Happy Holidays and New year from the EMDB! Please be advised that the EMDB team will be operating at reduced capacity between December 15th - January 12th. With this in mind we would ask that you be prepared for longer reply times through both our helpdesk system and the OneDep deposition system. well done on a productive 2025, wishing you all the best and we will see you in 2026!
Resources
EM validation services
• Fourier Shell Correlation (FSC) server
• Tilt-pair validation server
Test Data
2D picked particle sets
| Name | Description | Image size | Voxel size | Format |
|---|---|---|---|---|
| Birkbeck_GroEL_MDH_MODEL | 3 stacks of 2781 model images each with different SNR | 256x256 | 1.4Å | CCP4 |
| Birkbeck_GroEL_MDH_REAL | 2781 CTF-corrected GroEL-MDF images | 160x160 | 2.8Å | Spider |
| SPIDER_FRANK_data | 70S E. coli ribosome with (image 1-5000) and without (images 5001-10000) Elongation factor G (EF-G) provided by Haixiao Gao and J Frank. | 130x130 | 2.82Å | Spider |
PDBeShape
| Name | Description | Format | Size |
|---|---|---|---|
| PDBeShape test set | 200 entries of eukaryotic ribosomes, prokaryotic ribosomes, chaperonines, and viruses | Tar | 27 Gb |
Pairs of 3D volumes for testing FSC server
| Test case | Voxel size | Map 1 | Map 2 | Result |
|---|---|---|---|---|
| GroEL dataset publicly available (Stagg et al., J. Struct. Biol. 163:29-39, 2008) |
1.63 Å | 14 MB (MRC format) download | 14 MB (MRC format) download | View FSC plot |
Datasets for testing Tilt-pair validation server
| Parameter | Icosahedral Bacillus stearothermophilus pyruvate dehydrogenase E2 core, 1.5 MDa, Rosenthal and Henderson, 2003 | Chicken anemia virus (CAV), 2.7 MDa, Crowther et al., 2003 | ß-galactosidase, 450 kDa, Chen et al., 2013 |
|---|---|---|---|
| Map | e2map.mrc | cav_3d.mrc | Bgal_3d.mrc |
| Untilted stack | stack1.mrc | cav6216_stk.mrc | Bgal_untilt_stk.mrc |
| Parameters | stack1.par | cav6216.par | Bgal_untilt.par |
| Parameter file type | Frealign | Frealign | Frealign |
| Tilted stack | stack2.mrc | cav6217_stk.mrc | Bgal_tilt_stk.mrc |
| Voxel size | 4.98 Å | 3.62 Å | 2.98 Å |
| Mask radius | 20 pixels | 24 pixels | 30 pixels |
| Tilt range | (-20°, 20°) | (-30°, 30°) | (-20°, 20°) |
| Resolution range | (100 Å, 15 Å) | (100 Å, 25 Å) | (150 Å, 35 Å) |
| Voltage | 300 | 300 | 80 |
| Defocus | 59000 | 29000 | 31500 |
| Spherical aberration | 2 mm | 2 mm | 2 mm |
| Amplitude contrast | 0.07 | 0 | 0 |
| Results | View | View | View |
Quick links
Recent Entries
(Show all)
The structure of the complex formed by two FIPV-II S proteins and two cat APN proteins.
Immune complex of P5-1C8 Fab binding the RBD of Omicron BA.1 6p spike protein (2 Fab)
Cryo-EM structure of SARS-CoV-2 WT 6p spike protein in complex with P5-1C8 IgG (1.5 IgG)
Immune complex of P5-1C8 Fab binding the RBD of Omicron BA.1 6p spike protein (1 Fab)
Immune complex of P5-1C8 IgG binding the RBD of SARS-CoV-2 WT 6p spike protein
Structure of the MOR/Gi/Mitragynine Pseudoindoxil Complex, GTP-bound G-ACT-3
Structure of the MOR/Gi/Mitragynine Pseudoindoxil Complex, GTP-bound G-Primed, AHD 3DVA Sorted
Structure of the MOR/Gi/Mitragynine Pseudoindoxil Complex, GTP-bound G-ACT-2
CRISPR-associated deaminase Cad1 in cA4 bound form, symmetry expanded dimer, CARF domain focus refined map
CRISPR-associated deaminase Cad1 in cA4 bound form, symmetry expanded dimer, deaminase domain focus refined map
CRISPR-associated deaminase Cad1 in cA4 bound form, symmetry expanded dimer, refined against a composite map
CRISPR-associated deaminase Cad1 in cA4 bound form, symmetry expanded dimer, consensus map
Structures and mechanism of the nicotinamide nucleotide transhydrogenase from E. coli
positive allosteric modulator(BMS986187)-bound delta-opioid receptor-Gi complex
Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk
5-fold pentamer reconstruction of SFTSV virus complexed with hA5-6 (W30B/W53) Fab
2-fold hexamer reconstruction of SFTSV virus complexed with hA5-6 (W30B/W53) Fab
Cryo-EM structure of the human A2A adenosine receptor in complex with a Fab antibody fragment
Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 200 nM ivermectin
Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 0.02 mM ivermectin
Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 2000 nM ivermectin
Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 500 nM ivermectin
The cryo-EM structure of amyloid fibrils from abdominal fat of a multiple myeloma patient (case 1)- polymorph 1.
The cryo-EM structure of amyloid fibrils from abdominal fat of a multiple myeloma patient (case 2).
The cryo-EM structure of amyloid fibrils from abdominal fat of a multiple myeloma patient (case 1)- polymorph 2.
Immune complex of P5-1C8 IgG binding the RBD of Omicron BA.1 6p spike protein
chimera map of bundle-shaped phycobilisome with short rod from thylakoid-lacking cyanobacterium Gloeobacter violaceus PCC 7421
Immune complex of P5-1C8 Fab binding the RBD of Omicron JN.1 6p spike protein
Cryo-EM structure of SARS-CoV-2 WT 6p spike protein in complex with P5-1C8 IgG (1 IgG)
Immune complex of P5-1C8 Fab binding the RBD of SARS-CoV-2 WT 6p spike protein