[English] 日本語
Yorodumi
- PDB-6een: Crystal structure of a designer Pentatrico Peptide RNA binding pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6een
TitleCrystal structure of a designer Pentatrico Peptide RNA binding protein, bound to a complex RNA target and featuring an infinite superhelix and microheterogeneity.
Components
  • (Designer Pentatricopeptide Protein ...) x 4
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • RNA (5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')
  • RNA (5'-R(P*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsRNA BINDING PROTEIN/RNA / Complex / PPR / RNA / Helical disorder / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homologyRNA
Function and homology information
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsSchmidberger, J.W. / Bond, C.S.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: Crystal structure of a designer Pentatrico Peptide RNA binding protein, bound to a complex RNA target and featuring an infinite superhelix and microheterogeneity.
Authors: Schmidberger, J.W. / Bond, C.S.
History
DepositionAug 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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: Designer Pentatricopeptide Protein dPPR10
B: Designer Pentatricopeptide Protein dPPR10
C: Designer Pentatricopeptide Protein dPPR10
D: Designer Pentatricopeptide Protein dPPR10
F: RNA (5'-R(P*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')
G: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
H: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
I: RNA (5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)151,1118
Polymers151,1118
Non-polymers00
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry, The protein is observed to bind to the RNA target. The actual target is GUAUCCUUAACCAUUUC. It was built as superposed poly X chains with occupancies ...Evidence: isothermal titration calorimetry, The protein is observed to bind to the RNA target. The actual target is GUAUCCUUAACCAUUUC. It was built as superposed poly X chains with occupancies matching their frequency in the actual sequence mentioned above.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.347, 51.647, 51.972
Angle α, β, γ (deg.)118.120, 97.210, 96.000
Int Tables number1
Space group name H-MP1
Detailsthis protein:RNA dimer assembly is represented as an octameric assembly due to structural disorder/microheterogeneity resulting in the structure being refined as 4 protein chains (partially occupied) + 4 RNA chains (partially occupied)

-
Components

-
Designer Pentatricopeptide Protein ... , 4 types, 4 molecules ABCD

#1: Protein Designer Pentatricopeptide Protein dPPR10


Mass: 34936.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli)
#2: Protein Designer Pentatricopeptide Protein dPPR10


Mass: 35053.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli)
#3: Protein Designer Pentatricopeptide Protein dPPR10


Mass: 34927.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli)
#4: Protein Designer Pentatricopeptide Protein dPPR10


Mass: 34801.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli)

-
RNA chain , 4 types, 4 molecules FGHI

#5: RNA chain RNA (5'-R(P*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')


Mass: 3061.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Zea mays (maize)
#6: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 2710.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Zea mays (maize)
#7: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2917.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Zea mays (maize)
#8: RNA chain RNA (5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')


Mass: 2701.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Zea mays (maize)

-
Non-polymers , 1 types, 214 molecules

#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsThe structure features an infinite superhelix that has inherent helical disorder. This means we ...The structure features an infinite superhelix that has inherent helical disorder. This means we don't know where it begins and ends. This leads to map averaging at each position in the repeating helix. The highly redundant design of the protein means this averaging is not an issues except at positions 5 and 35 of each repeat that change to bind different bases in the target RNA. Also, the target RNA will average out. The solution to this was to build the structure as four superposed chains for the protein and four superposed chains for the RNA. Each case adding up to an occupancy of 1.
Sequence detailsProtein is designed based on a consensus sequence of many PPR proteins. Chains A to D are ...Protein is designed based on a consensus sequence of many PPR proteins. Chains A to D are repetitions of the same single chain with microheterogeneity at positions 5 and 35. The protein is observed to bind to the RNA target. The actual target sequence is GUAUCCUUAACCAUUUC. Because of infinite nature of superhelix, it was built as superposed poly X chains with occupancies matching their frequency in the actual sequence mentioned above.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Mg Acetate, 0.05 M MES pH 5.6, 20% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953737 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953737 Å / Relative weight: 1
ReflectionResolution: 2.01→44.92 Å / Num. obs: 25127 / % possible obs: 97 % / Redundancy: 2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.049 / Rrim(I) all: 0.074 / Net I/σ(I): 9 / Num. measured all: 50507
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.01-2.061.60.305288417870.7860.2770.4132.190.8
8.98-44.921.90.0365442850.9850.0340.04924.299.7

-
Processing

Software
NameVersionClassification
REFMACrefinement
Aimless0.5.31data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5i9f

5i9f


Resolution: 2.01→44.92 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2435 / WRfactor Rwork: 0.177 / FOM work R set: 0.8049 / SU B: 17.923 / SU ML: 0.477 / SU Rfree: 0.3423 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 1207 4.8 %RANDOM
Rwork0.1832 ---
obs0.1862 23919 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.79 Å2 / Biso mean: 32.183 Å2 / Biso min: 11.54 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å2-1.12 Å2-1.42 Å2
2---0.06 Å2-0.17 Å2
3----0.53 Å2
Refinement stepCycle: final / Resolution: 2.01→44.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9776 765 0 214 10755
Biso mean---35.37 -
Num. residues----1269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01410736
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710111
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.62914599
X-RAY DIFFRACTIONr_angle_other_deg1.2061.68823703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.9535.2341283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.55825.172435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.49151979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0191536
X-RAY DIFFRACTIONr_chiral_restr0.0780.21422
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211807
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021769
LS refinement shellResolution: 2.008→2.06 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 60 -
Rwork0.295 1719 -
all-1779 -
obs--90.58 %

+
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