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)Non-catalytic site depleted and epsilon C-terminal domain deleted FoF1-ATPase from Bacillus PS3,state2,nucleotide depleted condition
CryoEM structure of the symmetric Pho90 dimer from yeast without substrates.
Refinement Focused on the 3rd Body of a 1033 Scaffold-Based DNA Origami Nanostructure V4 with TBA
Non-catalytic site depleted and epsilon C-terminal domain deleted FoF1-ATPase from Bacillus PS3,state3,under ATP saturated condition
transcription complex paused at ops site and bound to autoinhibited RfaH, not fully complementary scaffold
Cryo-EM structure of the light-driven sodium pump ErNaR in the pentameric form at pH 8.0
Structure of the native y-Tubulin Ring Complex (yTuRC) capping microtubule minus ends at the spindle pole body
70S ribosome with A, P and E-site tRNAs in chloramphenicol-treated Mycoplasma pneumoniae cells, K3 data
Herpes simplex virus 1 nuclear egress complex (WT) determined in situ from perinuclear vesicles
Hemagglutinin-neuraminidase from Human parainfluenza virus type 3: complex with rPIV3-23 and rPIV3-28 Fabs
E. coli transcription complex paused at ops site with fully recruited RfaH
Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assembled in peptidiscs
E. coli RNA polymerase paused at ops site (non-complementary scaffold)
Cryo-EM structure of Pyrococcus furiosus apo form RNA polymerase contracted clamp conformation with Spt4/5
Structure of the y-Tubulin Small Complex (yTuSC) as part of the native y-Tubulin Ring Complex (yTuRC) capping microtubule minus ends at the spindle pole body
Non-catalytic site depleted and epsilon C-terminal domain deleted FoF1-ATPase from Bacillus PS3,state1,nucleotide depleted condition
Structure of a 1033 Scaffold Base DNA Origami Nanostructure V4 with Desalted Purified Staples
Structure of apo form of human gamma-secretase PSEN1 APH-1B isoform reconstituted into lipid nanodisc
70S ribosome with A* and P/E-site tRNAs in chloramphenicol-treated Mycoplasma pneumoniae cells, K3 data
Human Amylin1 Receptor in Complex with Gs and human Calcitonin Gene-Related Peptide
in situ subtomogram average of C. elegans microtubules in mitotic centrosomes
fully recruited RfaH bound to E. coli transcription complex paused at ops site (alternative state of RfaH)
CRISPR-Cas type III-D effector complex bound to a target RNA consensus map
Refinement Focused on the 1st Body of a 1033 Scaffold-Based DNA Origami Nanostructure V4 with TBA
Cryo-EM structure of the human parainfluenza virus hPIV3 L-P polymerase in dimeric form
Cryo-EM structure of the light-driven sodium pump ErNaR in the pentameric form at pH 4.3
Human 3-methylcrotonyl-CoA carboxylase in BCCP-CTS state with substrate
Consensus map: CW Flagellar Switch Complex - FliF, FliG, FliM, and FliN forming the C-ring from Salmonella
Cryo-EM structure of human high-voltage activated L-type calcium channel CaV1.2 (apo)
CRISPR-Cas type III-D effector complex bound to self-target RNA in a post-cleavage state
Influenza virus neuraminidase N1 NC13 ectodomain with a tetrabrachio-domain stalk
Low-dose cryo-electron ptychographic reconstruction of TMV recorded with CSA of 6.1 mrad
Cryo-EM structure of synthetic claudin-4 complex with Clostridium perfringens enterotoxin C-terminal domain, sFab COP-2, and Nanobody
Human parainfluenza virus type 3 prefusion F trimer in complex with rPIV3-18 Fab
Cryo-EM structure of human high-voltage activated L-type calcium channel CaV1.2 in complex with benidipine (BEN)
Structure of a 1033 Scaffold Base DNA Origami Nanostructure V4 with HPLC Purified Staples
Structure of the SFTSV L protein in a transcription-priming state with bound capped RNA [TRANSCRIPTION-PRIMING]
in-situ subtomogram average of C. elegans centrioles in centrosomes
Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP45 Class B
polysome/di-ribosome class I in chloramphenicol-treated Mycoplasma pneumoniae cells
Structure of human gamma-secretase PSEN1 APH-1B isoform reconstituted into lipid nanodisc in complex with Ab46
Cryo-EM structure of pre-subcore from in vitro assembled particles
70S ribosome with A and P-site tRNAs in chloramphenicol-treated Mycoplasma pneumoniae cells, K3 data
Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP63 Class C
CryoEM map of a de novo designed T=4 icosahedral nanocage hierarchically built from pseudosymmetric trimers; design Ico(T=4)-4
CRISPR-Cas type III-D effector complex bound to a target RNA local refinement map
Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP63 Class E1
backtracked E. coli transcription complex paused at ops site and bound to RfaH
in situ subtomogram average of C. elegans gamma-tubulin ring complexes in mitotic centrosomes
SARS-CoV-2 Omicron BQ.1.1 Variant Spike Protein Complexed with MO11 Fab
Cryo-EM structure of Pyrococcus furiosus apo form RNA polymerase open clamp conformation
CryoEM structure of the asymmetric Pho90 dimer from yeast without substrates.
Structure of the SFTSV L protein stalled in a transcription-specific early elongation state with bound capped RNA [TRANSCRIPTION-EARLY-ELONGATION]
Non-catalytic site depleted and epsilon C-terminal domain deleted FoF1-ATPase from Bacillus PS3,state3,nucleotide depleted condition
fully recruited RfaH bound to E. coli transcription complex paused at ops site (not fully complementary scaffold; alternative state of RfaH)
Non-catalytic site depleted and epsilon C-terminal domain deleted FoF1-ATPase from Bacillus PS3,state1,under ATP saturated condition
70S ribosome with a, P and E-site tRNAs in chloramphenicol-treated Mycoplasma pneumoniae cells, K3 data
Herpes simplex virus 1 capsid (WT) vertices in perinuclear NEC-coated vesicles determined in situ
Structure of the SFTSV L protein in a transcription-priming state without capped RNA [TRANSCRIPTION-PRIMING (in vitro)]
CRISPR-Cas type III-D effector complex bound to a self-target RNA in the pre-cleavage state
Cryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructure V4 and TBA
CryoEM structure of the symmetric Pho90 dimer from yeast with substrates.
E. coli transcription complex paused at ops site and bound to RfaH and NusA
Cryo-EM structure of Pyrococcus furiosus apo form RNA polymerase contracted clamp conformation
70S ribosome with a and P-site tRNAs in chloramphenicol-treated Mycoplasma pneumoniae cells, K3 data
Refinement Focused on the 2nd Body of a 1033 Scaffold-Based DNA Origami Nanostructure V4 with TBA
Structure of the native microtubule lattice nucleated from the yeast spindle pole body
Cryo-EM structure of Pyrococcus furiosus transcription elongation complex bound to Spt4/5
Cryo-EM structure of the human parainfluenza virus hPIV3 L-P polymerase in monomeric form
Non-catalytic site depleted and epsilon C-terminal domain deleted FoF1-ATPase from Bacillus PS3,state2,under ATP saturated condition
Cryo-EM structure of human high-voltage activated L-type calcium channel CaV1.2 in complex with tetrandrine (TET)
autoinhibited RfaH bound to E. coli transcription complex paused at ops site (encounter complex)
70S ribosome with EF-Tu-tRNA and P-site tRNA in chloramphenicol-treated Mycoplasma pneumoniae cells, K3 data
Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP45 Class C1
70S ribosome with EF-Tu-tRNA, P and E-site tRNAs in chloramphenicol-treated Mycoplasma pneumoniae cells, K3 data
fully recruited RfaH bound to E. coli transcription complex paused at ops site (not complementary scaffold)