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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Recent Entries
(Show all)CryoEM structure of A/Shanghai/1/2013 H7 in complex with polyclonal Fab from mice immunized with H7 stem nanoparticles-15 days post-immunization
Cryo-EM map of the nucleosome region of Rpd3S-nucleosome complex in State 3
Cryo-EM map of the nucleosome region of Rpd3S-nucleosome complex in State 2
Locally refined SARS-CoV-2 BA-2.86 Spike receptor binding domain (RBD) complexed with angiotensin converting enzyme 2 (ACE2)
PHF filament generated from 4E-Tau(297-407) under neutral Mg2+ condition
CryoEM structure of A/Michigan/45/2015 H1 in complex with flu HA central stem VH1-18 antibody 09-1B12
Cryo-EM structure of human invariant chain in complex with HLA-DR15
nhTMEM16 A444P mutant in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (long TM6/short TM6)
TRPV1 in nanodisc bound with 2 LPA molecules in neighboring monomers
Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with broadly neutralizing llama nanobody R27 targeting the CD4-binding site
nhTMEM16 lipid scramblase in lipid nanodiscs with MSP1E3 scaffold protein in the absence of Ca2+
CryoEM structure of A/Michigan/45/2015 H1 in complex with flu HA central stem VH1-18 antibody UCA6_N55T
TRPV1 in nanodisc bound with two LPA molecules in opposite monomers
T cell receptor delta 2 gamma 9 with TCRD TM domain chimera of TRAC
Cryo-EM map of the Rpd3S region of Rpd3S-nucleosome complex in State 3
Structure of avian H5N1 influenza A polymerase in complex with human ANP32B.
T cell receptor delta 2 gamma 9 with F283A, F290A, and F291A (DeepEMhancer)
TRPV1 in nanodisc bound with empty vanilloid binding pocket at 25C
Cryo-EM map of the human CTF18-RFC-PCNA binary complex in the four-subunit binding state (state 3)
nhTMEM16 lipid scramblase in lipid nanodiscs with MSP2N2 scaffold protein in the presence of Ca2+ (open state)
Cryo-EM map of the Rpd3S region of Rpd3S-nucleosome complex in State1
Cryo-EM structure of TRPM2 chanzyme in the presence of EDTA (apo state)
CryoEM structure of A/Shanghai/1/2013 H7 in complex with polyclonal Fab from mice immunized with H7 stem nanoparticles-28 days post immunization
Structural insights into cellular control of the human CPEB3 prion, functionally regulated by a labile-amyloid-forming segment
CRYO-EM CONSENSUS MAP OF LEISHMANIA MAJOR 80S RIBOSOME : PARENTAL STRAIN
Structure of human oligosaccharyltransferase OST-A complex bound to NGI-1
Cryo-EM map of the human CTF18-RFC-PCNA-DNA ternary complex with cracked and closed PCNA (state 7)
TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 2 (monomer)
Cryo-EM map of the human CTF18-RFC alone in the apo state (State 1)
nhTMEM16 lipid scramblase in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (closed state)
nhTMEM16 A444P mutant in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (bent TM6)
Cryo-EM structure of the DNA polymerase holoenzyme E9-A20-D4 of vaccinia virus
nhTMEM16 lipid scramblase in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (closed state) (consensus map)
nhTMEM16 R432A mutant in lipid nanodiscs with MSP2N2 scaffold protein in the presence of Ca2+
Influence of lipid bilayer on structure of acetylcholine receptor
Cryo-EM map of the human CTF18-RFC-PCNA-DNA ternary complex in the five-subunit binding state (state 4)
Influence of lipid bilayer on structure of acetylcholine receptor
CryoEM structure of A/Perth/16/2009 H3 in complex with polyclonal Fab from mice immunized with H3 stem nanoparticles-15 days post immunization
Influence of lipid bilayer on structure of acetylcholine receptor
Langya henipavirus postfusion fusion protein in complex with 4G5 Fab (global refinement)
SARS-CoV-2 Omicron BA.1 spike protein in complex with a self-assembling trivalent nanobody Tr67
Cryo-EM structure of TRPM2 chanzyme in the presence of Magnesium, Adenosine monophosphate, and Ribose-5-phosphate
CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : PARENTAL STRAIN
CryoEM structure of A/Perth/16/2009 H3 in complex with flu HA central stem VH1-18 antibody UCA6
Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with broadly neutralizing bi-specific antibody CAP256L-R27 targeting the CD4-binding site and the V2-apex
nhTMEM16 lipid scramblase in lipid nanodiscs with MSP2N2 scaffold protein in the presence of Ca2+ (intermediate state)
Cryo-EM co-structure of AcrB with the CU232 efflux pump inhibitor
Cryo-EM map of the human CTF18-RFC-PCNA-DNA ternary complex with narrow PCNA opening state II (state 6)
Influence of lipid bilayer on structure of acetylcholine receptor
Influence of lipid bilayer on structure of acetylcholine receptor
TRPV1 in Nanodisc bound with lysophosphatidic acid in all four monomers
1.4A Tobacco Mosaic Virus (CryoSPARC processing from Falcon 4 data)
Structure of avian H5N1 influenza A polymerase dimer in complex with human ANP32B (Encapsidase focused).
Cryo-EM map of the human CTF18-RFC-PCNA binary complex in the three-subunit binding state (state 2)
Monkeypox virus DNA replication holoenzyme F8, A22 and E4 in complex with a DNA duplex and cidofovir diphosphate
Cryo-EM structure of TRPM2 chanzyme in the presence of EDTA and ADP-ribose
Structure of avian H5N1 influenza A polymerase dimer in complex with human ANP32B (Consensus map)
nhTMEM16 A444P mutant in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (long TM6)
nhTMEM16 lipid scramblase in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (open state)
Cryo-EM structure of TRPM2 chanzyme in the presence of Calcium and ADP-ribose
Influence of lipid bilayer on structure of acetylcholine receptor
Influence of lipid bilayer on structure of acetylcholine receptor
nhTMEM16 lipid scramblase in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (closed state)(local refined monomer map)
T cell receptor delta 2 gamma 9 with TCRD TM domain chimera of TRAC (DeepEMhancer)
Cryo-EM map of the Rpd3S region of Rpd3S-Nulceosome complex in State 2
Influence of lipid bilayer on structure of acetylcholine receptor
Cryo-EM structure of Myxococcus xanthus EncA encapsulin shell loaded with EncD cargo
Cryo-EM map of the nucleosome region of Rpd3S-nucleosome complex in State 1
Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with broadly neutralizing llama nanobody G36 targeting the CD4-binding site
Structure of avian H5N1 influenza A polymerase dimer in complex with human ANP32B.
nhTMEM16 A444P mutant in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (short TM6)
Langya henipavirus postfusion F protein in complex with 4G5 Fab, local refinement of the viral membrane proximal region
Cryo-EM map of the human CTF18-RFC-PCNA-DNA ternary complex with narrow PCNA opening state I (state 5)
Langya henipavirus postfusion F protein in complex with the 4G5 Fab, local refinement of the viral membrane distal region
Influence of lipid bilayer on structure of acetylcholine receptor
Influence of lipid bilayer on structure of acetylcholine receptor
Cryo-EM structure of human invariant chain in complex with HLA-DQ
TRPV1 in nanodisc bound with empty vanilloid binding pocket at 4C
TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 1 (monomer)
Influence of lipid bilayer on structure of acetylcholine receptor
Influence of lipid bilayer on structure of acetylcholine receptor
Subtomogram average of immature PhiKZ Major Capsid Protein from tubular arrays
Influence of lipid bilayer on structure of acetylcholine receptor
Monkeypox virus DNA replication holoenzyme F8, A22 and E4 in complex with a DNA duplex and dCTP
Influence of lipid bilayer on structure of acetylcholine receptor
CRYO-EM FOCUSED REFINEMENT MAP OF LEISHMANIA MAJOR 80S RIBOSOME : PARENTAL STRAIN
MD65 N332-GT5 SOSIP in complex with RM_N332_08 Fab and RM20A3 Fab
Cryo-EM co-structure of AcrB with the EPM35 efflux pump inhibitor
Influence of lipid bilayer on structure of acetylcholine receptor
Structure of avian H5N1 influenza A polymerase dimer in complex with human ANP32B (Replicase focused).
CryoEM structure of A/Perth/16/2009 H3 in complex with polyclonal Fab from mice immunized with H3 stem nanoparticles-28 days post immunization
Cryo-EM co-structure of AcrB with the CU032 efflux pump inhibitor
Influence of lipid bilayer on structure of acetylcholine receptor