[English] 日本語
Yorodumi
- PDB-3sn2: Crystal structure analysis of iron regulatory protein 1 in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sn2
TitleCrystal structure analysis of iron regulatory protein 1 in complex with transferrin receptor IRE B RNA
Components
  • Cytoplasmic aconitate hydratase
  • transferrin receptor iron regulatory element B RNA
KeywordsLYASE/RNA / RNA binding / iron sulfur cluster binding / phosphorylation / LYASE-RNA complex
Function / homology
Function and homology information


aconitate hydratase / aconitate hydratase activity / iron-responsive element binding / citrate metabolic process / response to iron(II) ion / tricarboxylic acid cycle / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
Aconitase/Iron-responsive element-binding protein 2 / Aconitase A, swivel domain / Aconitase; domain 3 / Aconitase, domain 3 / Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain / Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 / Aconitase family, 4Fe-4S cluster binding site / Aconitase, iron-sulfur domain / Aconitase family (aconitate hydratase) / Aconitase family signature 1. ...Aconitase/Iron-responsive element-binding protein 2 / Aconitase A, swivel domain / Aconitase; domain 3 / Aconitase, domain 3 / Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain / Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 / Aconitase family, 4Fe-4S cluster binding site / Aconitase, iron-sulfur domain / Aconitase family (aconitate hydratase) / Aconitase family signature 1. / Aconitase family signature 2. / Aconitase; domain 4 / Aconitase, domain 4 / Aconitase A/isopropylmalate dehydratase small subunit, swivel domain / Aconitase C-terminal domain / Aconitase/3-isopropylmalate dehydratase, swivel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Cytoplasmic aconitate hydratase
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsVolz, K. / Selezneva, A.I. / Walden, W.E.
Citation
Journal: Febs Lett. / Year: 2012
Title: Accommodating variety in iron-responsive elements: Crystal structure of transferrin receptor 1 B IRE bound to iron regulatory protein 1.
Authors: Walden, W.E. / Selezneva, A. / Volz, K.
#1: Journal: Science / Year: 2006
Title: Structure of dual function iron regulatory protein 1 complexed with ferritin IRE-RNA.
Authors: Walden, W.E. / Selezneva, A.I. / Dupuy, J. / Volbeda, A. / Fontecilla-Camps, J.C. / Theil, E.C. / Volz, K.
History
DepositionJun 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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 / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytoplasmic aconitate hydratase
B: transferrin receptor iron regulatory element B RNA


Theoretical massNumber of molelcules
Total (without water)110,0222
Polymers110,0222
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-16 kcal/mol
Surface area36200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.675, 101.675, 281.349
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Cytoplasmic aconitate hydratase / Iron regulatory protein 1 / IRP1 / Aconitase / Citrate hydro-lyase / Ferritin repressor protein / ...Iron regulatory protein 1 / IRP1 / Aconitase / Citrate hydro-lyase / Ferritin repressor protein / Iron-responsive element-binding protein 1 / IRE-BP 1


Mass: 100776.734 Da / Num. of mol.: 1 / Mutation: C437S/C503S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ACO1, FRP, IREB1, IREBP, IRP1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5465 / References: UniProt: Q01059, aconitate hydratase
#2: RNA chain transferrin receptor iron regulatory element B RNA


Mass: 9245.521 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS STATE THAT THE SEQUENCE PROVIDED FOR CHAINS A AND B IS CORRECT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.7 M sodium citrate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 6, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→32.7 Å / Num. all: 30782 / Num. obs: 30703 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 106.1 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.99-3.0972.190.55090.75312398199.4
3.097-3.2212.190.45531.04312327199.6
3.221-3.3682.180.35251.46712402199.6
3.368-3.5452.190.24862.39312433199.6
3.545-3.7672.160.18043.66212324199.7
3.767-4.0582.140.12955.81612162199.7
4.058-4.4672.140.08639.87512183199.6
4.467-5.1132.160.072813.58312168199.6
5.113-6.4422.130.068815.1912139199.5
6.442-32.72.020.039430.85311254197.2

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IPY

2ipy
PDB Unreleased entry


Resolution: 2.99→32.643 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 33.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2748 1993 6.5 %RANDOM
Rwork0.2272 ---
obs0.2303 30644 99.61 %-
all-30644 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 95.345 Å2 / ksol: 0.406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-17.5764 Å20 Å2-0 Å2
2--17.5764 Å20 Å2
3----35.1527 Å2
Refinement stepCycle: LAST / Resolution: 2.99→32.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6632 611 0 146 7389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057875
X-RAY DIFFRACTIONf_angle_d0.80110272
X-RAY DIFFRACTIONf_dihedral_angle_d14.9442868
X-RAY DIFFRACTIONf_chiral_restr0.0471171
X-RAY DIFFRACTIONf_plane_restr0.0041231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.06480.40771370.40061977X-RAY DIFFRACTION99
3.0648-3.14760.38581400.36981997X-RAY DIFFRACTION100
3.1476-3.24010.36631380.31741999X-RAY DIFFRACTION99
3.2401-3.34460.35041400.29592027X-RAY DIFFRACTION100
3.3446-3.4640.38621390.27051997X-RAY DIFFRACTION100
3.464-3.60250.36561400.24922033X-RAY DIFFRACTION100
3.6025-3.76620.26281420.22822038X-RAY DIFFRACTION100
3.7662-3.96450.26151410.21482014X-RAY DIFFRACTION100
3.9645-4.21240.25271430.19312055X-RAY DIFFRACTION100
4.2124-4.53680.25231430.18582044X-RAY DIFFRACTION100
4.5368-4.9920.23311430.17392050X-RAY DIFFRACTION100
4.992-5.7110.26061450.19142104X-RAY DIFFRACTION100
5.711-7.18260.25061480.21192114X-RAY DIFFRACTION100
7.1826-32.64520.23961540.21732202X-RAY DIFFRACTION98

+
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