EMPIAR-12772 - Progesterone-bound DB3 Fab in complex with computationally designed DBPro1156_2 protein binder [multiple data sets in MRC format]

EMPIAR-12772

Progesterone-bound DB3 Fab in complex with computationally designed DBPro1156_2 protein binder [multiple data sets in MRC format]

Publication:

Targeting protein-ligand neosurfaces with a generalizable deep learning tool

Marchand A, Buckley S, Schneuing A, Pacesa M, Elia M, Gainza P, Elizarova E, Neeser RM, Lee PW, Reymond L, Miao Y, Scheller L, Georgeon S, Schmidt J, Schwaller P, Maerkl SJ, Bronstein M, Correia BE

Nature (2025)

PMID: 39814890

DOI: 10.1038/s41586-024-08435-4

Related EMDB entry:

EMD-50522

Deposited:

2025-02-11

Released:

2025-10-29

Last modified:

2025-10-29

Imageset size:

14.63 TB

Imageset DOI:

10.6019/EMPIAR-12772

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
micrographs - single frame

Image Sets

1. Unaligned multi-frame movies of Progesterone-bound DB3 Fab in complex with computationally designed DBPro1156_2 protein binder

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

34507

Image size:

(4096, 4096)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.658, 0.658)

Details:

---

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

Depending on the number and size of files to be downloaded, this can take an enormous amount of time. Also, this feature is unstable and may not work properly, and checksums of downloaded files are not verified.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

2. Aligned dose-weighted micrographs of Progesterone-bound DB3 Fab in complex with computationally designed DBPro1156_2 protein binder

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

34507

Image size:

(4096, 4096)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.658, 0.658)

Details:

---

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

Browse All Files

Quick Links

Browse EMPIAR

Sample Preparation Widget

Volume Browser

Tomo Viewer Prototype

Claim entries to your ORCiD

Talks and Tutorials

EMPIAR Quick tour

Publications

Re-use study

Statistics

EMPIAR in the news

COVID-19 Data Portal

EMDB

BioImage Archive

PDBe

EMNavigator@PDBj

PDBj

Citations

CryoTriplane: triplane-based neural radiance field representation for high-resolution cryo-EM 3D homogeneous reconstruction.

Cheng Y, He B, Zeng Q, Zhang F, Han R. (2026)

Structural identification of the RY12 domain of RyR1 as an ADP sensor and the target of the malignant hyperthermia therapeutic dantrolene.

Kim K, Li H, Yuan Q, Melville Z, Zalk R, des Georges A, Frank J, Hendrickson WA, Marks AR, Clarke OB. (2026)

Post-acquisition super resolution for cryo-electron microscopy.

Burton Smith RN, Murata K. (2026)

Structural heterogeneity of CTE Type I tau filaments with an interface-shifted polymorph

Watanabe R, Lee EB. (2026)

Agentic cryo-EM structure determination with CryoPilot

--- (2026)

Ligand-induced activation of RyR1 in native membranes.

Mikirtumov V, Golusik S, Huo R, Sprink T, Balyschew N, Yang W, Diebolder C, Yuan S, Kotecha A, Kudryashev M. (2026)

QwenCryoMarker: a universal post-processing framework for contamination-aware particle cleaning.

Sun Y, Zhao J, Xu N, Wang L, Ding W, Li M. (2026)

An unattended image-processing pipeline for on-the-fly quality assessment and 3D exploration in cryo-EM.

Marchán Torres D, Conesa P, Garcia A, Iceta M, Broche L, Gragera M, Linares R, Kwong HS, Chichón FJ, Svensson O, Arranz R, Effantin G, Kandiah E, Carazo JM, Sorzano COS. (2026)

CryoMV: Structure-Prior-Guided Modeling and Real-Particle Validation of Continuous Conformational Transitions in Cryo-EM

Li F, Dong H, Tang S, Wang X, Zhang C, Ji C, Han R, Zhang F, Wan X. (2026)

Easymode: general pretrained networks for cellular cryo-ET enable flexible approaches to subtomogram averaging

So-Last MGF, Burt A, Hale T, Allegretti M. (2026)

See all citations

Protein Data Bank Japan News

[2020-07-15]

PDBj는 2020 년 7 월에 20 주년을 맞이했습니다.

[2019-02-20]

[wwPDB] 고분자결정구조 등록 시 PDBx/mmCIF 형식 파일만 허용됩니다.

[2017-11-16]

11 월 24 일 ~ 26 일, 텔레콤 센터 빌딩 (도쿄 오다이바)에서 개최되는 「사이언스 아고라 2017」에 출전합니다

[2016-01-28]

News on 2016-1-11

See all news