[English] 日本語
Yorodumi
- PDB-7szu: Crystal structure of Pepper RNA aptamer in complex with HBC ligan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7szu
TitleCrystal structure of Pepper RNA aptamer in complex with HBC ligand and Fab BL3-6
Components
  • BL3-6 Fab heavy chain
  • BL3-6 Fab light chain
  • RNA aptamer
KeywordsIMMUNE SYSTEM/RNA / fluorogenic / IMMUNE SYSTEM-RNA complex
Function / homologyChem-J8F / RNA / RNA (> 10)
Function and homology information
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsRees, H.C. / Piccirilli, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM102489 United States
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Structural Basis for Fluorescence Activation by Pepper RNA.
Authors: Rees, H.C. / Gogacz, W. / Li, N.S. / Koirala, D. / Piccirilli, J.A.
History
DepositionNov 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
R: RNA aptamer
H: BL3-6 Fab heavy chain
L: BL3-6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0647
Polymers68,6893
Non-polymers3754
Water9,836546
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, EMSA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.609, 96.992, 148.255
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
RNA chain , 1 types, 1 molecules R

#1: RNA chain RNA aptamer


Mass: 21734.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Antibody , 2 types, 2 molecules HL

#2: Antibody BL3-6 Fab heavy chain


Mass: 23749.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Antibody BL3-6 Fab light chain


Mass: 23204.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 4 types, 550 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: Chemical ChemComp-J8F / 4-[(~{Z})-1-cyano-2-[4-[2-hydroxyethyl(methyl)amino]phenyl]ethenyl]benzenecarbonitrile


Mass: 303.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C19H17N3O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.02 M Magnesium sulfate hydrate 0.002 M Cobalt(II) chloride hexahydrate 0.05 M Sodium cacodylate trihydrate pH 6.0 25% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.0005 M Spermine

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.239→148.255 Å / Num. obs: 43646 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 62.32 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.9
Reflection shellResolution: 2.24→2.31 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.449 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3937 / CC1/2: 0.605 / Rpim(I) all: 0.593 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Cootmodel building
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KZD

4kzd


Resolution: 2.24→58.9 Å / SU ML: 0.3874 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.6424
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2626 1999 4.59 %
Rwork0.2194 41547 -
obs0.2213 43546 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.89 Å2
Refinement stepCycle: LAST / Resolution: 2.24→58.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 1407 58 546 5314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00255009
X-RAY DIFFRACTIONf_angle_d0.58157125
X-RAY DIFFRACTIONf_chiral_restr0.0375849
X-RAY DIFFRACTIONf_plane_restr0.0034658
X-RAY DIFFRACTIONf_dihedral_angle_d14.36692005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.290.41111390.35082903X-RAY DIFFRACTION98.51
2.29-2.360.40171420.33412918X-RAY DIFFRACTION99.9
2.36-2.430.37881400.31032924X-RAY DIFFRACTION99.93
2.43-2.50.35441410.30662923X-RAY DIFFRACTION99.8
2.5-2.590.33451410.28412928X-RAY DIFFRACTION100
2.59-2.70.371420.29572942X-RAY DIFFRACTION99.97
2.7-2.820.39541410.2982949X-RAY DIFFRACTION99.97
2.82-2.970.36391430.27362960X-RAY DIFFRACTION100
2.97-3.150.26191420.24012951X-RAY DIFFRACTION99.94
3.16-3.40.28871410.24012956X-RAY DIFFRACTION99.81
3.4-3.740.26771430.20862983X-RAY DIFFRACTION99.9
3.74-4.280.23811460.1933001X-RAY DIFFRACTION99.94
4.28-5.390.18971450.16753044X-RAY DIFFRACTION99.94
5.4-58.90.23261530.20363165X-RAY DIFFRACTION99.55

+
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://pdbjlvh1.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