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)Local EM map of Prp19 subcomplex of Chlamydomonas C* complex from Prp19-Flag dataset
Cryo EM structure of human phosphate channel XPR1 at intermediate state
Cryo EM structure of human phosphate channel XPR1 in complex with IP7
Complex of FMDV O/18074 and inter-serotype broadly neutralizing antibodies pOA-2
Complex of FMDV A/WH/CHA/09 and inter-serotype broadly neutralizing antibodies pOA-2
Cryo EM structure of human phosphate channel XPR1 at intermediate state
Cryo EM structure of human phosphate channel XPR1 in complex with IP6
Cryo EM structure of human phosphate channel XPR1 at open and inward-facing state
Cryo EM structure of human phosphate channel XPR1 at inward-facing state
Structure of the Position 1 to 3 Open gamma-Tubulin Ring Complex from Pig Brain
In situ structure of mitochondrial ATPsynthase in whole Polytomella cells
Density for a protein trimer unit bound to RNA from a single-layered nucleoprotein-RNA helical assembly from Marburg virus
Structure of rabbit RyR1 reconstituted into lipid liposomes in open state in complex with Ca2+, ATP, caffeine and Nb9657.
Structure of the Position 8 to 9 CMG-decorated gamma-Tubulin Ring Complex from Pig Brain
Structure of the Position 13 to 14 CMG-decorated gamma-Tubulin Ring Complex from Pig Brain
Structure of the Position 10 to 12 Open gamma-Tubulin Ring Complex from Pig Brain
Structure of a gp140 SpyTag-SpyCatcher mi3 nanoparticle including mi3 density only.
Cryo-EM structure of single-layered nucleoprotein-RNA helical assembly from Marburg virus, trimeric repeat unit
Structure of RyR1 in detergent in open state in complex with Ca2+, ATP, caffeine and Nb9657.
Unmasked HIV-1 envelope trimer gp140 SpyTag SpyCatcher mi3 nanoparticle.
Structure of mouse RyR2 solubilised in detergent in open state in complex with Ca2+, ATP, caffeine and Nb9657.
Structure of RyR1 reconstituted into lipid nanodisc in primed state in complex with Ca2+, ATP, caffeine and Nb9657
CRYO-EM FOCUSED REFINED MAP OF LEISHMANIA MAJOR 80S RIBOSOME : LM32Cs1C1 Mutant snoRNA overexpression class 4
Structure of the peripheral stalk of the Polytomella ATPsynthase dimer in whole cells
Combined map of Candida albicans 80S ribosome in complex with mefloquine
Structure of RyR1 reconstituted into lipid liposomes in primed state in complex with Ca2+, ATP, caffeine and Nb9657.
Structure of the Position 10 to 12 CMG-decorated gamma-Tubulin Ring Complex from Pig Brain
Structure of the Position 1 to 3 CMG-decorated gamma-Tubulin Ring Complex from Pig Brain
Human RNF213 (consensus refinement without accounting for flexibility)
40S head focused map of Candida albicans 80S ribosome in complex with mefloquine
CRYO-EM CONSENSUS MAP OF LEISHMANIA MAJOR 80S RIBOSOME : LM32Cs1C1 Mutant snoRNA overexpression class 4
40S body focused map of Candida albicans 80S ribosome in complex with mefloquine
Structure of RyR1 solubilised in detergent in primed state in complex with Ca2+, ATP, caffeine and Nb9657
CryoEM structure of Gs-coupled GPBAR with small molecule agonist P395
Structure of the Position 4 to 7 CMG-decorated gamma-Tubulin Ring Complex from Pig Brain
Structure of the Position 4 to 11 Open gamma-Tubulin Ring Complex from Pig Brain
C1 turret to capsid interface of full Haloferax tailed virus 1 adjacent to the portal-capsid interface.
Structure of RyR1 in detergent in close state in complex with FKBP and Nb9657.
Human RNF213: focused refinement of carbohydrate binding module (CBM) domain
CryoEM structure of Komagataella pastoris Cytochrome c oxidase (9 subunits) in complex with human VMAT2 and Amphetamine
Tyrocidine synthetase modules 1 and 2 crosslinked in the condensation state, complex A
Cryo-EM structure of native SWR1 bound to nucleosome (composite structure)
Cryo-EM structure of native SWR1 bound to DNA in the absence of nucleotide (composite structure)
Cryo-EM structure of native SWR1 bound to DNA in the absence of nucleotide (consensus map)
Acinetobacter baumannii Tse15 Rhs effector, toxin cleavage mutant (D1369N, D1391N)
Swc3-Swc2 subcomplex from SWR1-nucleosome complex (focused refinement)
Tyrocidine synthetase modules 1 and 2 crosslinked in the condensation state, complex C
Tyrocidine synthetase modules 1 and 2 crosslinked in the condensation state, complex B
Cryo-EM structure of native SWR1, free complex (composite structure)
Cryo-EM structure of mouse PI(4,5)P2-bound TRPML1 channel at 2.46 Angstrom resolution
Swr1 ATPase domain from SWR1(apo)-DNA complex (focused refinement)
Subtomogram average of the ribonucleoprotein of the rabies virus CVS-27 strain
Komagataella pastoris Cytochrome c oxidase in complex with human VMAT2 and Tetrabenazine
Nucleosome and bound Swr1 ATPase from SWR1-nucleosome complex (focused refinement)
Komagataella pastoris Cytochrome c oxidase in complex with human VMAT2 and Reserpine
CryoEM structure of Komagataella pastoris Cytochrome c oxidase (11 subunits) in complex with human VMAT2
Cryo-EM structure of mouse TRPML1 channel Y404W at 2.86 Angstrom resolution
Cryo-EM structure of native SWR1 bound to DNA (composite structure)
Cryo-EM structure of the human P2X1 receptor in the apo closed state
Komagataella pastoris Cytochrome c oxidase (9 subunits) in complex with human VMAT2
Mycobacteriophage Bxb1 C1 Capsid and Portal - Composite map and model
Cryo-EM structure of native SWR1, free complex (consensus map filtered by local resolution)
Komagataella pastoris Cytochrome c oxidase in complex with human VMAT2 and Histamine
RuvBL-associated core from SWR1-nucleosome complex (focused refinement)
Cryo-EM structure of the desensitised ATP-bound human P2X1 receptor
Cryo-EM structure of the human P2X1 receptor in the NF449-bound inhibited state
Cryo-EM structure of Rab12-LRRK2 complex in the LRRK2 dimer state
E. coli RNA polymerase consensus volume with a bound fluoride riboswitch in the ligand-bound state
Cryo-EM structure of Rab12-LRRK2 complex in the LRRK2 monomer state
Cryo-EM structure of native SWR1 bound to DNA (unmasked refinement filtered by local resolution)
Komagataella pastoris Cytochrome c oxidase in complex with human VMAT2 and Serotonin
Cryo-EM structure of the human P2X1 receptor in the ATP-bound desensitized state
Structure of recombinantly assembled murine alpha-synuclein fibrils
Structural basis for adhesin secretion by the outer-membrane usher in type 1 pili
Cryo-EM structure of native SWR1 bound to nucleosome (consensus map filtered by local resolution)
Structure of SARS-CoV-2 BA.2.86 spike RBD in complex with ACE2 (down state)
Cryo-EM structure of E.coli spermidine transporter PotD-PotABC in pre-translocation state
Cryo-EM structure of histamine H2 receptor in complex with histamine and miniGq
Cryo-EM structure of histamine H2 receptor in complex with histamine and miniGs
Cryo-EM structure of histamine H4 receptor in complex with immepip and Gi
Cryo-EM structure of E.coli spermidine transporter PotABC in nanodisc
Structure of SARS-CoV-2 JN.1 spike glycoprotein in complex with ACE2 (2-up and 1-down state)
Structure of SARS-CoV-2 JN.1 spike RBD in complex with ACE2 (up state)
Cryo-EM structure of E.coli spermidine transporter PotABC with spermidine
Neutralization antibody CUP2G3 bound with SARS-CoV-2 Omicron BA.5 spike trimer
SARS-CoV-2 Omicron Spike in complex with XGV004, XGV016 and XGV030
Neutralization antibody ZCP3B4 bound with SARS-CoV-2 Omicron BA.5 RBD
Local EM map of Prp19 subcomplex of Chlamydomonas C* complex from Cdc5L-Flag dataset
Cryo-EM structure of E.coli spermidine transporter PotD-PotABC in translocation intermidiate state
Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (2-up and 1-down state)
Cryo-EM structure of histamine H1 receptor in complex with histamine and miniGq
Cryo-EM structure of the inhibitor-bound Vo complex from Enterococcus hirae
Local EM map of U5 snRNP of Chlamydomonas C* complex from Cdc5L-Flag dataset
Cryo-EM map of the Chlamydomonas C* complex from Cdc5L-Flag dataset
Overall EM map of the Chlamydomonas C* complex from Prp19-Flag dataset
Cryo-EM structure of histamine H3 receptor in complex with imetit and Gi
Cryo-EM structure of histamine H3 receptor in complex with histamine and Gi
Cryo-electron microscopic structure of an amide hydrolase from Pseudoxanthomonas wuyuanensis
Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (2-up state)
Structure of SARS-CoV-2 BA.2.86 spike RBD in complex with ACE2 (up state)
Structure of the SARS-CoV-2 BA.2.86 spike glycoprotein (closed state)
Local EM map of N-ter of Prp17 of Chlamydomonas C* complex from Cdc5L-Flag dataset
Neutralization antibody ZCP4C9 bound with SARS-CoV-2 Omicron BA.5 RBD
Neutralization antibody ZCP4D5 bound with SARS-CoV-2 Omicron BA.5 spike trimer
Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (1 highly-open RBD and 1 partially-open RBD)
Structure of SARS-CoV-2 JN.1 spike glycoprotein in complex with ACE2 (2-up state)
Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (3-up state)
SARS-CoV-2 Omicron Spike in complex with XGV018,XGV038 and XGV042
Local EM map of N-ter of Prp17 of Chlamydomonas C* from Prp19-Flag dataset