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- EMDB-27537: Spatial Definition of the Human Progesterone Receptor-B Transcrip... -

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Basic information

Entry
Database: EMDB / ID: EMD-27537
TitleSpatial Definition of the Human Progesterone Receptor-B Transcriptional Complex
Map dataCryo-EM map of PRE-DNA/PR-B
Sample
  • Complex: PRE-DNA/PR-B 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: 10.91 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

Downloads & links

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Map

FileDownload / File: emd_27537.map.gz / Format: CCP4 / Size: 113.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of PRE-DNA/PR-B
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 310 pix.
= 300.08 Å
0.97 Å/pix.
x 310 pix.
= 300.08 Å
0.97 Å/pix.
x 310 pix.
= 300.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.968 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.28515884 - 1.2925155
Average (Standard dev.)0.01847755 (±0.08439577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions310310310
Spacing310310310
CellA=B=C: 300.08 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 with a Fab binding...

Fileemd_27537_additional_1.map
AnnotationCryo-EM map of PRE-DNA/PR-B with a Fab binding to its N-terminal AF3 region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Cryo-EM map of PRE-DNA/PR-B with a Fab binding...

Fileemd_27537_additional_2.map
AnnotationCryo-EM map of PRE-DNA/PR-B with a Fab binding to its C-terminal LBD region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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

Fileemd_27537_half_map_1.map
AnnotationCryo-EM half map of PRE-DNA/PR-B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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

Fileemd_27537_half_map_2.map
AnnotationCryo-EM half map of PRE-DNA/PR-B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : PRE-DNA/PR-B complex

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

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Supramolecule #1: PRE-DNA/PR-B complex

SupramoleculeName: PRE-DNA/PR-B complex / type: complex / ID: 1 / Parent: 0 / Details: Progesterone Receptor and DNA complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 370 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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 7011 / Average exposure time: 8.0 sec. / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -0.0026000000000000003 µm / Nominal defocus min: -0.001 µm

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Image processing

Particle selectionNumber selected: 341819
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION (ver. 3.1), cryoSPARC (ver. 3.3.2)) / Number images used: 42619
Initial angle assignmentType: COMMON LINE / Software - Name: EMAN2 (ver. 2.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: RELION (ver. 3.1), cryoSPARC (ver. 3.3.2))
Final 3D classificationSoftware: (Name: RELION (ver. 3.1), cryoSPARC (ver. 3.3.2))

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