-0.1684-0.1555-0.0455-0.55860.23930.14410.1079-0.07130.189-0.11460.2355-20.62433.68553.919
41.09831.22481.39954.26631.37582.5779-0.06040.17120.1149-0.18650.1567-0.3043-0.01970.0316-0.09640.1248-0.05530.01540.13850.03460.2223-5.11517.74836.716
56.4038-1.79010.76177.4504-4.004111.6575-0.01030.2439-0.80120.16040.0055-0.33610.2132-0.30620.00470.0972-0.16170.07090.3006-0.19280.243913.34117.9641.187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A729 - 841
2X-RAY DIFFRACTION2B730 - 841
3X-RAY DIFFRACTION3C736 - 839
4X-RAY DIFFRACTION4D731 - 839
5X-RAY DIFFRACTION5E736 - 838

+
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