[English] 日本語
Yorodumi
- PDB-7rzz: Crystal structure of FBF-2 in complex with LST-1 site A peptide a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rzz
TitleCrystal structure of FBF-2 in complex with LST-1 site A peptide and compact FBE RNA
Components
  • Fem-3 mRNA-binding factor 2
  • Lateral Signaling Target
  • RNA
KeywordsRNA BINDING PROTEIN / Pumilio RNA-binding proteins
Function / homology
Function and homology information


sex differentiation / P granule / post-transcriptional regulation of gene expression / G-protein alpha-subunit binding / mRNA 3'-UTR binding / regulation of gene expression / cell differentiation / negative regulation of translation / nucleus / cytoplasm
Similarity search - Function
Pumilio, RNA binding domain / Pumilio homology domain / Pumilio homology domain (PUM-HD) profile. / Pumilio-family RNA binding repeat / Pumilio RNA-binding repeat profile. / Pumilio RNA-binding repeat / Pumilio-like repeats / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
RNA / Lateral Signaling Target / Fem-3 mRNA-binding factor 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsQiu, C. / Hall, T.M.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Bipartite interaction sites differentially modulate RNA-binding affinity of a protein complex essential for germline stem cell self-renewal.
Authors: Qiu, C. / Wine, R.N. / Campbell, Z.T. / Hall, T.M.T.
History
DepositionAug 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 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
A: Fem-3 mRNA-binding factor 2
B: RNA
C: Lateral Signaling Target


Theoretical massNumber of molelcules
Total (without water)53,8713
Polymers53,8713
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-6 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.169, 93.169, 111.278
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

-
Components

#1: Protein Fem-3 mRNA-binding factor 2


Mass: 47019.055 Da / Num. of mol.: 1 / Fragment: UNP residues 164-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: fbf-2, F21H12.5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09312
#2: RNA chain RNA


Mass: 2872.750 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Caenorhabditis elegans (invertebrata)
#3: Protein/peptide Lateral Signaling Target


Mass: 3979.517 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: lst-1, CELE_T22A3.3, T22A3.3 / Production host: Escherichia coli (E. coli) / References: UniProt: P91820
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30% (v/v) PEG 400, 0.1 M CHES, pH 9.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→35.7 Å / Num. obs: 26102 / % possible obs: 99.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 42.65 Å2 / Rpim(I) all: 0.031 / Net I/σ(I): 14.5
Reflection shellResolution: 2.39→2.48 Å / Num. unique obs: 2118 / Rpim(I) all: 0.186 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.19.2-4158refinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3k5q

3k5q


Resolution: 2.39→35.7 Å / SU ML: 0.2743 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.4784
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2151 1991 9.21 %
Rwork0.171 19632 -
obs0.1751 21623 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.93 Å2
Refinement stepCycle: LAST / Resolution: 2.39→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3266 171 0 95 3532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213519
X-RAY DIFFRACTIONf_angle_d0.44634782
X-RAY DIFFRACTIONf_chiral_restr0.033557
X-RAY DIFFRACTIONf_plane_restr0.0038581
X-RAY DIFFRACTIONf_dihedral_angle_d8.4225539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.450.26371340.23041364X-RAY DIFFRACTION99.07
2.45-2.510.30681450.21891402X-RAY DIFFRACTION99.42
2.51-2.590.27321420.19841414X-RAY DIFFRACTION99.62
2.59-2.670.25231450.20651361X-RAY DIFFRACTION99.67
2.67-2.770.26121500.19961418X-RAY DIFFRACTION99.81
2.77-2.880.26381430.20391391X-RAY DIFFRACTION99.87
2.88-3.010.25691440.20631430X-RAY DIFFRACTION99.49
3.01-3.170.2231420.19161388X-RAY DIFFRACTION99.54
3.17-3.370.25931450.18561403X-RAY DIFFRACTION99.49
3.37-3.630.23771440.17411393X-RAY DIFFRACTION99.55
3.63-3.990.19531360.15521401X-RAY DIFFRACTION99.29
3.99-4.560.16441360.1411416X-RAY DIFFRACTION99.42
4.57-5.740.18711410.15281412X-RAY DIFFRACTION99.11
5.75-35.720.17651440.15031439X-RAY DIFFRACTION99.56
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)
12.95818630386-1.62519842941-2.249155732623.802727133833.87432736037.13913028150.1232625354470.165553070254-0.0810606567157-0.087695556119-0.0352283108631-0.1232757255740.0331430498270.0980036218996-0.09141001361360.244693019810.0542163308309-0.00534533419240.3024360583730.005328434495510.368037574234-21.8803068662-17.3906133288-8.25083208411
20.253211937137-1.51231157224-0.1618931404453.903619423921.06474529840.467319194879-0.092456230186-0.1081701314940.02321876098050.1004758128540.198178196134-0.0123701253963-0.006844588455860.0195632235139-0.1075313555470.364584101222-0.01627520526010.05974290075880.321523224158-0.006632941591680.339113255209-45.12054778589.8990464571419.4695999588
38.96857946674-7.81569634142-5.385080962227.994653331555.762218138475.8559812956-0.114206368763-0.3834947496360.300586659970.6153659364830.0696676103454-0.6233954446370.3880336039480.3938208650060.03032972693360.565794844429-0.0560584168120.1934335649660.373766869326-0.05384490685010.404619515392-34.775464174612.03891140834.1247726283
49.220630416646.13340013414-6.119340574289.78524950405-5.478486478424.41771375918-0.2233323153530.458353059446-0.504196443863-0.234529572052-0.0786556046282-0.4475735736920.753097316808-0.01392945569740.5917303445040.5015857693180.0381323466361-0.0621239560010.58522519893-0.0304958237440.434741509387-38.229260270123.881659655728.7708249999
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 168 through 323 )AA168 - 3231 - 151
22chain 'A' and (resid 324 through 568 )AA324 - 566152 - 394
33chain 'B' and (resid 1 through 9 )BB1 - 9
44chain 'C' and (resid 27 through 41 )CC27 - 411 - 15

+
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