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- EMDB-27540: Spatial Definition of the Human Progesterone Receptor-B Transcrip... -

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Basic information

Entry
Database: EMDB / ID: EMD-27540
TitleSpatial Definition of the Human Progesterone Receptor-B Transcriptional Complex
Map dataCryo-EM half map of PRE-DNA/PR-B/SRC-2/p300
Sample
  • Complex: PRE-DNA/PR-B/SRC-2/p300 complex
KeywordsProgesterone receptor-B / nuclear receptor isoforms / steroid receptor coactivator-2 / p300-CBP / transcriptional complex / cryo-EM / activation domain / quaternary structure / HORMONE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 19.1 Å
AuthorsYu X / Yi P
Funding support United States, 9 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)HD8818 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)HD07857 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)NIDDK59820 United States
Welch FoundationQ-1967-20180324 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM143380 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL162842 United States
Department of Defense (DOD, United States)DAMD W81WH-21-1-0404 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080139 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01HD042311 United States
CitationJournal: iScience / Year: 2022
Title: Spatial definition of the human progesterone receptor-B transcriptional complex.
Authors: Xinzhe Yu / Ping Yi / Anil K Panigrahi / Lance Edward V Lumahan / John P Lydon / David M Lonard / Steven J Lutdke / Zhao Wang / Bert W O'Malley /
Abstract: We report the quaternary structure of core transcriptional complex for the full-length human progesterone receptor-B (PR-B) homodimer with primary coactivator steroid receptor coactivator-2 (SRC-2) ...We report the quaternary structure of core transcriptional complex for the full-length human progesterone receptor-B (PR-B) homodimer with primary coactivator steroid receptor coactivator-2 (SRC-2) and the secondary coactivator p300/CREB-binding protein (CBP). The PR-B homodimer engages one SRC-2 mainly through its activation function 1 (AF1) in N-terminus. SRC-2 is positioned between PR-B and p300 leaving space for direct interaction between PR-B and p300 through PR-B's C-terminal AF2 and its unique AF3. Direct AF3/p300 interaction provides long-desired structural insights into the known functional differences between PR-B and the PR-A isoform lacking AF3. We reveal the contributions of each AF and demonstrate their structural basis in forming the PR-B dimer interface and PR-B/coactivator complex. Comparison of the PR-B/coactivator complex with other steroid receptor (estrogen receptor and androgen receptor) complexes also shows that each receptor has its unique mechanism for recruiting coactivators due to the highly variable N-termini among receptors.
History
DepositionJul 8, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27540.png

Downloads & links

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Map

FileDownload / File: emd_27540.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM half map of PRE-DNA/PR-B/SRC-2/p300
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.25876367 - 1.350223
Average (Standard dev.)0.004565169 (±0.050039407)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 448.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cryo-EM map of PRE-DNA/PR-B/SRC-2/p300 with C-terminal Fab binding...

Fileemd_27540_additional_1.map
AnnotationCryo-EM map of PRE-DNA/PR-B/SRC-2/p300 with C-terminal Fab binding to LBD domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM map of PRE-DNA/PR-B/SRC-2/p300

Fileemd_27540_half_map_1.map
AnnotationCryo-EM map of PRE-DNA/PR-B/SRC-2/p300
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half map of PRE-DNA/PR-B/SRC-2/p300

Fileemd_27540_half_map_2.map
AnnotationCryo-EM half map of PRE-DNA/PR-B/SRC-2/p300
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PRE-DNA/PR-B/SRC-2/p300 complex

EntireName: PRE-DNA/PR-B/SRC-2/p300 complex
Components
  • Complex: PRE-DNA/PR-B/SRC-2/p300 complex

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Supramolecule #1: PRE-DNA/PR-B/SRC-2/p300 complex

SupramoleculeName: PRE-DNA/PR-B/SRC-2/p300 complex / type: complex / ID: 1 / Parent: 0 / Details: PRE DNA-bound PR-B/SRC-2/p300 complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 830 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: -0.0026000000000000003 µm / Nominal defocus min: -0.001 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 1201 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 194158
Startup modelType of model: NONE
Initial angle assignmentType: COMMON LINE / Software - Name: EMAN2 (ver. 2.3)
Final 3D classificationSoftware: (Name: RELION (ver. 3.1), cryoSPARC (ver. 3.3.2))
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: RELION (ver. 3.1), cryoSPARC (ver. 3.3.2))
Final reconstructionResolution.type: BY AUTHOR / Resolution: 19.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION (ver. 3.1), cryoSPARC (ver. 3.3.2)) / Number images used: 15779

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