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)Focused map used to visualize the endonuclease of Hantaan virus polymerase apo dimer
Cryo-EM structure of long form insulin receptor (IR-B) in the apo state
ELIC with Propylamine in spNW15 nanodiscs with 2:1:1 POPC:POPE:POPG
The rotavirus VP5*/VP8* conformational transition permeabilizes membranes to Ca2+ (class 6 reconstruction)
Structure of the E. coli clamp loader bound to the beta clamp in an Altered-Collar conformation
Cryo-Electron Tomography of a Cryo-Lamella Milled Inside a Mouse Brain Tissue Biopsy
SARS-CoV-2 S (C.37 Lambda variant) plus S309, S2L20, and S2X303 Fabs
Structure of the E. coli clamp loader bound to the beta clamp in an Initial-Binding conformation
SARS-CoV-2 S RBD (C.37 Lambda variant) plus S309 Fab, local refinement
Refined density map of gamma tubulin ring complex capped microtubule
A mechanistic understanding of protective influenza B neuraminidase mAbs at the airway interface
Atomic structure of wheat ribosome reveals unique features of the plant ribosomes
Backbone model of de novo-designed chlorophyll-binding nanocage O32-15
Structure of coxsackievirus B5 capsid (mutant CVB5F.cas.genogroupB) - F particle
E. coli SIR2-HerA complex (hexamer HerA bound with dodecamer Sir2)
Cryo-EM consensus map of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex
Cryo-EM structure of the ClpP degradation system in Streptomyces hawaiiensis
Structure of coxsackievirus B5 capsid (mutant CVB5F.cas.genogroupB) - E particle
A mechanistic understanding of protective influenza B neuraminidase mAbs at the airway interface
Cytoplasmic dynein-1 motor domain bound to dynactin-p150glued and LIS1
Atomic structure of wheat ribosome reveals unique features of the plant ribosomes
Atomic structure of wheat ribosome reveals unique features of the plant ribosomes
Structure of coxsackievirus B5 capsid (mutant CVB5F.cas.genogroupB) - A particle
Local map of B3SB3L in complex with two-RBD-up state I of soluble SARS-CoV-2 Spike trimer
ELIC5 with Propylamine in spNW15 nanodiscs with 2:1:1 POPC:POPE:POPG
Cryo-EM structure of short form insulin receptor (IR-A) with three IGF2 bound, asymmetric conformation.
Tobacco mosaic virus from scanning transmission electron microscopy at CSA=2.0 mrad
E. coli clamp loader with open clamp on primed template DNA (form 2)
Trehalose Synthase (TreS) of Mycobacterium tuberculosis in complex with 6-TreAz compound
The cryo-EM structure of the nonameric RAD51 ring bound to the nucleosome with the linker DNA binding
Cryo-EM structure of the ClpC1:ClpP1P2 degradation complex in Streptomyces hawaiiensis
Cryo-EM map focused on the external protomers and one internal protomer of Hantaan virus polymerase hexamer
Cryo-EM structure of short form insulin receptor (IR-A) with four IGF2 bound, symmetric conformation.
The cryo-EM structure of the RAD51 L1 and L2 loops bound to the linker DNA with the sticky end of the nucleosome
In situ structure of RNA-dependent RNA polymerase in full BAV particles
1918 H1N1 Viral polymerase heterotrimer in complex with 4 repeat serine-5 phosphorylated PolII peptide
Cytoplasmic dynein-A heavy chain bound to dynactin-p150glued and IC-LC tower
5'vRNA-bound Hantaan virus polymerase in monomeric intermediate state
The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without the linker DNA binding
A mechanistic understanding of protective influenza B neuraminidase mAbs at the airway interface
E. coli SIR2-HerA complex (dodecamer SIR2 bound 4 protomers of HerA)
SARS-CoV-2 S NTD (C.37 Lambda variant) plus S2L20 and S2X303 Fabs, local refinement
Atomic structure of wheat ribosome reveals unique features of the plant ribosomes
Tomogram of GBP1 coatomers assembled on brain polar lipid-derived small unilamellar vesicles.
The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with the linker DNA binding
Focused map of Pex region of Trypanosoma docking complex, (MDH)4-(Pex5)1-(Pex14)1
Cryo-EM structure of the ClpC1:ClpP1P2 degradation complex in Streptomyces hawaiiensis
Tomogram of GBP1 coatomers assembled on brain polar lipid-derived small unilamellar vesicles.
hOCT1 in complex with nb5660 in inward facing partially open 2 conformation
E. coli clamp loader with open clamp on primed template DNA (form 1)
Cryo-EM structure of long form insulin receptor (IR-B) with four IGF2 bound, symmetric conformation.
Cryo-EM structure of long form insulin receptor (IR-B) with three IGF2 bound, asymmetric conformation.
Structure of the E. coli clamp loader bound to the beta clamp in a Closed-DNA1 conformation
The cryo-EM structure of the RAD51 N-terminal lobe domain bound to the histone H4 tail of the nucleosome
hOCT1 in complex with nb5660 in inward facing partially open 1 conformation
Cryo-EM structure of ClpP1P2 in complex with ADEP1 from Streptomyces hawaiiensis
Symmetry expanded map of 2 gamma-tubulins bound to 2 alpha tubulins in gamma tubulin ring complex capped microtubule end.
The cryo-EM structure of the RAD51 L1 and L2 loops bound to the linker DNA with the blunt end of the nucleosome
Cryo-EM structure of H. thermophilus GroEL-GroES2 asymmetric football complex
autophagosome and autolysosomes are empty next to fibrillar polyQ
Cryo-EM structure of SARS-CoV-2 prototype spike protein receptor-binding domain in complex with hippopotamus ACE2
Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with hippopotamus ACE2
Cryo-EM structure of H. thermoluteolus GroEL-GroES2 football complex
Structure of the E. coli clamp loader bound to the beta clamp in a Closed-DNA2 conformation
Cryo-EM structure of the [Pyr1]-apelin-13-bound human APLNR-Gi complex
Focused map of Hantaan virus polymerase dimer used to refine the cap-binding domain
Structure of the E. coli clamp loader bound to the beta clamp in a Semi-Open conformation
Structure of the E. coli clamp loader bound to the beta clamp in a Open-RNAp/t conformation
Computationally Designed, Expandable O4 Octahedral Handshake Nanocage
Structure of the E. coli clamp loader bound to the beta clamp in a Fully-Open conformation
hOCT1 in complex with nb5660 in inward facing fully open conformation
The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding
The cryo-EM structure of the RAD51 filament bound to the nucleosome
hOCT1 in complex with spironolactone in inward facing occluded conformation
The cryo-EM structure of the RAD51 L2 loop bound to the linker DNA with the blunt end of the nucleosome
hOCT1 in complex with spironolactone in outward facing partially occluded conformation
Tomogram of GBP1 coatomers assembled on brain polar lipid-derived small unilamellar vesicles.
Structure of the gamma tubulin ring complex nucleated microtubule protofilament.
1918 H1N1 Viral polymerase heterotrimer in complex with 4 repeat serine-5 phosphorylated PolII peptide with ordered PB2 C-terminal domains
Cryo-Electron Tomography of a Cryo-Lamella cut inside a Mouse Kidney Tissue Biopsy
Chimeric cryo-EM map of Hantaan virus polymerase in hexameric state
Structure of the E. coli clamp loader bound to the beta clamp in a Open-DNAp/t conformation
The rotavirus VP5*/VP8* conformational transition permeabilizes membranes to Ca2+ (class 5 reconstruction)