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Basic information

Entry
Database: PDB / ID: 3snp
TitleCrystal structure analysis of iron regulatory protein 1 in complex with ferritin H IRE RNA
Components
  • Cytoplasmic aconitate hydratase
  • ferritin H IRE 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: 2.8 Å
AuthorsVolz, K. / Selezneva, A.I. / Walden, W.E.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and preliminary X-ray diffraction analysis of iron regulatory protein 1 in complex with ferritin IRE RNA.
Authors: Selezneva, A.I. / Cavigiolio, G. / Theil, E.C. / Walden, W.E. / Volz, K.
History
DepositionJun 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
SupersessionAug 3, 2011ID: 2IPY
Revision 1.1Aug 3, 2011Group: Advisory
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Cytoplasmic aconitate hydratase
C: ferritin H IRE RNA
D: ferritin H IRE RNA


Theoretical massNumber of molelcules
Total (without water)220,6914
Polymers220,6914
Non-polymers00
Water10,034557
1
A: Cytoplasmic aconitate hydratase
C: ferritin H IRE RNA


Theoretical massNumber of molelcules
Total (without water)110,3452
Polymers110,3452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-13 kcal/mol
Surface area36790 Å2
MethodPISA
2
B: Cytoplasmic aconitate hydratase
D: ferritin H IRE RNA


Theoretical massNumber of molelcules
Total (without water)110,3452
Polymers110,3452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-12 kcal/mol
Surface area36790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.555, 80.851, 142.873
Angle α, β, γ (deg.)90.00, 92.03, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2 / 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 ferritin H IRE RNA


Mass: 9568.674 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.06
Details: 220 mM ammonium phosphate monobasic, 50 mM sodium acetate, pH 5.06, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→99 Å / Num. all: 61046 / Num. obs: 61046 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 67.5 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 7.6
Reflection shellResolution: 2.8→2.91 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.359 / % possible all: 91.1

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2B3X AND 2B3Y

2b3x

2b3y


Resolution: 2.8→99 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3117 -RANDOM
Rwork0.198 ---
all0.199 61074 --
obs0.199 57957 91.1 %-
Displacement parametersBiso max: 8.51 Å2 / Biso mean: 54.3928 Å2 / Biso min: 126.12 Å2
Refinement stepCycle: LAST / Resolution: 2.8→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13314 1242 0 557 15113

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