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- EMDB-10443: Virion of native gene transfer agent (GTA) particle -

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Basic information

Entry
Database: EMDB / ID: EMD-10443
TitleVirion of native gene transfer agent (GTA) particle
Map datavirion of native GTA particle
SampleRhodobacter capsulatus DE442 != Rhodobacter capsulatus SB 1003

Rhodobacter capsulatus DE442

  • Virus: Rhodobacter capsulatus SB 1003 (bacteria)
    • Complex: Capsid
      • Protein or peptide: x 3 types
    • Complex: Head spike
    • Complex: Connector
      • Protein or peptide: x 2 types
    • Complex: Tail
      • Protein or peptide: x 4 types
    • Complex: BaseplateTripod (photography)
      • Protein or peptide: x 2 types
  • Ligand: x 1 types
Function / homology
Function and homology information


Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Bacteriophage phiJL001, Gp84, N-terminal / GTA TIM-barrel-like domain / Phage conserved hypothetical protein BR0599 / Uncharacterized conserved protein (DUF2163) / GTA TIM-barrel-like domain / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Phage conserved hypothetical protein ...Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Bacteriophage phiJL001, Gp84, N-terminal / GTA TIM-barrel-like domain / Phage conserved hypothetical protein BR0599 / Uncharacterized conserved protein (DUF2163) / GTA TIM-barrel-like domain / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Phage conserved hypothetical protein / Tail completion protein / Protein of unknown function (DUF3168) / Gene transfer agent, major tail protein / Phage portal protein, HK97 / Bacteriophage SPP1, head-tail adaptor / Phage head-tail joining protein / Tip attachment protein J / Putative phage tail protein / Bacteriophage SPP1, head-tail adaptor superfamily / Bacteriophage/Gene transfer agent portal protein / Phage portal protein / Phage major tail protein TP901-1 / Phage tail tube protein / Phage capsid / Phage capsid family / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein / Phage portal protein, HK97 family / Phage major capsid protein, HK97 family / Gene transfer agent protein / Head-tail adaptor protein / DUF3168 domain-containing protein / Phage major tail protein, TP901-1 family / TIGR02217 family protein / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesRhodobacter capsulatus SB 1003 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.54 Å
AuthorsBardy P / Fuzik T / Hrebik D / Pantucek R / Beatty JT / Plevka P
Funding support Czech Republic, 7 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Czech Republic)LQ1601 Czech Republic
European Regional Development FundCZ.1.05/1.1.00/02.0070 Czech Republic
Ministry of Education (MoE, Czech Republic)LM2011033 Czech Republic
Czech Science Foundation15-21631Y Czech Republic
Czech Science Foundation18-17810S Czech Republic
European Molecular Biology Organization (EMBO)3041 Czech Republic
Grant Agency of the Czech Republic18-13064S Czech Republic
CitationJournal: Nat Commun / Year: 2020
Title: Structure and mechanism of DNA delivery of a gene transfer agent.
Authors: Pavol Bárdy / Tibor Füzik / Dominik Hrebík / Roman Pantůček / J Thomas Beatty / Pavel Plevka /
Abstract: Alphaproteobacteria, which are the most abundant microorganisms of temperate oceans, produce phage-like particles called gene transfer agents (GTAs) that mediate lateral gene exchange. However, the ...Alphaproteobacteria, which are the most abundant microorganisms of temperate oceans, produce phage-like particles called gene transfer agents (GTAs) that mediate lateral gene exchange. However, the mechanism by which GTAs deliver DNA into cells is unknown. Here we present the structure of the GTA of Rhodobacter capsulatus (RcGTA) and describe the conformational changes required for its DNA ejection. The structure of RcGTA resembles that of a tailed phage, but it has an oblate head shortened in the direction of the tail axis, which limits its packaging capacity to less than 4,500 base pairs of linear double-stranded DNA. The tail channel of RcGTA contains a trimer of proteins that possess features of both tape measure proteins of long-tailed phages from the family Siphoviridae and tail needle proteins of short-tailed phages from the family Podoviridae. The opening of a constriction within the RcGTA baseplate enables the ejection of DNA into bacterial periplasm.
History
DepositionNov 1, 2019-
Header (metadata) releaseJul 22, 2020-
Map releaseJul 22, 2020-
UpdateJul 14, 2021-
Current statusJul 14, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tba
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10443.png

Downloads & links

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Map

FileDownload / File: emd_10443.map.gz / Format: CCP4 / Size: 3.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationvirion of native GTA particle
Voxel sizeX=Y=Z: 1.063 Å
Density
Contour LevelBy AUTHOR: 4.5 / Movie #1: 4.5
Minimum - Maximum0.0 - 37.205704
Average (Standard dev.)0.03369573 (±0.41731745)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions960960960
Spacing960960960
CellA=B=C: 1020.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0631.0631.063
M x/y/z960960960
origin x/y/z0.0000.0000.000
length x/y/z1020.4801020.4801020.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS960960960
D min/max/mean0.00037.2060.034

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Supplemental data

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Sample components

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Entire : Rhodobacter capsulatus DE442

EntireName: Rhodobacter capsulatus DE442 (bacteria)
Components
  • Virus: Rhodobacter capsulatus SB 1003 (bacteria)
    • Complex: Capsid
      • Protein or peptide: Phage major capsid protein, HK97 family
      • Protein or peptide: Uncharacterized protein
      • Protein or peptide: Uncharacterized protein
    • Complex: Head spike
    • Complex: Connector
      • Protein or peptide: Uncharacterized protein
      • Protein or peptide: Portal protein Rcc01684
    • Complex: Tail
      • Protein or peptide: Uncharacterized protein
      • Protein or peptide: Uncharacterized protein
      • Protein or peptide: Phage major tail protein, TP901-1 family
      • Protein or peptide: Uncharacterized protein
    • Complex: BaseplateTripod (photography)
      • Protein or peptide: Uncharacterized protein
      • Protein or peptide: Uncharacterized protein
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster

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Supramolecule #1: Rhodobacter capsulatus SB 1003

SupramoleculeName: Rhodobacter capsulatus SB 1003 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Details: phage-like particle mediating high-frequency horisontal gene transfer in Rhodobacterales species
NCBI-ID: 272942 / Sci species name: Rhodobacter capsulatus SB 1003 / Sci species strain: Gene transfer agent / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 880 KDa
Virus shellShell ID: 1 / Name: HK97-like oblate capsid / Diameter: 945.0 Å / T number (triangulation number): 3

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Supramolecule #2: Capsid

SupramoleculeName: Capsid / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 / Details: Oblate T=3 capsid
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria) / Strain: Gene transfer agent

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Supramolecule #3: Head spike

SupramoleculeName: Head spike / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 / Details: penton protrusion of the capsid
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria) / Strain: Gene transfer agent

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Supramolecule #4: Connector

SupramoleculeName: Connector / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5
Details: special 5-fold vertex of the capsid, interconnecting capsid to tail
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria) / Strain: Gene transfer agent

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Supramolecule #5: Tail

SupramoleculeName: Tail / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #6-#8, #11
Details: tubular structure interconnecting capsid to baseplate (host-recognition device)
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria) / Strain: Gene transfer agent

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Supramolecule #6: Baseplate

SupramoleculeName: Baseplate / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #9-#10
Details: host-recognition device present at the tip of the tail
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria) / Strain: Gene transfer agent

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Macromolecule #1: Phage major capsid protein, HK97 family

MacromoleculeName: Phage major capsid protein, HK97 family / type: protein_or_peptide / ID: 1 / Number of copies: 145 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 40.894988 KDa
SequenceString: MPEGADPVAE VKTALAGFLK EVKGFQDDVK TRLQQQEERV TMLQTKTYAG RHALAAAATE EAPHQKAFAA YLRTGDDDGL RGLSLEGKA LNSAVAAEGG YLVDPQTSET IRGVLRSTAS LRQIASVVNV EATSFDVLVD KTDMGSGWAS ETAALSETAT P QIDRITIP ...String:
MPEGADPVAE VKTALAGFLK EVKGFQDDVK TRLQQQEERV TMLQTKTYAG RHALAAAATE EAPHQKAFAA YLRTGDDDGL RGLSLEGKA LNSAVAAEGG YLVDPQTSET IRGVLRSTAS LRQIASVVNV EATSFDVLVD KTDMGSGWAS ETAALSETAT P QIDRITIP LHELAAMPKA SQRLLDDSAF DIETWLANRI ADKFARAEAA AFISGDGVDK PTGFLTKTKV ANGAWAWGSL GY VATGAAG DFAAVNASDA VVDLVYALGA EYRANASFVM NSKTAGAVRK MKDADGRFLW ADSLAAGEPA RLMGYPVLIA EDM PDIAAN AYAIAFGDFG NGYTIAERPD LRVLRDPFSA KPHVLFYASK RVGGDVSDFA AIKLLKFAA

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Macromolecule #2: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 2 / Number of copies: 55 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 9.104348 KDa
SequenceString:
MDVFAKHAVS LESPAVRHYE ITPSDSTDLA RRPRALRVQT GGTLVLRDET GITVTYTVFA GEILPVRPVR VLATGTTATA VGWE

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Macromolecule #3: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 3 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 32.996828 KDa
SequenceString: MIALGLGLGL AANGGPALRR YAVNGVAPVA VLDFERHFLS HPLALTRATS ATYADALRAV QTAPADTPRY DYSTGKRALL LEASATNLL PNSAQFEAAS WGKTRASVLA NAALAPNGTM TADKLVEDTS NNSHFVARTG TQIAAGTSVT ASIFVKAAER R WFALVTAD ...String:
MIALGLGLGL AANGGPALRR YAVNGVAPVA VLDFERHFLS HPLALTRATS ATYADALRAV QTAPADTPRY DYSTGKRALL LEASATNLL PNSAQFEAAS WGKTRASVLA NAALAPNGTM TADKLVEDTS NNSHFVARTG TQIAAGTSVT ASIFVKAAER R WFALVTAD SANAFRTTYF DLQTGTLGVV SQGAAGHVAQ IVAAGNGWYR CSVTQTQAAS GNFNFYPSVA SANGATSYPG DG ASGLYLW GAQLEAGAAV SSVIPTEAAA VTRAADLASV AVAAGSYDLR RVDAAGTAVT KGVAHPGGAL TIGAGSLYLL SLF PAGAL

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Macromolecule #4: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 20.956354 KDa
SequenceString: MMLNEVTAVP GTALPVAEFR DHLRLGTGFA DLGAEDAALL SYLRAAIAAI EGRTAKALIS RGFRLALTAW RWGDMQTLPI APVATVTAL RLVDAAGVET PVAAGWRLVP DMARPRIEAL GAMLPMIPTG GRVEIDFTAG FGASWSALPV DLAQAVFLLA A QYYELRHD ...String:
MMLNEVTAVP GTALPVAEFR DHLRLGTGFA DLGAEDAALL SYLRAAIAAI EGRTAKALIS RGFRLALTAW RWGDMQTLPI APVATVTAL RLVDAAGVET PVAAGWRLVP DMARPRIEAL GAMLPMIPTG GRVEIDFTAG FGASWSALPV DLAQAVFLLA A QYYELRHD GAAEGGAMPF GVMALIERWR TVRVLGGRP

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Macromolecule #5: Portal protein Rcc01684

MacromoleculeName: Portal protein Rcc01684 / type: protein_or_peptide / ID: 5 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 42.84691 KDa
SequenceString: MGLNFFRKAA PEVRTEPVAE RKASVTGRIV AMASGAGRPV WGPRDTVSLM RTGFAGNPVG FRSVKLIAEA TAAVPLICQD AERRYEIHP VLDLLRRPNA GQGRAELFEA LIGQILLSGN GYLEAVCPEP GVPRELHVLR SDRMAVVPGA DGWPVGYDYT V GGRKHRFD ...String:
MGLNFFRKAA PEVRTEPVAE RKASVTGRIV AMASGAGRPV WGPRDTVSLM RTGFAGNPVG FRSVKLIAEA TAAVPLICQD AERRYEIHP VLDLLRRPNA GQGRAELFEA LIGQILLSGN GYLEAVCPEP GVPRELHVLR SDRMAVVPGA DGWPVGYDYT V GGRKHRFD MTGHPDPICH IKSFHPTDDH YGLSPMQAAA VALDVHNAAS AWSKALLDNA ARPSGAIIYK GADGQGVLAP EQ YERLIFE METHHQGARN AGRPMLLEGG LDWKPMGFSP SDMEFHETKA AAAREIALAF GVPPMLIGIP GDATYANYAE ANR AFYRLT VLPLLTRVSA ALAWWLSGYL GAQIELKPDL DQVPALAVER DQLWARIGAA GFLSNSEKRV LLGLPPTAEG

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Macromolecule #6: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 13.871859 KDa
SequenceString:
MSYAVAGALQ AAVYQQLRAD AVLAALVGTA VYDAVPPGPL AGTYVSLGPE DVADASDKTG AGAVHDFVIS VITDAAGFAT AKAAAAAVS DALVGADLVL SRGRLVGLWF LRAKARRVEK ADMRRIDLVF RARVEG

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Macromolecule #7: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 7 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 12.403123 KDa
SequenceString:
MSRPRLNRLL VLEEAVRVAD GAGGHRLDWQ AKGEVWAEVT AGSGSERAGE FVTLASVPFT IVVRAAPVGA ARRPRPEQRF REGARIFRI LAVAERDREG HYLSCFAREE VVA

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Macromolecule #8: Phage major tail protein, TP901-1 family

MacromoleculeName: Phage major tail protein, TP901-1 family / type: protein_or_peptide / ID: 8 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 14.420007 KDa
SequenceString:
MAAQNGKDLL IKLDLTGSGQ FETIAGLRAT RISFNAETVD VTSLESQGGW RELLGGAGVR SASISGAGVF KDADTDERAR QIFFDGEVP EFQVIIPDFG IVQGPFMITS IDYAGSHNGE ASYELAMASA GALSFTAI

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Macromolecule #9: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 31.690734 KDa
SequenceString: MAYPESLKAH LQGGVTTLAR AWALARADGR VLGFTDHDVV LRFDGISFEP GSGMTAKAVL QGTGLSVDNT ESYGALSSEA ITEADLLAG RYDGAAVTVW LVNWADPAMR AVIFRGHLGE VSRGAGAFTA ELRGLTAALG QEQGRIYHPR CAAVLGDGRC R FDLTKDGY ...String:
MAYPESLKAH LQGGVTTLAR AWALARADGR VLGFTDHDVV LRFDGISFEP GSGMTAKAVL QGTGLSVDNT ESYGALSSEA ITEADLLAG RYDGAAVTVW LVNWADPAMR AVIFRGHLGE VSRGAGAFTA ELRGLTAALG QEQGRIYHPR CAAVLGDGRC R FDLTKDGY ALEAALGGVD EAVVLRLAEG AGFEDRWFEK GRLVVLDGAA AGLIGVVKND RLQADGSRLI ELWQRLGANP VA GDRVRIE PGCDKRAGTC RLKFDNFLNF RGFPHIPGED WMVSYPVQSG TNDGGSLFR

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Macromolecule #10: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 10 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 138.527359 KDa
SequenceString: MATILLSAAG AAIGGGFGGT VLGLSGAVIG RAVGATLGRV IDQRLLGSGS QSVETGRVDR LRLSSASEGE AVGRLWGRMR VAGQVIWAT RFFESASVEK SGKGVPRATV TSYSYSLSLA LALCEGEILR VGRVWADGSE IEVSGLNMRV YRGGEDQLPD P KIAAVEGA ...String:
MATILLSAAG AAIGGGFGGT VLGLSGAVIG RAVGATLGRV IDQRLLGSGS QSVETGRVDR LRLSSASEGE AVGRLWGRMR VAGQVIWAT RFFESASVEK SGKGVPRATV TSYSYSLSLA LALCEGEILR VGRVWADGSE IEVSGLNMRV YRGGEDQLPD P KIAAVEGA EAAPAYRGIA YVVLEDLQLA PFGNRVPQFT FEVVRAAQGA LAEAEPDLTR GLRAVALIPG TGEYALATTP VY LATGSGV TATQGVANQN APGGQTDLVA ALERLDEELP NCGAVSLVVS WFGDDLRCGA CDVKPKVASV AEEGANMPWR VAG LERAGA EEVPRLSGQS VYGGTPADAA VIEAIAALRA AGKAVTFYPF ILMAQLAGNG LPDPWNPGSA QPALPWRGRI TLSV APGRA GSPDGTAAAE AQVAGFFGAA SPGDSAIAGG EVVYSGPEEW SMRRFILHYA HLCQLAGGVD AFCIGTEMVA LTQIR GPSN SFPAVAAFRQ LAGEVKAILG PGCKIGYAAD WSEYWGYAPG NGERFFHLDP LWADENIDFI GIDNYLPLSD WRDGAD HAD AGWGSIHALD YLRSNIEGGE YYDWFYAAPE HRAAQIRTPI TDGDHDEPWI WRAKDLRNWW LNDHHERVGG LRSEVAT AW VPQSKPIWFT EMGCAAIDKG TNQPNKFLDP KSSESGLPHH SDGRRDELIQ MQYLRAMTGY WGEAARNPVS AVYGGPML D MSRAHVWAWD ARPWPQFPLN TALWSDGENY ARGHWISGRA VAQPLASVVA EICGAAGITE IDVSGLYGLV RGYTMTGDQ TGRAGLQALM LAYGFEALER DGQLVFRMRD GRVAADLAAA DLALGEGEAV VETVRAAEAE IAGRVRLAYV EAEGDFEVKA VEAVFPDAA AGAAAGSELS LALTRAQAQG IVGRWLAEAR VARDTARFAL PPSRGHLGTG DVVRLDLPEG KRRYRIDRVE Q AGLIQVEA VRVEPGIYAP ADEVEDPASL RPFAAPVPVT AVFLDLPLMK GDEDPVAPHL AVTATPWPGT VAVWSSDEDA GY ALNASLG TRAVIGQTLT PLFRARPGVW DRGAALRVRL ASGALDSATA AKVLNGANAM AIGDGSSENW EVFQFAEAAL VEG KIWDIS LRLRGQLGTD ALMPEVWPEG SVVVALNGAP EQILLPSAAR GLARHYRIGA AVRSYDDPSF VHRIEAFAGA GLRP FSPCH LRAEPGASGW AFRWVRRTRI DGDSWQGYEV PLGETAELYL VRVLEGTAVK REVTVGEASW SYPAALQAAD GIAGA FTLE VAQVSDVYGP GLAARITVGA

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Macromolecule #11: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 11 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 22.985713 KDa
SequenceString: MAFHEVRFPA NLSFGSVGGP ERRTEIVTLS SGHEERNSPW AHSRRHYDAG VGLRSLDDVE RLIAFFEARG GQLHGFRWKD WADFKSCPA SRAVAHEDQL IGMGDGVTTA FQLVKTYVSG GQSYLRPIVK PVEGTVKLGI AGDHQAEAVN FAVDHATGIV S FNEPPPQG ...String:
MAFHEVRFPA NLSFGSVGGP ERRTEIVTLS SGHEERNSPW AHSRRHYDAG VGLRSLDDVE RLIAFFEARG GQLHGFRWKD WADFKSCPA SRAVAHEDQL IGMGDGVTTA FQLVKTYVSG GQSYLRPIVK PVEGTVKLGI AGDHQAEAVN FAVDHATGIV S FNEPPPQG ARVTAGFEFD VPVRFDTDRI AVSVQSFQAG DLPQVPVVEV RI

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Macromolecule #12: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 12 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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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

Concentration20 mg/mL
BufferpH: 7.8
Component:
ConcentrationNameFormula
10.0 mMTris
1.0 mMNaClSodium chloride
1.0 mMMgCl2
1.0 mMCaCl2
0.01 mg/mlBovine serum albumin

Details: G-buffer, doi: 10.1016/0003-9861(77)90508-2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 11.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 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 opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -3.0 µm / Nominal defocus min: -1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 42.75 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 53432
CTF correctionSoftware - Name: RELION (ver. 2.1)
Startup modelType of model: INSILICO MODEL / Details: gradient descent method implemented in RELION
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0)
Details: Map is generated from merged maps of GTA capsid (EMD-10442), neck (EMD-10477), tail tube (EMD-10478) and baseplate (EMD-10490). Internal map regions corresponds to the genome from asymmetric ...Details: Map is generated from merged maps of GTA capsid (EMD-10442), neck (EMD-10477), tail tube (EMD-10478) and baseplate (EMD-10490). Internal map regions corresponds to the genome from asymmetric reconstruction (EMD-10568) and tape-measure protein density from C3 reconstruction of tail tube (EMD-10570). Shown resoluton value corresponds to the map with lowest resolution (C3 tail tube).
Number images used: 27724
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6tba:
Virion of native gene transfer agent (GTA) particle

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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