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- PDB-3sn2: Crystal structure analysis of iron regulatory protein 1 in comple... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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.

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Experimental details

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Experiment

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

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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

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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

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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

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