The PDBeShape website has been retired
You have followed an old link to the website of PDBeShape, but both the project and the website no longer exist. PDBeShape was a project funded by the EU's BioMedBridges project which aimed to build data bridges from biology to medicine. PDBeShape was a collaboration between the Elixir and Instruct research infrastructures, carried out jointly by EMBL-EBI and STFC.
The description on the now defunct website of what PDBeShape was and aimed to enable said:
"PDBeShape contains structural biology volume data obtained from electron microscopy, subtomogram averaging, crystallography, and potentially other techniques. Structural alignments between the volumes have been pre-calculated, and these can be searched in PDBeShape to find volumes with similar morphology. Differences between otherwise similar volumes are highlighted, and may reveal conformational changes or location of additional components. This first release contains high quality volume data for prokaryotic and eukaryotic ribosomes, and class I and II chaperonins, taken from EMDB and PDB. In later releases, we will include a wider range of volumes. To get started, enter the EMDB or PDB code of a volume of interest in the search box. Alternatively, you can use EMsearch or EMbrowse to look for suitable examples. After displaying an initial selection of results, you will be able to investigate further, looking for other matches, or varying search/scoring parameters."
Basically, the idea was to provide shape-based searches of EMDB and PDB, for instance to try and identify unidentified objects in a cryo-EM map or tomogram. Unfortunately, the technology was not there yet at the time of the project but the problem it hoped to address is still a highly relevant one!
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(Show all)MicroED structure of bovine liver catalase with missing cone solved by suspended drop
Asymmetric unit of the PARIS Immune Complex at 3.2 Angstrom Resolution
Mycobacteriophage Bxb1 portal and connector assembly - C3 consensus refinement
Soluble ectodomain of human cytomegalovirus (HCMV) glycoprotein B (gB) stabilized in a prefusion-like conformation in complex with 1G2 and 7H3, composite map (global and local) and model
Mycobacteriophage Bxb1 tail tube segment - Core C1 local refinement
Structure of HIV-1 CH119 SOSIP.664 trimer in complex with CD4 molecules
Respiratory complex CI:CIII2, type II, Wild type mouse under cold temperature
Respiratory complex Peripheral Arm of CI, focus-refined map of type II, Wild type mouse under cold temperature
Respiratory complex Membrane domain of CI, focused map of type I, Wild type mouse under thermoneutral temperature
Respiratory complex Peripheral Arm of CI, focus-refined map of type IA, Wild type mouse under cold temperature
Respiratory complex Peripheral Arm of CI, focus-refined map of type IB, Wild type mouse under cold temperature
Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, bound to collagen alpha-1(I) chain
Cryo-EM structure of the tethered agonist-bound human PAR1-Gq complex
Respiratory complex Membrane domain of CI, focus-refined of type IB, Wild type mouse under cold temperature
Cryo-EM structure of the retatrutide-bound human GLP-1R-Gs complex
Respiratory complex Membrane domain of CI, focus-refined of type I, PERK -/- mouse under cold temperature
Cryo-EM structure of ATP-bound human very long-chain fatty acid ABC transporter ABCD3
Respiratory complex CIII2, focus-refined of type IB, Wild type mouse under cold temperature
Respiratory complex CI:CIII2, type I, PERK -/- mouse under cold temperature
Human collagen prolyl processing enzyme complex, P3H1/CRTAP heterodimer
Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, in its dual-ternary state
Structure of Nipah virus Bangladesh string G protein ectodomain tetramer bound to single-domain antibody n425 at 5.87 Angstroms overall resolution
Respiratory complex CIII2, focus-refined of type I, Wild type mouse under thermoneutral temperature
Cryo-EM structure of Hepatitis B virus surface antigen subviral particle with D2 symmetry
Respiratory complex CI:CIII2, type I, Wild type mouse under thermoneutral temperature
Respiratory complex Membrane domain of CI, focus-refined of type II, Wild type mouse under cold temperature
Localized reconstruction of Hepatitis B virus surface antigen dimer in the subviral particle with D2 symmetry from dataset A0
The structure of Candida albicans Cdr1 in milbemycin oxime-inhibited state
Cryo-EM structure of the tethered agonist-bound human PAR1-Gi complex
Cryo-EM structure of Phytanoyl-CoA-bound human very long-chain fatty acid ABC transporter ABCD3
Respiratory complex CIII2, focus-refined of type II, Wild type mouse under cold temperature
Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, in its apo state
Structure of Nipah virus Malaysia string G protein ectodomain monomer bound to single-domain antibody n425 at 3.63 Angstroms overall resolution
Cryo-EM structure of Hepatitis B virus surface antigen subviral particle (ellipsoidal shape with C1 symmetry)
Respiratory complex CIII2, focus-refined of type IA, Wild type mouse under cold temperature
Respiratory complex Membrane domain of CI, focus-refined of type IA, Wild type mouse under cold temperature
Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, bound to 2-oxoglutarate
Localized reconstruction of Hepatitis B virus surface antigen dimer in the subviral particle with D2 symmetry from dataset A
Respiratory complex CI:CIII2, type IA, Wild type mouse under cold temperature
Cryo-EM structure of Hepatitis B virus surface antigen subviral particle with D4 symmetry
Respiratory complex CIII2, focus-refined of type I, PERK -/- mouse under cold temperature
Respiratory complex Peripheral Arm of CI, focus-refined map of type I, Wild type mouse under thermoneutral temperature
Structure of Nipah virus Bangladesh string G protein ectodomain monomer bound to single-domain antibody n425 at 3.22 Angstroms overall resolution
Respiratory complex Peripheral Arm of CI, focus-refined map of type I, PERK -/- mouse under cold temperature
Respiratory complex CI:CIII2, type IB, Wild type mouse under cold temperature
Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, bound to cyclosporin A
Structural organization of the palisade layer in intracellular mature vaccinia virions
Cryo-EM structure of the ATP-bound Mtb DppABCD with the D445A mutation of DppA
Structural organization of the palisade layer in isolated vaccinia virus cores
Cryo-EM structure of a protein-free RNA at 2.17 angstrom resolution from Biortus
Cryo-EM structure of apo ABCC4 at 2.20 angstrom resolution from Biortus
Cryo-EM structure of Mycobacterium tuberculosis DppABCD in apo form
96-nm repeat of axonemal doublet microtubules from bovine sperm, RS2-RS3 bridge local refinement
96-nm repeat of axonemal doublet microtubules from bovine sperm, ODA-DC local refinement
96-nm repeat of axonemal doublet microtubules from bovine sperm, IDAe local refinement
96-nm repeat of axonemal doublet microtubules from bovine sperm, N-DRC baseplate local refinement
96-nm repeat of axonemal doublet microtubules from bovine sperm, ODA local refinement
96-nm repeat of axonemal doublet microtubules from bovine sperm, RS1 head local refinement
Integrative Structure of the human intron lariat Spliceosome (ILS'')
96-nm repeat of axonemal doublet microtubules from bovine sperm, RS1 base local refinement
Nucleosome portion of Chd1-bound SHN103, unsharpened focused refinement.
Cryo-EM structure of Dopamine 3 Receptor:Go complex bound to bitopic FOB02-04A - Conformation A
96-nm repeat of axonemal doublet microtubules from bovine sperm, RS2 base local refinement
96-nm repeat of axonemal doublet microtubules from bovine sperm, RS2 stalk local refinement
Hexasome portion of Chd1-bound SHN103, unsharpened focused refinement.
96-nm repeat of axonemal doublet microtubules from bovine sperm, IDAab local refinement
Cryo-EM structure of the heat-irreversible amyloid fibrils of human lysozyme
Original nucleosome portion of DN103, unsharpened focused refinement
Structure of Chd1 bound to a dinucleosome with a dyad-to-dyad distance of 103 bp.
Cryo-EM structure of Vipp1 helical filament with lattice 1 (Vipp1_L1)
96-nm repeat of axonemal doublet microtubules from bovine sperm, RS1 barrel local refinement
96-nm repeat of axonemal doublet microtubules from bovine sperm, N-DRC distal lobe local refinement
Unsharpened consensus map of hexasome-nucleosome complex SHN103 bound by Chd1
96-nm repeat of axonemal doublet microtubules from bovine sperm, RS2 head local refinement
Cryo-EM structure of Vipp1-deltaH6_aa1-219 helical filament with lattice 2 (Vipp1-deltaH6_L2)
Structure of a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp.
CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with GABA and puerarin
96-nm repeat of axonemal doublet microtubules from bovine sperm, RS1 stalk local refinement
96-nm repeat of axonemal doublet microtubules from bovine sperm, ARMH1 subcomplex local refinement
Cryo-EM structure of Dopamine 3 receptor:Go complex bound to bitopic FOB02-04A - Conformation B
Sub-tomogram averaging results of pentameric 5-HT3A receptor on cell-derived vesicles
Structure of Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp.
96-nm repeat of axonemal doublet microtubules from bovine sperm, IDAf IC/LC local refinement
96-nm repeat of axonemal doublet microtubules from bovine sperm, IDAf motors pre-state local refinement part 1
In situ structure of the peripheral stalk of the mitochondrial ATPsynthase in whole Polytomella cells
96-nm repeat of axonemal doublet microtubules from bovine sperm, RS3 head local refinement
Restored Chd1-bound nucleosome portion of DN103, unsharpened focused refinement
Structure of a mononucleosome bound by one copy of Chd1 with the DBD on the exit-side DNA.
Cryo-EM structure of the heat-irreversible amyloid fibrils of hen egg-white lysozyme
sub-tomogram averaging results of tetrameric 5-HT3A receptor on cell-derived vesicles
96-nm repeat of axonemal doublet microtubules from bovine sperm, IDAf motors pre-state local refinement part 2
96-nm repeat of axonemal doublet microtubules from bovine sperm, RS3 stalk local refinement
96-nm repeat of axonemal doublet microtubules from bovine sperm, RS3 base local refinement
96-nm repeat of axonemal doublet microtubules from bovine sperm, IDAc local refinement
Soluble ectodomain of human cytomegalovirus (HCMV) glycoprotein B (gB) stabilized in a prefusion-like conformation in complex with 1G2 and 7H3, global refinement
Subtomogram averaging of Bxb1 phage tail tube (emptied) during the infection state
I1 symmetry applied adeno-associated virus-9 with human Interleukin 3
70S initiation complex (tRNA-fMet M1, initiation factor 2 + CUG start codon)
Mycobacteriophage Bxb1 tail tube segment - C1 consensus refinement
The mTORC1 cholesterol sensor LYCHOS (GPR155) - auxin bound, open state
The mTORC1 cholesterol sensor LYCHOS (GPR155) - monomer with auxin
Cryo-EM structure of the Nipah Virus polymerase (L) protein in complex with the tetrameric phosphoprotein (P)
Subtomogram averaging of Bxb1 phage portal (emptied) during the infection state
Subtomogram averaging of Bxb1 phage capsid (DNA-filled) during the infection state
Mycobacteriophage Bxb1 portal and connector assembly - Head-to-tail stopper and tail terminator C6 local refinement
Myxococcus xanthus EncA encapsulin engineered pore mutant with T=1 icosahedral symmetry
Soluble ectodomain of human cytomegalovirus (HCMV) glycoprotein B (gB) in the postfusion conformation in complex with 1G2 and 7H3 Fabs
3-fold symmetry face of adeno-associated virus-9 and human Interleukin 3 complex
Mycobacteriophage Bxb1 tail tube segment - CTE domain C1 local refinement
Subtomogram averaging of Bxb1 phage capsid (emptied) during the infection state
Cargo-loaded Myxococcus xanthus EncA encapsulin engineered pore mutant with T=3 icosahedral symmetry
Mycobacteriophage Bxb1 C1 Capsid and Portal - Portal C1 local refinement
Subtomogram averaging of Bxb1 phage portal (DNA-filled) during the infection state
Structure of closed state SARS-Cov2 spike protein from EMPIAR-10453
Soluble ectodomain of human cytomegalovirus (HCMV) glycoprotein B (gB) stabilized in a prefusion-like conformation in complex with 1G2 and 7H3, local refinement
Subtomogram averaging of Bxb1 phage tail tube (DNA-filled) during the infection state
Mycobacteriophage Bxb1 portal and connector assembly - Portal and head-to-tail adaptor C12 local refinement
Mycobacteriophage Bxb1 portal and connector assembly - Tail tube C3 local refinement
The mTORC1 cholesterol sensor LYCHOS (GPR155) - auxin bound, closed state