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- PDB-5awg: Crystal structure of Hg-bound SufB-SufC-SufD complex from Escheri... -

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Basic information

Entry
Database: PDB / ID: 5awg
TitleCrystal structure of Hg-bound SufB-SufC-SufD complex from Escherichia coli
Components
  • FeS cluster assembly protein SufB
  • FeS cluster assembly protein SufD
  • Probable ATP-dependent transporter SufC
KeywordsTRANSPORT PROTEIN/PROTEIN BINDING / Iron-Sulfur Clusters / Iron-Sulfur Proteins / ABC proteins / ABC ATPase / TRANSPORT PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


iron-sulfur cluster assembly complex / iron-sulfur cluster assembly / response to radiation / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
SUF system FeS cluster assembly, SufB / SUF system FeS cluster assembly, SufBD, N-terminal / SufBD protein N-terminal region / SUF system FeS cluster assembly, SufD / SUF system FeS cluster assembly, SufBD / SUF system FeS cluster assembly, SufBD superfamily / SUF system FeS cluster assembly, SufBD / FeS cluster assembly SUF system, ATPase SufC / ABC transporter-like, conserved site / ABC transporters family signature. ...SUF system FeS cluster assembly, SufB / SUF system FeS cluster assembly, SufBD, N-terminal / SufBD protein N-terminal region / SUF system FeS cluster assembly, SufD / SUF system FeS cluster assembly, SufBD / SUF system FeS cluster assembly, SufBD superfamily / SUF system FeS cluster assembly, SufBD / FeS cluster assembly SUF system, ATPase SufC / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Probable ATP-dependent transporter SufC / FeS cluster assembly protein SufB / Iron-sulfur cluster assembly protein SufD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 4.278 Å
AuthorsHirabayashi, K. / Wada, K.
CitationJournal: J Biol Chem / Year: 2015
Title: Functional Dynamics Revealed by the Structure of the SufBCD Complex, a Novel ATP-binding Cassette (ABC) Protein That Serves as a Scaffold for Iron-Sulfur Cluster Biogenesis.
Authors: Kei Hirabayashi / Eiki Yuda / Naoyuki Tanaka / Sumie Katayama / Kenji Iwasaki / Takashi Matsumoto / Genji Kurisu / F Wayne Outten / Keiichi Fukuyama / Yasuhiro Takahashi / Kei Wada /
Abstract: ATP-binding cassette (ABC)-type ATPases are chemomechanical engines involved in diverse biological pathways. Recent genomic information reveals that ABC ATPase domains/subunits act not only in ABC ...ATP-binding cassette (ABC)-type ATPases are chemomechanical engines involved in diverse biological pathways. Recent genomic information reveals that ABC ATPase domains/subunits act not only in ABC transporters and structural maintenance of chromosome proteins, but also in iron-sulfur (Fe-S) cluster biogenesis. A novel type of ABC protein, the SufBCD complex, functions in the biosynthesis of nascent Fe-S clusters in almost all Eubacteria and Archaea, as well as eukaryotic chloroplasts. In this study, we determined the first crystal structure of the Escherichia coli SufBCD complex, which exhibits the common architecture of ABC proteins: two ABC ATPase components (SufC) with function-specific components (SufB-SufD protomers). Biochemical and physiological analyses based on this structure provided critical insights into Fe-S cluster assembly and revealed a dynamic conformational change driven by ABC ATPase activity. We propose a molecular mechanism for the biogenesis of the Fe-S cluster in the SufBCD complex.
History
DepositionJul 3, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Aug 11, 2021Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FeS cluster assembly protein SufB
B: FeS cluster assembly protein SufD
C: Probable ATP-dependent transporter SufC
D: Probable ATP-dependent transporter SufC
E: FeS cluster assembly protein SufB
F: FeS cluster assembly protein SufD
G: Probable ATP-dependent transporter SufC
H: Probable ATP-dependent transporter SufC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,62512
Polymers313,8238
Non-polymers8024
Water0
1
A: FeS cluster assembly protein SufB
B: FeS cluster assembly protein SufD
C: Probable ATP-dependent transporter SufC
D: Probable ATP-dependent transporter SufC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,3136
Polymers156,9114
Non-polymers4012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-93 kcal/mol
Surface area52160 Å2
MethodPISA
2
E: FeS cluster assembly protein SufB
F: FeS cluster assembly protein SufD
G: Probable ATP-dependent transporter SufC
H: Probable ATP-dependent transporter SufC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,3136
Polymers156,9114
Non-polymers4012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-66 kcal/mol
Surface area51920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.848, 139.379, 124.414
Angle α, β, γ (deg.)90.00, 113.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FeS cluster assembly protein SufB


Mass: 54800.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: sufB, ynhE, b1683, JW5273 / Production host: Escherichia coli (E. coli) / References: UniProt: P77522
#2: Protein FeS cluster assembly protein SufD


Mass: 46884.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: sufD, ynhC, b1681, JW1671 / Production host: Escherichia coli (E. coli) / References: UniProt: P77689
#3: Protein
Probable ATP-dependent transporter SufC


Mass: 27613.332 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: sufC, ynhD, b1682, JW1672 / Production host: Escherichia coli (E. coli) / References: UniProt: P77499
#4: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.48 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: pentaerythritol propoxylate (5/4 PO/OH), sodium citrate, potassium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.95 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 28, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 4.278→50 Å / Num. obs: 50117 / % possible obs: 99.3 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 6.6
Reflection shellResolution: 4.3→4.45 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 5.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data scaling
PHENIXphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 4.278→43.942 Å / SU ML: 0.63 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 37.87 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.3404 2511 5.01 %Random selection
Rwork0.2948 ---
obs0.2973 50117 98.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.278→43.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18804 0 4 0 18808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00719142
X-RAY DIFFRACTIONf_angle_d1.67225886
X-RAY DIFFRACTIONf_dihedral_angle_d16.957047
X-RAY DIFFRACTIONf_chiral_restr0.072917
X-RAY DIFFRACTIONf_plane_restr0.0073395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2783-4.36050.37291210.32112422X-RAY DIFFRACTION91
4.3605-4.44940.42441630.31922689X-RAY DIFFRACTION100
4.4494-4.54610.42741280.29442665X-RAY DIFFRACTION100
4.5461-4.65170.32471380.27992686X-RAY DIFFRACTION100
4.6517-4.76790.33731610.27352675X-RAY DIFFRACTION100
4.7679-4.89670.35871250.29562637X-RAY DIFFRACTION100
4.8967-5.04060.35781410.29942710X-RAY DIFFRACTION100
5.0406-5.2030.41891470.3072703X-RAY DIFFRACTION100
5.203-5.38870.35571320.31582699X-RAY DIFFRACTION100
5.3887-5.6040.37151460.32122639X-RAY DIFFRACTION100
5.604-5.85850.43571320.31832705X-RAY DIFFRACTION100
5.8585-6.16660.36951400.32952667X-RAY DIFFRACTION100
6.1666-6.55180.37061500.35072674X-RAY DIFFRACTION99
6.5518-7.05570.38261440.33312685X-RAY DIFFRACTION99
7.0557-7.76230.34161340.32192623X-RAY DIFFRACTION98
7.7623-8.87740.30911380.27792648X-RAY DIFFRACTION98
8.8774-11.15430.25241390.22672564X-RAY DIFFRACTION96
11.1543-43.9440.2461320.27112515X-RAY DIFFRACTION94

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