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- EMDB-4069: RadA dodecamer on ssDNA -

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Basic information

Entry
Database: EMDB / ID: EMD-4069
TitleRadA dodecamer on ssDNA
Map data
Sample
  • Complex: Complex of RadA with ssDNA
    • Protein or peptide: RadA
    • DNA: M13mp18
Biological speciesStreptococcus pneumoniae (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsRapisarda C / Fronzes R
CitationJournal: To be published
Title: RadA dodecamer on ssDNA
Authors: Rapisarda C / Fronzes R
History
DepositionJul 22, 2016-
Header (metadata) releaseFeb 8, 2017-
Map releaseJan 17, 2018-
UpdateJan 24, 2018-
Current statusJan 24, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4069.png

Downloads & links

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Map

FileDownload / File: emd_4069.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.99 Å
Density
Contour LevelBy AUTHOR: 0.039 / Movie #1: 0.04
Minimum - Maximum-0.04329799 - 0.107960224
Average (Standard dev.)0.00038854362 (±0.0075932513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 390.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.991.991.99
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z390.040390.040390.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS196196196
D min/max/mean-0.0430.1080.000

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Supplemental data

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Sample components

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Entire : Complex of RadA with ssDNA

EntireName: Complex of RadA with ssDNA
Components
  • Complex: Complex of RadA with ssDNA
    • Protein or peptide: RadA
    • DNA: M13mp18

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Supramolecule #1: Complex of RadA with ssDNA

SupramoleculeName: Complex of RadA with ssDNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptococcus pneumoniae (bacteria) / Strain: R6
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21 / Recombinant plasmid: pASK IBA13
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: RadA

MacromoleculeName: RadA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pneumoniae (bacteria) / Strain: R6
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASWSHPQFE KSGGGGGLVP RGSKKKATFV CQNCGYNSPK YLGRCPNCGS WSSFVEEVEV AEVKNARVSL TGEKTKPMKL AEVTSINVNR TKTEMEEFNR VLGGGVVPGS LVLIGGDPGI GKSTLLLQVS TQLSQVGTVL YVSGEESAQQ IKLRAERLGD IDSEFYLYAE ...String:
MASWSHPQFE KSGGGGGLVP RGSKKKATFV CQNCGYNSPK YLGRCPNCGS WSSFVEEVEV AEVKNARVSL TGEKTKPMKL AEVTSINVNR TKTEMEEFNR VLGGGVVPGS LVLIGGDPGI GKSTLLLQVS TQLSQVGTVL YVSGEESAQQ IKLRAERLGD IDSEFYLYAE TNMQSVRAEV ERIQPDFLII DSIQTIMSPE ISGVQGSVSQ VREVTAELMQ LAKTNNIAIF IVGHVTKEGT LAGPRMLEHM VDTVLYFEGE RHHTFRILRA VKNRFGSTNE IGIFEMQSGG LVEVLNPSQV FLEERLDGAT GSSIVVTMEG TRPILAEVQA LVTPTMFGNA KRTTTGLDFN RASLIMAVLE KRAGLLLQNQ DAYLKSAGGV KLDEPAIDLA VAVAIASSYK DKPTNPQECF VGELGLTGEI RRVNRIEQRI NEAAKLGFTK IYVPKNSLTG ITLPKEIQVI GVTTIQEVLK KVF

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Macromolecule #2: M13mp18

MacromoleculeName: M13mp18 / type: dna / ID: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString: AATGCTACTA CTATTAGTAG AATTGATGCC ACCTTTTCAG CTCGCGCCCC AAATGAAAAT ATAGCTAAAC AGGTTATTGA CCATTTGCG AAATGTATCT AATGGTCAAA CTAAATCTAC TCGTTCGCAG AATTGGGAAT CAACTGTTAT ATGGAATGAA A CTTCCAGA ...String:
AATGCTACTA CTATTAGTAG AATTGATGCC ACCTTTTCAG CTCGCGCCCC AAATGAAAAT ATAGCTAAAC AGGTTATTGA CCATTTGCG AAATGTATCT AATGGTCAAA CTAAATCTAC TCGTTCGCAG AATTGGGAAT CAACTGTTAT ATGGAATGAA A CTTCCAGA CACCGTACTT TAGTTGCATA TTTAAAACAT GTTGAGCTAC AGCATTATAT TCAGCAATTA AGCTCTAAGC CA TCCGCAA AAATGACCTC TTATCAAAAG GAGCAATTAA AGGTACTCTC TAATCCTGAC CTGTTGGAGT TTGCTTCCGG TCT GGTTCG CTTTGAAGCT CGAATTAAAA CGCGATATTT GAAGTCTTTC GGGCTTCCTC TTAATCTTTT TGATGCAATC CGCT TTGCT TCTGACTATA ATAGTCAGGG TAAAGACCTG ATTTTTGATT TATGGTCATT CTCGTTTTCT GAACTGTTTA AAGCA TTTG AGGGGGATTC AATGAATATT TATGACGATT CCGCAGTATT GGACGCTATC CAGTCTAAAC ATTTTACTAT TACCCC CTC TGGCAAAACT TCTTTTGCAA AAGCCTCTCG CTATTTTGGT TTTTATCGTC GTCTGGTAAA CGAGGGTTAT GATAGTG TT GCTCTTACTA TGCCTCGTAA TTCCTTTTGG CGTTATGTAT CTGCATTAGT TGAATGTGGT ATTCCTAAAT CTCAACTG A TGAATCTTTC TACCTGTAAT AATGTTGTTC CGTTAGTTCG TTTTATTAAC GTAGATTTTT CTTCCCAACG TCCTGACTG GTATAATGAG CCAGTTCTTA AAATCGCATA AGGTAATTCA CAATGATTAA AGTTGAAATT AAACCATCTC AAGCCCAATT TACTACTCG TTCTGGTGTT TCTCGTCAGG GCAAGCCTTA TTCACTGAAT GAGCAGCTTT GTTACGTTGA TTTGGGTAAT G AATATCCG GTTCTTGTCA AGATTACTCT TGATGAAGGT CAGCCAGCCT ATGCGCCTGG TCTGTACACC GTTCATCTGT CC TCTTTCA AAGTTGGTCA GTTCGGTTCC CTTATGATTG ACCGTCTGCG CCTCGTTCCG GCTAAGTAAC ATGGAGCAGG TCG CGGATT TCGACACAAT TTATCAGGCG ATGATACAAA TCTCCGTTGT ACTTTGTTTC GCGCTTGGTA TAATCGCTGG GGGT CAAAG ATGAGTGTTT TAGTGTATTC TTTTGCCTCT TTCGTTTTAG GTTGGTGCCT TCGTAGTGGC ATTACGTATT TTACC CGTT TAATGGAAAC TTCCTCATGA AAAAGTCTTT AGTCCTCAAA GCCTCTGTAG CCGTTGCTAC CCTCGTTCCG ATGCTG TCT TTCGCTGCTG AGGGTGACGA TCCCGCAAAA GCGGCCTTTA ACTCCCTGCA AGCCTCAGCG ACCGAATATA TCGGTTA TG CGTGGGCGAT GGTTGTTGTC ATTGTCGGCG CAACTATCGG TATCAAGCTG TTTAAGAAAT TCACCTCGAA AGCAAGCT G ATAAACCGAT ACAATTAAAG GCTCCTTTTG GAGCCTTTTT TTTGGAGATT TTCAACGTGA AAAAATTATT ATTCGCAAT TCCTTTAGTT GTTCCTTTCT ATTCTCACTC CGCTGAAACT GTTGAAAGTT GTTTAGCAAA ATCCCATACA GAAAATTCAT TTACTAACG TCTGGAAAGA CGACAAAACT TTAGATCGTT ACGCTAACTA TGAGGGCTGT CTGTGGAATG CTACAGGCGT T GTAGTTTG TACTGGTGAC GAAACTCAGT GTTACGGTAC ATGGGTTCCT ATTGGGCTTG CTATCCCTGA AAATGAGGGT GG TGGCTCT GAGGGTGGCG GTTCTGAGGG TGGCGGTTCT GAGGGTGGCG GTACTAAACC TCCTGAGTAC GGTGATACAC CTA TTCCGG GCTATACTTA TATCAACCCT CTCGACGGCA CTTATCCGCC TGGTACTGAG CAAAACCCCG CTAATCCTAA TCCT TCTCT TGAGGAGTCT CAGCCTCTTA ATACTTTCAT GTTTCAGAAT AATAGGTTCC GAAATAGGCA GGGGGCATTA ACTGT TTAT ACGGGCACTG TTACTCAAGG CACTGACCCC GTTAAAACTT ATTACCAGTA CACTCCTGTA TCATCAAAAG CCATGT ATG ACGCTTACTG GAACGGTAAA TTCAGAGACT GCGCTTTCCA TTCTGGCTTT AATGAGGATT TATTTGTTTG TGAATAT CA AGGCCAATCG TCTGACCTGC CTCAACCTCC TGTCAATGCT GGCGGCGGCT CTGGTGGTGG TTCTGGTGGC GGCTCTGA G GGTGGTGGCT CTGAGGGTGG CGGTTCTGAG GGTGGCGGCT CTGAGGGAGG CGGTTCCGGT GGTGGCTCTG GTTCCGGTG ATTTTGATTA TGAAAAGATG GCAAACGCTA ATAAGGGGGC TATGACCGAA AATGCCGATG AAAACGCGCT ACAGTCTGAC GCTAAAGGC AAACTTGATT CTGTCGCTAC TGATTACGGT GCTGCTATCG ATGGTTTCAT TGGTGACGTT TCCGGCCTTG C TAATGGTA ATGGTGCTAC TGGTGATTTT GCTGGCTCTA ATTCCCAAAT GGCTCAAGTC GGTGACGGTG ATAATTCACC TT TAATGAA TAATTTCCGT CAATATTTAC CTTCCCTCCC TCAATCGGTT GAATGTCGCC CTTTTGTCTT TGGCGCTGGT AAA CCATAT GAATTTTCTA TTGATTGTGA CAAAATAAAC TTATTCCGTG GTGTCTTTGC GTTTCTTTTA TATGTTGCCA CCTT TATGT ATGTATTTTC TACGTTTGCT AACATACTGC GTAATAAGGA GTCTTAATCA TGCCAGTTCT TTTGGGTATT CCGTT ATTA TTGCGTTTCC TCGGTTTCCT TCTGGTAACT TTGTTCGGCT ATCTGCTTAC TTTTCTTAAA AAGGGCTTCG GTAAGA TAG CTATTGCTAT TTCATTGTTT CTTGCTCTTA TTATTGGGCT TAACTCAATT CTTGTGGGTT ATCTCTCTGA TATTAGC GC TCAATTACCC TCTGACTTTG TTCAGGGTGT TCAGTTAATT CTCCCGTCTA ATGCGCTTCC CTGTTTTTAT GTTATTCT C TCTGTAAAGG CTGCTATTTT CATTTTTGAC GTTAAACAAA AAATCGTTTC TTATTTGGAT TGGGATAAAT AATATGGCT GTTTATTTTG TAACTGGCAA ATTAGGCTCT GGAAAGACGC TCGTTAGCGT TGGTAAGATT CAGGATAAAA TTGTAGCTGG GTGCAAAAT AGCAACTAAT CTTGATTTAA GGCTTCAAAA CCTCCCGCAA GTCGGGAGGT TCGCTAAAAC GCCTCGCGTT C TTAGAATA CCGGATAAGC CTTCTATATC TGATTTGCTT GCTATTGGGC GCGGTAATGA TTCCTACGAT GAAAATAAAA AC GGCTTGC TTGTTCTCGA TGAGTGCGGT ACTTGGTTTA ATACCCGTTC TTGGAATGAT AAGGAAAGAC AGCCGATTAT TGA TTGGTT TCTACATGCT CGTAAATTAG GATGGGATAT TATTTTTCTT GTTCAGGACT TATCTATTGT TGATAAACAG GCGC GTTCT GCATTAGCTG AACATGTTGT TTATTGTCGT CGTCTGGACA GAATTACTTT ACCTTTTGTC GGTACTTTAT ATTCT CTTA TTACTGGCTC GAAAATGCCT CTGCCTAAAT TACATGTTGG CGTTGTTAAA TATGGCGATT CTCAATTAAG CCCTAC TGT TGAGCGTTGG CTTTATACTG GTAAGAATTT GTATAACGCA TATGATACTA AACAGGCTTT TTCTAGTAAT TATGATT CC GGTGTTTATT CTTATTTAAC GCCTTATTTA TCACACGGTC GGTATTTCAA ACCATTAAAT TTAGGTCAGA AGATGAAA T TAACTAAAAT ATATTTGAAA AAGTTTTCTC GCGTTCTTTG TCTTGCGATT GGATTTGCAT CAGCATTTAC ATATAGTTA TATAACCCAA CCTAAGCCGG AGGTTAAAAA GGTAGTCTCT CAGACCTATG ATTTTGATAA ATTCACTATT GACTCTTCTC AGCGTCTTA ATCTAAGCTA TCGCTATGTT TTCAAGGATT CTAAGGGAAA ATTAATTAAT AGCGACGATT TACAGAAGCA A GGTTATTC ACTCACATAT ATTGATTTAT GTACTGTTTC CATTAAAAAA GGTAATTCAA ATGAAATTGT TAAATGTAAT TA ATTTTGT TTTCTTGATG TTTGTTTCAT CATCTTCTTT TGCTCAGGTA ATTGAAATGA ATAATTCGCC TCTGCGCGAT TTT GTAACT TGGTATTCAA AGCAATCAGG CGAATCCGTT ATTGTTTCTC CCGATGTAAA AGGTACTGTT ACTGTATATT CATC TGACG TTAAACCTGA AAATCTACGC AATTTCTTTA TTTCTGTTTT ACGTGCAAAT AATTTTGATA TGGTAGGTTC TAACC CTTC CATTATTCAG AAGTATAATC CAAACAATCA GGATTATATT GATGAATTGC CATCATCTGA TAATCAGGAA TATGAT GAT AATTCCGCTC CTTCTGGTGG TTTCTTTGTT CCGCAAAATG ATAATGTTAC TCAAACTTTT AAAATTAATA ACGTTCG GG CAAAGGATTT AATACGAGTT GTCGAATTGT TTGTAAAGTC TAATACTTCT AAATCCTCAA ATGTATTATC TATTGACG G CTCTAATCTA TTAGTTGTTA GTGCTCCTAA AGATATTTTA GATAACCTTC CTCAATTCCT TTCAACTGTT GATTTGCCA ACTGACCAGA TATTGATTGA GGGTTTGATA TTTGAGGTTC AGCAAGGTGA TGCTTTAGAT TTTTCATTTG CTGCTGGCTC TCAGCGTGG CACTGTTGCA GGCGGTGTTA ATACTGACCG CCTCACCTCT GTTTTATCTT CTGCTGGTGG TTCGTTCGGT A TTTTTAAT GGCGATGTTT TAGGGCTATC AGTTCGCGCA TTAAAGACTA ATAGCCATTC AAAAATATTG TCTGTGCCAC GT ATTCTTA CGCTTTCAGG TCAGAAGGGT TCTATCTCTG TTGGCCAGAA TGTCCCTTTT ATTACTGGTC GTGTGACTGG TGA ATCTGC CAATGTAAAT AATCCATTTC AGACGATTGA GCGTCAAAAT GTAGGTATTT CCATGAGCGT TTTTCCTGTT GCAA TGGCT GGCGGTAATA TTGTTCTGGA TATTACCAGC AAGGCCGATA GTTTGAGTTC TTCTACTCAG GCAAGTGATG TTATT ACTA ATCAAAGAAG TATTGCTACA ACGGTTAATT TGCGTGATGG ACAGACTCTT TTACTCGGTG GCCTCACTGA TTATAA AAA CACTTCTCAG GATTCTGGCG TACCGTTCCT GTCTAAAATC CCTTTAATCG GCCTCCTGTT TAGCTCCCGC TCTGATT CT AACGAGGAAA GCACGTTATA CGTGCTCGTC AAAGCAACCA TAGTACGCGC CCTGTAGCGG CGCATTAAGC GCGGCGGG T GTGGTGGTTA CGCGCAGCGT GACCGCTACA CTTGCCAGCG CCCTAGCGCC CGCTCCTTTC GCTTTCTTCC CTTCCTTTC TCGCCACGTT CGCCGGCTTT CCCCGTCAAG CTCTAAATCG GGGGCTCCCT TTAGGGTTCC GATTTAGTGC TTTACGGCAC CTCGACCCC AAAAAACTTG ATTTGGGTGA TGGTTCACGT AGTGGGCCAT CGCCCTGATA GACGGTTTTT CGCCCTTTGA C GTTGGAGT CCACGTTCTT TAATAGTGGA CTCTTGTTCC AAACTGGAAC AACACTCAAC CCTATCTCGG GCTATTCTTT TG ATTTATA AGGGATTTTG CCGATTTCGG AACCACCATC AAACAGGATT TTCGCCTGCT GGGGCAAACC AGCGTGGACC GCT TGCTGC AACTCTCTCA GGGCCAGGCG GTGAAGGGCA ATCAGCTGTT GCCCGTCTCA CTGGTGAAAA GAAAAACCAC CCTG GCGCC CAATACGCAA ACCGCCTCTC CCCGCGCGTT GGCCGATTCA TTAATGCAGC TGGCACGACA GGTTTCCCGA CTGGA AAGC GGGCAGTGAG CGCAACGCAA TTAATGTGAG TTAGCTCACT CATTAGGCAC CCCAGGCTTT ACACTTTATG CTTCCG GCT CGTATGTTGT GTGGAATTGT GAGCGGATAA CAATTTCACA CAGGAAACAG CTATGACCAT GATTACGAAT TCGAGCT CG GTACCCGGGG ATCCTCTAGA GTCGACCTGC AGGCATGCAA GCTTGGCACT GGCCGTCGTT TTACAACGTC GTGACTGG G AAAACCCTGG CGTTACCCAA CTTAATCGCC TTGCAGCACA TCCCCCTTTC GCCAGCTGGC GTAATAGCGA AGAGGCCCG CACCGATCGC CCTTCCCAAC AGTTGCGCAG CCTGAATGGC GAATGGCGCT TTGCCTGGTT TCCGGCACCA GAAGCGGTGC CGGAAAGCT GGCTGGAGTG CGATCTTCCT GAGGCCGATA CTGTCGTCGT CCCCTCAAAC TGGCAGATGC ACGGTTACGA T GCGCCCAT CTACACCAAC GTGACCTATC CCATTACGGT CAATCCGCCG TTTGTTCCCA CGGAGAATCC GACGGGTTGT TA CTCGCTC ACATTTAATG TTGATGAAAG CTGGCTACAG GAAGGCCAGA CGCGAATTAT TTTTGATGGC GTTCCTATTG GTT AAAAAA TGAGCTGATT TAACAAAAAT TTAATGCGAA TTTTAACAAA ATATTAACGT TTACAATTTA AATATTTGCT TATA CAATC TTCCTGTTTT TGGGGCTTTT CTGATTATCA ACCGGGGTAC ATATGATTGA CATGCTAGTT TTACGATTAC CGTTC ATCG ATTCTCTTGT TTGCTCCAGA CTCTCAGGCA ATGACCTGAT AGCCTTTGTA GATCTCTCAA AAATAGCTAC CCTCTC CGG CATTAATTTA TCAGCTAGAA CGGTTGAATA TCATATTGAT GGTGATTTGA CTGTCTCCGG CCTTTCTCAC CCTTTTG AA TCTTTACCTA CACATTACTC AGGCATTGCA TTTAAAATAT ATGAGGGTTC TAAAAATTTT TATCCTTGCG TTGAAATA A AGGCTTCTCC CGCAAAAGTA TTACAGGGTC ATAATGTTTT TGGTACAACC GATTTAGCTT TATGCTCTGA GGCTTTATT GCTTAATTTT GCTAATTCTT TGCCTTGCCT GTATGATTTA TTGGATGTT

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.04 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMKCLPotassium Chloride
0.5 mMDTTDithiothreitol
2.0 mMMgAcMagnesium acetate
2.0 mMATPySAdenosine 5'-(y-Thiotriphosphate)
StainingType: NEGATIVE / Material: Uranyl Acetate
GridModel: EMS / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Number grids imaged: 1 / Number real images: 500 / Average exposure time: 1.0 sec. / Average electron dose: 11.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 18000
CTF correctionSoftware - Name: EMAN
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: EMAN (ver. 2)
Final 3D classificationNumber classes: 2 / Avg.num./class: 9000 / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 9000
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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