To accommodate the rapid growth of EMDB depositions, the EMDB ID format will be extended to six-digits
www.rcsb.org/news/fe...
www.rcsb.org/news/fe...
Extension to EMDB Accession Codes
To accommodate the rapid growth of EMDB depositions, the EMDB ID format will be extended to six-digits
www.rcsb.org
June 27, 2025 at 4:12 PM
To accommodate the rapid growth of EMDB depositions, the EMDB ID format will be extended to six-digits
www.rcsb.org/news/fe...
www.rcsb.org/news/fe...
The EMDB wishes you a very Merry Christmas, a Happy New Year and we are delighted to share our jointly designed EMDB/PDBe Christmas card with you. It has been a busy year, we look forward to seeing you in the New Year here! Card: A mixture of #cryoEM and X-ray diffraction structures.
December 18, 2025 at 2:01 PM
The EMDB wishes you a very Merry Christmas, a Happy New Year and we are delighted to share our jointly designed EMDB/PDBe Christmas card with you. It has been a busy year, we look forward to seeing you in the New Year here! Card: A mixture of #cryoEM and X-ray diffraction structures.
This week we had International Day of Women and Girls in Science 👩🔬 🥼 🔬
There are many women working to provided the resources at PDBe, AlphaFoldDB, EMDB and EMPIAR. Lets met a few of them!
#IDWGS #WomeninSTEM #WomenInScience #WhatAScientistLooksLike
There are many women working to provided the resources at PDBe, AlphaFoldDB, EMDB and EMPIAR. Lets met a few of them!
#IDWGS #WomeninSTEM #WomenInScience #WhatAScientistLooksLike
February 14, 2025 at 5:30 PM
This week we had International Day of Women and Girls in Science 👩🔬 🥼 🔬
There are many women working to provided the resources at PDBe, AlphaFoldDB, EMDB and EMPIAR. Lets met a few of them!
#IDWGS #WomeninSTEM #WomenInScience #WhatAScientistLooksLike
There are many women working to provided the resources at PDBe, AlphaFoldDB, EMDB and EMPIAR. Lets met a few of them!
#IDWGS #WomeninSTEM #WomenInScience #WhatAScientistLooksLike
Happy Holidays from PDBe (PDBe.org), EMDB (ebi.ac.uk/emdb) & EMPIAR (ebi.ac.uk/empiar)!
May your holidays be full of joy, peace, rest & rejuvenation.
Enjoy this structural #biology generated #christmastree.
We look forward to all the new structures to come!
🧵 1 of 5
May your holidays be full of joy, peace, rest & rejuvenation.
Enjoy this structural #biology generated #christmastree.
We look forward to all the new structures to come!
🧵 1 of 5
December 25, 2024 at 11:35 PM
Happy Holidays from PDBe (PDBe.org), EMDB (ebi.ac.uk/emdb) & EMPIAR (ebi.ac.uk/empiar)!
May your holidays be full of joy, peace, rest & rejuvenation.
Enjoy this structural #biology generated #christmastree.
We look forward to all the new structures to come!
🧵 1 of 5
May your holidays be full of joy, peace, rest & rejuvenation.
Enjoy this structural #biology generated #christmastree.
We look forward to all the new structures to come!
🧵 1 of 5
Structural biology data to inspire a snowflake:
#PDBe:
pdbe.org/8g30
#EMDB:
emdb-empiar.org/EMD-29686
🧵 5 of 5
#PDBe:
pdbe.org/8g30
#EMDB:
emdb-empiar.org/EMD-29686
🧵 5 of 5
December 25, 2024 at 11:35 PM
Structural biology data to inspire a snowflake:
#PDBe:
pdbe.org/8g30
#EMDB:
emdb-empiar.org/EMD-29686
🧵 5 of 5
#PDBe:
pdbe.org/8g30
#EMDB:
emdb-empiar.org/EMD-29686
🧵 5 of 5
The wwPDB just hit a major milestone: 𝟏𝟎,𝟎𝟎𝟎 𝐄𝐌𝐃𝐁 𝐞𝐧𝐭𝐫𝐢𝐞𝐬 𝐫𝐞𝐥𝐞𝐚𝐬𝐞𝐝 𝐢𝐧 𝐚 𝐬𝐢𝐧𝐠𝐥𝐞 𝐲𝐞𝐚𝐫. To put this in context, the entire EMDB reached 10,000 entries total in 2019 — now the archive 𝐡𝐚𝐬 𝐬𝐮𝐫𝐩𝐚𝐬𝐬𝐞𝐝 𝟓𝟎,𝟎𝟎𝟎. Huge credit to the community driving 3DEM forward!
www.wwpdb.org/news/news?ye...
#3DEM #EMDB
www.wwpdb.org/news/news?ye...
#3DEM #EMDB
EMDB Surpasses 10,000 Entries in a Year
wwPDB: Worldwide Protein Data Bank
www.wwpdb.org
January 20, 2026 at 10:18 AM
The wwPDB just hit a major milestone: 𝟏𝟎,𝟎𝟎𝟎 𝐄𝐌𝐃𝐁 𝐞𝐧𝐭𝐫𝐢𝐞𝐬 𝐫𝐞𝐥𝐞𝐚𝐬𝐞𝐝 𝐢𝐧 𝐚 𝐬𝐢𝐧𝐠𝐥𝐞 𝐲𝐞𝐚𝐫. To put this in context, the entire EMDB reached 10,000 entries total in 2019 — now the archive 𝐡𝐚𝐬 𝐬𝐮𝐫𝐩𝐚𝐬𝐬𝐞𝐝 𝟓𝟎,𝟎𝟎𝟎. Huge credit to the community driving 3DEM forward!
www.wwpdb.org/news/news?ye...
#3DEM #EMDB
www.wwpdb.org/news/news?ye...
#3DEM #EMDB
Finally out! Working with this team was a fantastic learning experience. Also I was excited to determine the in situ clathrin structure for this project! That’s my first EM-structure upload to EMDB. Can I tell my mom I am a structural biologist now? 😁 #cryoET
January 6, 2025 at 6:00 PM
Finally out! Working with this team was a fantastic learning experience. Also I was excited to determine the in situ clathrin structure for this project! That’s my first EM-structure upload to EMDB. Can I tell my mom I am a structural biologist now? 😁 #cryoET
Validation of helical symmetry parameters in EMDB www.biorxiv.org/content/10.1101/2025.05.18.654508v1 #cryoem
May 24, 2025 at 11:21 AM
Validation of helical symmetry parameters in EMDB www.biorxiv.org/content/10.1101/2025.05.18.654508v1 #cryoem
With 8 composite cryo-EM maps (totaling 47 EMDB entries) and several biochemical assays, we demonstrate the mechanistic basis for the positioning of H3K36me3 within actively transcribed regions. Surprisingly, SETD2 must be relieved of auto inhibition by the transcription machinery!
Ever wondered how transcription choreographs histone modifications? Our work reveals the basis of co-transcriptional H3K36me3 by SETD2. We visualize how a histone writer coordinates with the transcription machinery! This is the magnus opus of @jonmarkert.bsky.social!
tinyurl.com/setd2
tinyurl.com/setd2
December 12, 2024 at 7:54 PM
With 8 composite cryo-EM maps (totaling 47 EMDB entries) and several biochemical assays, we demonstrate the mechanistic basis for the positioning of H3K36me3 within actively transcribed regions. Surprisingly, SETD2 must be relieved of auto inhibition by the transcription machinery!
Want to try LocScale-2.0 without installing locally?
Check out ColabScale: just upload your maps or enter your favourite EMDB ID and run LocScale-2.0 in the cloud.
edu.nl/ur3ge
Check out ColabScale: just upload your maps or enter your favourite EMDB ID and run LocScale-2.0 in the cloud.
edu.nl/ur3ge
May 22, 2025 at 11:05 AM
Want to try LocScale-2.0 without installing locally?
Check out ColabScale: just upload your maps or enter your favourite EMDB ID and run LocScale-2.0 in the cloud.
edu.nl/ur3ge
Check out ColabScale: just upload your maps or enter your favourite EMDB ID and run LocScale-2.0 in the cloud.
edu.nl/ur3ge
Proud to be one of the authors of the highest-resolution SARS-CoV-2 #cryoEM entry on EMDB 😄 This came out of a fun collaboration with Bicycle Therapeutics, where we used cryo-EM to validate binding of their biparatopic (EMD-51660) and homotrimeric (EMD-51659) Bicycle molecules 🔬
April 4, 2025 at 11:38 AM
Proud to be one of the authors of the highest-resolution SARS-CoV-2 #cryoEM entry on EMDB 😄 This came out of a fun collaboration with Bicycle Therapeutics, where we used cryo-EM to validate binding of their biparatopic (EMD-51660) and homotrimeric (EMD-51659) Bicycle molecules 🔬
First Bluesky post! Our MTHFR maps and models are now online
www.ebi.ac.uk/emdb/EMD-18298
www.ebi.ac.uk/emdb/EMD-18299
www.ebi.ac.uk/emdb/EMD-18300
www.ebi.ac.uk/emdb/EMD-18298
www.ebi.ac.uk/emdb/EMD-18299
www.ebi.ac.uk/emdb/EMD-18300
Dynamic inter-domain transformations mediate the allosteric regulation of human 5, 10-methylenetetra...
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
November 18, 2023 at 9:37 PM
First Bluesky post! Our MTHFR maps and models are now online
www.ebi.ac.uk/emdb/EMD-18298
www.ebi.ac.uk/emdb/EMD-18299
www.ebi.ac.uk/emdb/EMD-18300
www.ebi.ac.uk/emdb/EMD-18298
www.ebi.ac.uk/emdb/EMD-18299
www.ebi.ac.uk/emdb/EMD-18300
On this International Women’s ♀️ Day, we celebrate the diverse talented women who support #structuralbiology resources, such as:
🧪 PDBe & AlphaFoldDB
🧪 EMDB
🧪 EMPIAR
Leaders & more... Let's meet some of them!
🧵 (1 of 16)
#InternationalWomensDay #WomenInTech #WomenInScience
🧪 PDBe & AlphaFoldDB
🧪 EMDB
🧪 EMPIAR
Leaders & more... Let's meet some of them!
🧵 (1 of 16)
#InternationalWomensDay #WomenInTech #WomenInScience
March 8, 2025 at 2:00 PM
On this International Women’s ♀️ Day, we celebrate the diverse talented women who support #structuralbiology resources, such as:
🧪 PDBe & AlphaFoldDB
🧪 EMDB
🧪 EMPIAR
Leaders & more... Let's meet some of them!
🧵 (1 of 16)
#InternationalWomensDay #WomenInTech #WomenInScience
🧪 PDBe & AlphaFoldDB
🧪 EMDB
🧪 EMPIAR
Leaders & more... Let's meet some of them!
🧵 (1 of 16)
#InternationalWomensDay #WomenInTech #WomenInScience
The first time I heard about his habit I immediately flashed to Avery Bullock in American Dad and honestly I haven't been...fully dissuaded from the comparison since
www.youtube.com/watch?v=EmDB...
www.youtube.com/watch?v=EmDB...
American Dad - Avery a responsible drug user
YouTube video by My Head Movies
www.youtube.com
April 11, 2026 at 2:25 PM
The first time I heard about his habit I immediately flashed to Avery Bullock in American Dad and honestly I haven't been...fully dissuaded from the comparison since
www.youtube.com/watch?v=EmDB...
www.youtube.com/watch?v=EmDB...
Now on @biorxivpreprint.bsky.social: Dari Kimanius' paper on #Blush regularisation, a machine-learning based prior in #RELION5 trained on EMDB #cryoEM half-maps, which he uses to solve a #cryoEM data set of a 40 kDa protein:RNA complex that was previously intractable!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 24, 2023 at 12:40 PM
Now on @biorxivpreprint.bsky.social: Dari Kimanius' paper on #Blush regularisation, a machine-learning based prior in #RELION5 trained on EMDB #cryoEM half-maps, which he uses to solve a #cryoEM data set of a 40 kDa protein:RNA complex that was previously intractable!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
🎄✨ Season’s Greetings from PDBe ✨🎄
The PDBe wishes you a very Merry Christmas and a Happy New Year. We are delighted to share our jointly designed EMDB/PDBe Christmas card with you. It has been a busy year, and we look forward to seeing you in the New Year.
The PDBe wishes you a very Merry Christmas and a Happy New Year. We are delighted to share our jointly designed EMDB/PDBe Christmas card with you. It has been a busy year, and we look forward to seeing you in the New Year.
December 18, 2025 at 2:12 PM
🎄✨ Season’s Greetings from PDBe ✨🎄
The PDBe wishes you a very Merry Christmas and a Happy New Year. We are delighted to share our jointly designed EMDB/PDBe Christmas card with you. It has been a busy year, and we look forward to seeing you in the New Year.
The PDBe wishes you a very Merry Christmas and a Happy New Year. We are delighted to share our jointly designed EMDB/PDBe Christmas card with you. It has been a busy year, and we look forward to seeing you in the New Year.
Virus are fascinating !
#CryoEM of African swine fever virus (www.ebi.ac.uk/emdb/EMD-38214)
Homo 60-mer that assembles into a dodecahedron cage
#CryoEM of African swine fever virus (www.ebi.ac.uk/emdb/EMD-38214)
Homo 60-mer that assembles into a dodecahedron cage
January 31, 2024 at 9:00 AM
Virus are fascinating !
#CryoEM of African swine fever virus (www.ebi.ac.uk/emdb/EMD-38214)
Homo 60-mer that assembles into a dodecahedron cage
#CryoEM of African swine fever virus (www.ebi.ac.uk/emdb/EMD-38214)
Homo 60-mer that assembles into a dodecahedron cage
Validation of helical symmetry parameters in EMDB pubmed.ncbi.nlm.nih.gov/40475480/ #cryoem
June 7, 2025 at 9:57 PM
Validation of helical symmetry parameters in EMDB pubmed.ncbi.nlm.nih.gov/40475480/ #cryoem
pubpeer.com/publications...
Apparently non-existent density for a ligand in PDB 7yjj and EMDB 33872 is up for interpretation by readers and does not affect the robustness of the authors' paper......
Apparently non-existent density for a ligand in PDB 7yjj and EMDB 33872 is up for interpretation by readers and does not affect the robustness of the authors' paper......
August 20, 2025 at 10:16 AM
pubpeer.com/publications...
Apparently non-existent density for a ligand in PDB 7yjj and EMDB 33872 is up for interpretation by readers and does not affect the robustness of the authors' paper......
Apparently non-existent density for a ligand in PDB 7yjj and EMDB 33872 is up for interpretation by readers and does not affect the robustness of the authors' paper......
This is a fantastic example of how to begin as a newcomer to #cryoEM. Being proactive in getting advice from experienced scientists and going to any of the great workshops would likely lower the incidences of erroneous structures in the EMDB and PDB (There’s not a lot but there are a few).
Hassan Zafar et al.: Breaking barriers: transitioning from X-ray crystallography to cryo-EM for structural studies ##CryoElectronMicroscopyCryoEM##StructuralBiology##SingleParticleAnalysis@uvmvermont...##IUCrhttps://journals.iucr.org/paper?S205979832600080X
Breaking barriers: transitioning from X-ray crystallography to cryo-EM for structural studies
This article describes the transition of the Glass laboratory from X-ray crystallography to single-particle cryo-electron microscopy (cryo-EM) for structural studies of ATAD2B, a large AAA+ ATPase- and bromodomain-containing protein involved in chromatin regulation. It outlines practical strategies for protein expression, sample preparation, data processing and model building, offering a comprehensive workflow and troubleshooting guide for new cryo-EM users working with large, flexible macromolecular complexes.
journals.iucr.org
February 21, 2026 at 11:24 AM
This is a fantastic example of how to begin as a newcomer to #cryoEM. Being proactive in getting advice from experienced scientists and going to any of the great workshops would likely lower the incidences of erroneous structures in the EMDB and PDB (There’s not a lot but there are a few).
www.ebi.ac.uk/emdb/EMD-398... and another one not published yet.... 🫠 #cryoEM
May 2, 2025 at 8:48 AM
www.ebi.ac.uk/emdb/EMD-398... and another one not published yet.... 🫠 #cryoEM
In the authors' latest paper. doi.org/10.1016/j.bc... So I guess no one can request the data of www.ebi.ac.uk/emdb/EMD-39869 to be deposited into EMPIAR? #CryoEM
August 21, 2025 at 7:48 AM
In the authors' latest paper. doi.org/10.1016/j.bc... So I guess no one can request the data of www.ebi.ac.uk/emdb/EMD-39869 to be deposited into EMPIAR? #CryoEM
This week's release of 200 entries by the EMDB can be viewed at www.ebi.ac.uk/emdb. The running total for the month of May is 650 entries bringing the archive to a total of 57595 entries.
May 20, 2026 at 6:30 AM
This week's release of 200 entries by the EMDB can be viewed at www.ebi.ac.uk/emdb. The running total for the month of May is 650 entries bringing the archive to a total of 57595 entries.
This week's release of 288 entries by the EMDB can be viewed at www.ebi.ac.uk/emdb. The running total for the month of April is 1209 entries bringing the archive to a total of 56953 entries.
April 29, 2026 at 6:30 AM
This week's release of 288 entries by the EMDB can be viewed at www.ebi.ac.uk/emdb. The running total for the month of April is 1209 entries bringing the archive to a total of 56953 entries.