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- PDB-6ot9: Bimetallic dodecameric cage design 1 (BMC1) from cytochrome cb562 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ot9 | |||||||||||||||
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Title | Bimetallic dodecameric cage design 1 (BMC1) from cytochrome cb562 | |||||||||||||||
![]() | Soluble cytochrome b562 | |||||||||||||||
![]() | METAL BINDING PROTEIN / Supramolecular assembly / protein cage / bimetallic / metal binding | |||||||||||||||
Function / homology | ![]() electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Golub, E. / Esselborn, J. / Bailey, J.B. / Tezcan, F.A. | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Constructing protein polyhedra via orthogonal chemical interactions. Authors: Eyal Golub / Rohit H Subramanian / Julian Esselborn / Robert G Alberstein / Jake B Bailey / Jerika A Chiong / Xiaodong Yan / Timothy Booth / Timothy S Baker / F Akif Tezcan / ![]() Abstract: Many proteins exist naturally as symmetrical homooligomers or homopolymers. The emergent structural and functional properties of such protein assemblies have inspired extensive efforts in ...Many proteins exist naturally as symmetrical homooligomers or homopolymers. The emergent structural and functional properties of such protein assemblies have inspired extensive efforts in biomolecular design. As synthesized by ribosomes, proteins are inherently asymmetric. Thus, they must acquire multiple surface patches that selectively associate to generate the different symmetry elements needed to form higher-order architectures-a daunting task for protein design. Here we address this problem using an inorganic chemical approach, whereby multiple modes of protein-protein interactions and symmetry are simultaneously achieved by selective, 'one-pot' coordination of soft and hard metal ions. We show that a monomeric protein (protomer) appropriately modified with biologically inspired hydroxamate groups and zinc-binding motifs assembles through concurrent Fe and Zn coordination into discrete dodecameric and hexameric cages. Our cages closely resemble natural polyhedral protein architectures and are, to our knowledge, unique among designed systems in that they possess tightly packed shells devoid of large apertures. At the same time, they can assemble and disassemble in response to diverse stimuli, owing to their heterobimetallic construction on minimal interprotein-bonding footprints. With stoichiometries ranging from [2 Fe:9 Zn:6 protomers] to [8 Fe:21 Zn:12 protomers], these protein cages represent some of the compositionally most complex protein assemblies-or inorganic coordination complexes-obtained by design. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127 KB | Display | ![]() |
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PDB format | ![]() | 80.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ot4C ![]() 6ot7C ![]() 6ot8C ![]() 6ovhC ![]() 3m4bS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 4 molecules CDBA
#1: Protein | Mass: 11701.141 Da / Num. of mol.: 4 Mutation: E8H,A24T,Q25T,R34Q,L38Q,Q41W,K42S,K59S,H63C,D66W,I67E,V69I,D73N,D74A,K77H,N80K,E81Q,R98C,Y101C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Details (production host): pET20b for expression of BMC1 described here with background of pEC86 to provide machinery for c-type linkage of heme. Production host: ![]() ![]() |
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-Non-polymers , 5 types, 35 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/HAE.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HAE.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-HAE / #4: Chemical | ChemComp-HEC / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein solution: 2.1 mM protein, 1.05 mM Fe, 2 mM Zn added 1 hour prior to crystallisation. 1 ul + 1ul drops from protein solution and following mother liquor; 22.5% PEG400, 0.1 M HEPES pH 7.5, 0.2 M NaCl Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2018 Details: Mirror: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98008 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→39.92 Å / Num. obs: 38245 / % possible obs: 99.81 % / Redundancy: 10.29 % / Biso Wilson estimate: 51.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.061 / Rrim(I) all: 0.195 / Net I/σ(I): 8.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3M4B Resolution: 2.4→36.27 Å / SU ML: 0.3886 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.4761
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→36.27 Å
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Refine LS restraints |
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LS refinement shell |
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