Electron Microscopy Data Bank

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!

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author:"DiMaio F"

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Current Database

Current status

Sample type

Organism

Homo sapiens [39]
Saccharomyces cerevisiae [17]
Chaetomium thermophilum [16]
Synthetic construct [13]
Pseudomonas phage phi6 [11]
Saccharomyces cerevisiae [10]
Sus scrofa [10]
Escherichia coli [6]
Escherichia coli [6]
Salmonella phage p22 [5]
Middle east respiratory syndrome-related coronavirus [5]
Thermoplasma acidophilum [5]
Schizosaccharomyces pombe [5]
Bos taurus [5]
Human immunodeficiency virus 1 [4]
Middle east respiratory syndrome-related coronavirus [4]
Acinetobacter baumannii [4]
Mus musculus [3]
Nipah virus [3]
Escherichia coli [3]
Methanococcus maripaludis [3]
Escherichia coli [3]
Streptomyces coelicolor [2]
Mus sp. [2]
Leptospira licerasiae [2]
Streptomyces coelicolor [2]
Campylobacter jejuni [2]
Cricetus cricetus [1]
Rattus norvegicus [1]
Murine coronavirus [1]
Influenza a virus [1]
Sulfolobus islandicus [1]
Staphylococcus aureus [1]
Bacillus subtilis [1]
Sulfolobus islandicus rod-shaped virus 2 [1]
Mycobacterium tuberculosis [1]
Acidianus filamentous virus 1 [1]
Vibrio cholerae [1]
Human coronavirus nl63 [1]
Schizosaccharomyces pombe [1]
Bamboo mosaic virus [1]
Aequorea victoria [1]
Drosophila melanogaster [1]

EM Method

Resolution

Model molecular weight

Release Date

Author by name

Dimaio F [157]
Baker D [31]
Farrell DP [29]
Veesler D [28]
Kollman JM [17]
Eustermann S [15]
Hauptmann L [15]
Hoffmann T [15]
Hopfner KP [15]
Jungblut A [15]
Kolesnikova O [15]
Kunert F [15]
Lynch EM [15]
Metzner F [15]
Moldt M [15]
Zhang M [15]
Reggiano G [14]
Walz T [14]
Wang D [14]
Huiskonen JT [13]
Hansen JM [12]
Park YJ [12]
Egelman EH [11]
El Omari K [11]
Grimes JM [11]
Ilca SL [11]
Kotecha A [11]
Poranen MM [11]
Stuart DI [11]
Sun X [11]
Weis F [11]
De Haas F [11]
Borst AJ [10]
Frenz B [10]
Horowitz A [10]
Quispe J [10]
Seattle Structural Genomics Center For Infectious Disease Ssgcid [10]
Suzuki H [10]
Nogales E [9]
Walls AC [9]
Abrusci P [8]
Bohstedt T [8]
Burgess-brown NA [8]
Chi G [8]
Chiu W [8]
Ebenhoch R [8]
Li X [8]
Man H [8]
Mckinley G [8]
Mukhopadhyay SMM [8]
Wang Z [8]
Almeida FG [7]
Bergeron JRC [7]
Bosch BJ [7]
Bountra KD [7]
Durr KL [7]
Fernandez-cid A [7]
Garneau AP [7]
Isenring P [7]
Jazayeri A [7]
Lahiri I [7]
Lavoie JL [7]
Leschziner AE [7]
Liko I [7]
Moreau CP [7]
Mougous JD [7]
Qiu X [7]
Robinson CV [7]
Slimani S [7]
Tang H [7]
Tehan B [7]
Tortorici MA [7]
Tremblay LE [7]
Baek M [6]
Cianfrocco MA [6]
Li W [6]
Liao M [6]
Rapoport TA [6]
Tzokov SB [6]
Xu C [6]
Xu J [6]
Baker ML [5]
Bart SM [5]
Bera AK [5]
Carter L [5]
Castellano LM [5]
Chen D-H [5]
Chen DH [5]
Chen Z [5]
Cheng Y [5]
Chong J [5]
Dang HV [5]
Dervan PB [5]
Dougherty M [5]
Downing KH [5]
Egelman E [5]
Gates SN [5]
Haase-pettingell C [5]
Hare AA [5]
Hejab NMA [5]

Author by ORCID

Dimaio F [48]
Farrell DP [19]
Baker D [17]
Jungblut A [15]
Lynch EM [15]
Metzner F [15]
Hoffmann T [15]
Eustermann S [15]
Hopfner KP [15]
Zhang M [15]
Kunert F [15]
Kolesnikova O [15]
Hauptmann L [15]
Veesler D [14]
Huiskonen JT [13]
Kollman JM [13]
Walz T [13]
Hansen JM [12]
Grimes JM [11]
Kotecha A [11]
De Haas F [11]
Poranen MM [11]
Weis F [11]
Sun X [11]
Ilca SL [11]
Quispe J [10]
Park YJ [10]
Borst AJ [10]
Suzuki H [9]
Nogales E [9]
Wang Z [8]
Chiu W [8]
Lavoie JL [7]
Chi G [7]
Tortorici MA [7]
Durr KL [7]
Lahiri I [7]
Fernandez-cid A [7]
Bohstedt T [7]
Walls AC [7]
Garneau AP [7]
Ebenhoch R [7]
Tang H [7]
Egelman EH [7]
Tzokov SB [6]
Cianfrocco MA [6]
Bergeron JRC [6]
Li W [6]
Baek M [6]
Xu J [6]
Shorter J [5]
Wang AC [5]
Kobayashi Y [5]
Lin J [5]
Bera AK [5]
Jiang W [5]
Tse E [5]
Kawashima SA [5]
Downing KH [5]
Hryc CF [5]
Poepsel S [5]
Kellogg EH [5]
Carter L [5]
Rey FA [5]
Sauer MM [5]
Schmid MF [5]
Chen Z [5]
Ovchinnikov S [5]
Ferro LS [4]
Golcuk M [4]
Eshun-wilson L [4]
Milles LF [4]
Jack A [4]
Wicky BIM [4]
Stein A [4]
Mi W [4]
Fernandes J [4]
Weiss F [4]
Huijben T [4]
Mann D [4]
Courbet A [4]
Gur M [4]
Miller SI [4]
Mcguire AT [4]
Fang Q [4]
Valencia AM [4]
Luo J [4]
Kwong PD [4]
Yildiz A [4]
Broder CC [3]
Krupovic M [3]
Kang A [3]
Cambillau C [3]
Li X [3]
Addetia A [3]
Kibler RD [3]
Bethel NP [3]
Akkineni S [3]
Hickey AC [3]
Backovic M [3]

Journal

Software

Microscope

Electron Source

Film or detector model

EMPIAR Experiment type

EMPIAR Image category

External links

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Showing 1 - 10 of 166. Page 1 of 17

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EMDB [161]
EMPIAR [5]

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EMD-70396

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3D View

S. griseus TUA bound UmbA4 complexes

Release date: Dec. 17, 2025
Resolution: 3.4 Å
EM Method: Helical reconstruction
Fitted PDBs: 9oee
Q-score: 0.505

Zhao Q, Vlach J, Park YJ, Tan Y, Bertolli SK, Srinivas P, Liao P, Fitzpatrick CR, Dangl JL, Azadi P, DiMaio F, Peterson SB, Zhang D, Veesler D, Mougous JD

Cell (2025) [ DOI: doi:10.1016/j.cell.2025.10.044 Pubmed: 41338195 ]

EMD-73973

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Streptomyces coelicolor UmbA4 complex

Release date: Dec. 10, 2025
Resolution: 4.3 Å
EM Method: Single-particle

Zhao Q, Vlach J, Park YJ, Tan Y, Bertolli SK, Srinivas P, Liao P, Fitzpatrick CR, Dangl JL, Azadi P, DiMaio F, Peterson SB, Zhang D, Veesler D, Mougous JD

Cell (2025) [ DOI: doi:10.1016/j.cell.2025.10.044 Pubmed: 41338195 ]

EMPIAR-12689

Release date: July 10, 2025
Dataset size: 1.7 TB
Experiment type: EMDB

Roy A, Shi L, Chang A, Dong X, Fernandez A, Kraft JC, Li J, Le VQ, Winegar RV, Cherf GM, Slocum D, Poulson PD, Casper GE, Vallecillo-Zuniga ML, Valdoz JC, Miranda MC, Bai H, Kipnis Y, Olshefsky A, Priya T, Carter L, Ravichandran R, Chow CM, Johnson MR, Cheng S, Smith M, Overed-Sayer C, Finch DK, Lowe D, Bera AK, Matute-Bello G, Birkland TP, DiMaio F, Raghu G, Cochran JR, Stewart LJ, Campbell MG, Van Ry PM, Springer T, Baker D

Nat Commun (2023) 14 [ DOI: 10.1038/s41467-023-41272-z Pubmed: 37704610 ]

Image sets:

Unaligned multiframe micrographs of integrin avB6 headpiece in complex with minibinder

EMD-43736

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3D View

Umb1 umbrella toxin particle

Release date: April 17, 2024
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 8w20
Q-score: 0.295

Zhao Q, Bertolli S, Park YJ, Tan Y, Cutler KJ, Srinivas P, Asfahl KL, Fonesca-Garcia C, Gallagher LA, Li Y, Wang Y, Coleman-Derr D, DiMaio F, Zhang D, Peterson SB, Veesler D, Mougous JD

Nature (2024) 629 pp. 165-173 [ Pubmed: 38632398 DOI: doi:10.1038/s41586-024-07298-z ]

EMD-43737

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Umb1 umbrella toxin particle local refinement of UmbB1 bound ALF of UmbC1 and UmbA1

Release date: April 17, 2024
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8w22
Q-score: 0.386

Zhao Q, Bertolli S, Park YJ, Tan Y, Cutler KJ, Srinivas P, Asfahl KL, Fonesca-Garcia C, Gallagher LA, Li Y, Wang Y, Coleman-Derr D, DiMaio F, Zhang D, Peterson SB, Veesler D, Mougous JD

Nature (2024) 629 pp. 165-173 [ Pubmed: 38632398 DOI: doi:10.1038/s41586-024-07298-z ]

EMD-42070

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DpHF18 filament

Release date: April 10, 2024
Resolution: 3.6 Å
EM Method: Helical reconstruction
Fitted PDBs: 8uao
Q-score: 0.41

Shen H, Lynch EM, Akkineni S, Watson JL, Decarreau J, Bethel NP, Benna I, Sheffler W, Farrell D, DiMaio F, Derivery E, De Yoreo JJ, Kollman J, Baker D

Nat Nanotechnol (2024) 19 pp. 1016-1021 [ Pubmed: 38570702 DOI: doi:10.1038/s41565-024-01641-1 ]

EMD-42075

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DpHF7 filament

Release date: April 10, 2024
Resolution: 3.3 Å
EM Method: Helical reconstruction
Fitted PDBs: 8ub3
Q-score: 0.467

Shen H, Lynch EM, Akkineni S, Watson JL, Decarreau J, Bethel NP, Benna I, Sheffler W, Farrell D, DiMaio F, Derivery E, De Yoreo JJ, Kollman J, Baker D

Nat Nanotechnol (2024) 19 pp. 1016-1021 [ Pubmed: 38570702 DOI: doi:10.1038/s41565-024-01641-1 ]

EMD-42088

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DpHF19 filament

Release date: April 10, 2024
Resolution: 3.5 Å
EM Method: Helical reconstruction
Fitted PDBs: 8ubg
Q-score: 0.447

Shen H, Lynch EM, Akkineni S, Watson JL, Decarreau J, Bethel NP, Benna I, Sheffler W, Farrell D, DiMaio F, Derivery E, De Yoreo JJ, Kollman J, Baker D

Nat Nanotechnol (2024) 19 pp. 1016-1021 [ Pubmed: 38570702 DOI: doi:10.1038/s41565-024-01641-1 ]

EMD-41153

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Integrin alpha-v beta-8 in complex with minibinder B8_BP_dsulf

Release date: Sept. 27, 2023
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8tcf
Q-score: 0.493

Nat Commun (2023) 14 pp. 5660-5660 [ DOI: doi:10.1038/s41467-023-41272-z Pubmed: 37704610 ]

EMD-41154

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Raw data

Integrin alpha-v beta-6 in complex with minibinder B6_BP_dslf

Release date: Sept. 27, 2023
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8tcg
Q-score: 0.422

Nat Commun (2023) 14 pp. 5660-5660 [ DOI: doi:10.1038/s41467-023-41272-z Pubmed: 37704610 ]

Sort by: Download

Showing 1 - 10 of 166. Page 1 of 17

Display:

Statistics

Download

Select database:

EMDB [161]
EMPIAR [5]

Format:

Select the script type:

Shell (Unix-based) Batch (Windows-based)

Preview first 10

Download

Filter By

Current Database

Current status

Sample type

Organism

Homo sapiens [39]
Saccharomyces cerevisiae [17]
Chaetomium thermophilum [16]
Synthetic construct [13]
Pseudomonas phage phi6 [11]
Saccharomyces cerevisiae [10]
Sus scrofa [10]
Escherichia coli [6]
Escherichia coli [6]
Salmonella phage p22 [5]
Middle east respiratory syndrome-related coronavirus [5]
Thermoplasma acidophilum [5]
Schizosaccharomyces pombe [5]
Bos taurus [5]
Human immunodeficiency virus 1 [4]
Middle east respiratory syndrome-related coronavirus [4]
Acinetobacter baumannii [4]
Mus musculus [3]
Nipah virus [3]
Escherichia coli [3]
Methanococcus maripaludis [3]
Escherichia coli [3]
Streptomyces coelicolor [2]
Mus sp. [2]
Leptospira licerasiae [2]
Streptomyces coelicolor [2]
Campylobacter jejuni [2]
Cricetus cricetus [1]
Rattus norvegicus [1]
Murine coronavirus [1]
Influenza a virus [1]
Sulfolobus islandicus [1]
Staphylococcus aureus [1]
Bacillus subtilis [1]
Sulfolobus islandicus rod-shaped virus 2 [1]
Mycobacterium tuberculosis [1]
Acidianus filamentous virus 1 [1]
Vibrio cholerae [1]
Human coronavirus nl63 [1]
Schizosaccharomyces pombe [1]
Bamboo mosaic virus [1]
Aequorea victoria [1]
Drosophila melanogaster [1]

EM Method

Resolution

Model molecular weight

Release Date

Author by name

Dimaio F [157]
Baker D [31]
Farrell DP [29]
Veesler D [28]
Kollman JM [17]
Eustermann S [15]
Hauptmann L [15]
Hoffmann T [15]
Hopfner KP [15]
Jungblut A [15]
Kolesnikova O [15]
Kunert F [15]
Lynch EM [15]
Metzner F [15]
Moldt M [15]
Zhang M [15]
Reggiano G [14]
Walz T [14]
Wang D [14]
Huiskonen JT [13]
Hansen JM [12]
Park YJ [12]
Egelman EH [11]
El Omari K [11]
Grimes JM [11]
Ilca SL [11]
Kotecha A [11]
Poranen MM [11]
Stuart DI [11]
Sun X [11]
Weis F [11]
De Haas F [11]
Borst AJ [10]
Frenz B [10]
Horowitz A [10]
Quispe J [10]
Seattle Structural Genomics Center For Infectious Disease Ssgcid [10]
Suzuki H [10]
Nogales E [9]
Walls AC [9]
Abrusci P [8]
Bohstedt T [8]
Burgess-brown NA [8]
Chi G [8]
Chiu W [8]
Ebenhoch R [8]
Li X [8]
Man H [8]
Mckinley G [8]
Mukhopadhyay SMM [8]
Wang Z [8]
Almeida FG [7]
Bergeron JRC [7]
Bosch BJ [7]
Bountra KD [7]
Durr KL [7]
Fernandez-cid A [7]
Garneau AP [7]
Isenring P [7]
Jazayeri A [7]
Lahiri I [7]
Lavoie JL [7]
Leschziner AE [7]
Liko I [7]
Moreau CP [7]
Mougous JD [7]
Qiu X [7]
Robinson CV [7]
Slimani S [7]
Tang H [7]
Tehan B [7]
Tortorici MA [7]
Tremblay LE [7]
Baek M [6]
Cianfrocco MA [6]
Li W [6]
Liao M [6]
Rapoport TA [6]
Tzokov SB [6]
Xu C [6]
Xu J [6]
Baker ML [5]
Bart SM [5]
Bera AK [5]
Carter L [5]
Castellano LM [5]
Chen D-H [5]
Chen DH [5]
Chen Z [5]
Cheng Y [5]
Chong J [5]
Dang HV [5]
Dervan PB [5]
Dougherty M [5]
Downing KH [5]
Egelman E [5]
Gates SN [5]
Haase-pettingell C [5]
Hare AA [5]
Hejab NMA [5]

Author by ORCID

Dimaio F [48]
Farrell DP [19]
Baker D [17]
Jungblut A [15]
Lynch EM [15]
Metzner F [15]
Hoffmann T [15]
Eustermann S [15]
Hopfner KP [15]
Zhang M [15]
Kunert F [15]
Kolesnikova O [15]
Hauptmann L [15]
Veesler D [14]
Huiskonen JT [13]
Kollman JM [13]
Walz T [13]
Hansen JM [12]
Grimes JM [11]
Kotecha A [11]
De Haas F [11]
Poranen MM [11]
Weis F [11]
Sun X [11]
Ilca SL [11]
Quispe J [10]
Park YJ [10]
Borst AJ [10]
Suzuki H [9]
Nogales E [9]
Wang Z [8]
Chiu W [8]
Lavoie JL [7]
Chi G [7]
Tortorici MA [7]
Durr KL [7]
Lahiri I [7]
Fernandez-cid A [7]
Bohstedt T [7]
Walls AC [7]
Garneau AP [7]
Ebenhoch R [7]
Tang H [7]
Egelman EH [7]
Tzokov SB [6]
Cianfrocco MA [6]
Bergeron JRC [6]
Li W [6]
Baek M [6]
Xu J [6]
Shorter J [5]
Wang AC [5]
Kobayashi Y [5]
Lin J [5]
Bera AK [5]
Jiang W [5]
Tse E [5]
Kawashima SA [5]
Downing KH [5]
Hryc CF [5]
Poepsel S [5]
Kellogg EH [5]
Carter L [5]
Rey FA [5]
Sauer MM [5]
Schmid MF [5]
Chen Z [5]
Ovchinnikov S [5]
Ferro LS [4]
Golcuk M [4]
Eshun-wilson L [4]
Milles LF [4]
Jack A [4]
Wicky BIM [4]
Stein A [4]
Mi W [4]
Fernandes J [4]
Weiss F [4]
Huijben T [4]
Mann D [4]
Courbet A [4]
Gur M [4]
Miller SI [4]
Mcguire AT [4]
Fang Q [4]
Valencia AM [4]
Luo J [4]
Kwong PD [4]
Yildiz A [4]
Broder CC [3]
Krupovic M [3]
Kang A [3]
Cambillau C [3]
Li X [3]
Addetia A [3]
Kibler RD [3]
Bethel NP [3]
Akkineni S [3]
Hickey AC [3]
Backovic M [3]

Journal

Software

Microscope

Electron Source

Film or detector model

EMPIAR Experiment type

EMPIAR Image category

External links