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- EMDB-33097: Cryo-EM structure of PvrA-DNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-33097
TitleCryo-EM structure of PvrA-DNA complex
Map data
Sample
  • Complex: PvrA-DNA
    • DNA: fadD1
    • DNA: fadD1
    • Protein or peptide: Probable transcriptional regulator
KeywordsTetR / transcriptional regulator / DNA binding protein / TRANSCRIPTION
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
Tetracyclin repressor-like, C-terminal domain (WHG) / Tetracyclin repressor-like, C-terminal domain / : / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
Probable transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsZhu YB / Su ZM / Bao R
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81871615 China
CitationJournal: To be published
Title: The Pseudomonas aeruginosa regulator PvrA binds cooperatively to multiple pseudo-palindromic sites to efficiently stimulate target gene
Authors: Zhu YB / Luo BN / Song YJ / Su ZM / Bao R
History
DepositionMar 18, 2022-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33097.png

Downloads & links

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Map

FileDownload / File: emd_33097.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 400 pix.
= 340. Å		0.85 Å/pix.
x 400 pix.
= 340. Å		0.85 Å/pix.
x 400 pix.
= 340. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.547837 - 1.1801033
Average (Standard dev.)0.00027325604 (±0.020700783)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 340.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : PvrA-DNA

EntireName: PvrA-DNA
Components
  • Complex: PvrA-DNA
    • DNA: fadD1
    • DNA: fadD1
    • Protein or peptide: Probable transcriptional regulator

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Supramolecule #1: PvrA-DNA

SupramoleculeName: PvrA-DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: fadD1

MacromoleculeName: fadD1 / type: dna / ID: 1 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 13.225492 KDa
SequenceString:
(DG)(DA)(DC)(DC)(DG)(DT)(DG)(DA)(DC)(DC) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DA)(DT)(DG) (DT)(DC)(DT)(DC)(DG)(DG)(DT)(DC)(DA) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DG)(DA)(DC) (DC) (DG)(DA)(DA)

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Macromolecule #2: fadD1

MacromoleculeName: fadD1 / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 13.252534 KDa
SequenceString:
(DT)(DT)(DC)(DG)(DG)(DT)(DC)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DT)(DG)(DA)(DC)(DC)(DG) (DA)(DG)(DA)(DC)(DA)(DT)(DT)(DA)(DG) (DT)(DC)(DT)(DC)(DG)(DG)(DT)(DC)(DA)(DC) (DG) (DG)(DT)(DC)

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Macromolecule #3: Probable transcriptional regulator

MacromoleculeName: Probable transcriptional regulator / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Molecular weightTheoretical: 25.07177 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MQKEPRKVRE FRRREQEILD TALKLFLEQG EDSVTVEMIA DAVGIGKGTI YKHFKSKAEI YLRLMLDYER DLAALFHSED VARDKEALS RAYFEFRMRD PQRYRLFDRL EEKVVKTSQV PEMVEELHKI RASNFERLTQ LIKERIADGK LENVPPYFHY C AAWALVHG ...String:
MQKEPRKVRE FRRREQEILD TALKLFLEQG EDSVTVEMIA DAVGIGKGTI YKHFKSKAEI YLRLMLDYER DLAALFHSED VARDKEALS RAYFEFRMRD PQRYRLFDRL EEKVVKTSQV PEMVEELHKI RASNFERLTQ LIKERIADGK LENVPPYFHY C AAWALVHG AVALYHSPFW REVLEDQEGF FHFLMDIGVR MGNKRKREGD APSA

UniProtKB: Probable transcriptional regulator

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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

BufferpH: 7.8
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 58.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 883805
Startup modelType of model: OTHER / Details: Generated by ab-initio reconstruction in cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Software - details: Non-uniform reconstruction / Number images used: 391711
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 6 / Avg.num./class: 148962 / Software - Name: cryoSPARC (ver. 3.3.1)

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Atomic model buiding 1

Initial modelPDB ID:

5daj


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7xaq:
Cryo-EM structure of PvrA-DNA complex

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