[English] 日本語
Yorodumi
- EMDB-12029: Cryo-EM structure of the contractile injection system base plate ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12029
TitleCryo-EM structure of the contractile injection system base plate from Anabaena PCC7120
Map data
Sample
  • Complex: Base plate and spike complex (C3) of the Anabaena PCC7120 contractile injection system
    • Protein or peptide: x 11 types
Function / homology
Function and homology information


membrane => GO:0016020 / structural molecule activity
Similarity search - Function
YegP-like superfamily / Baseplate protein J-like / Baseplate J-like protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Type VI secretion system, RhsGE-associated Vgr protein / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / Gp5/Type VI secretion system Vgr protein, OB-fold domain ...YegP-like superfamily / Baseplate protein J-like / Baseplate J-like protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Type VI secretion system, RhsGE-associated Vgr protein / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Vgr protein, OB-fold domain superfamily / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
All3325 protein / All3324 protein / All3323 protein / Asl3322 protein / All3321 protein / All3320 protein / All3318 protein / All3317 protein / All3316 protein / All3315 protein / All3314 protein
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria) / Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsEisenstein F / Weiss GL / Pilhofer M
CitationJournal: Nat Microbiol / Year: 2022
Title: Structure of a thylakoid-anchored contractile injection system in multicellular cyanobacteria.
Authors: Gregor L Weiss / Fabian Eisenstein / Ann-Katrin Kieninger / Jingwei Xu / Hannah A Minas / Milena Gerber / Miki Feldmüller / Iris Maldener / Karl Forchhammer / Martin Pilhofer /
Abstract: Contractile injection systems (CISs) mediate cell-cell interactions by phage tail-like structures, using two distinct modes of action: extracellular CISs are released into the medium, while type 6 ...Contractile injection systems (CISs) mediate cell-cell interactions by phage tail-like structures, using two distinct modes of action: extracellular CISs are released into the medium, while type 6 secretion systems (T6SSs) are attached to the cytoplasmic membrane and function upon cell-cell contact. Here, we characterized a CIS in the multicellular cyanobacterium Anabaena, with features distinct from extracellular CISs and T6SSs. Cryo-electron tomography of focused ion beam-milled cells revealed that CISs were anchored in thylakoid membrane stacks, facing the cell periphery. Single particle cryo-electron microscopy showed that this unique in situ localization was mediated by extensions of tail fibre and baseplate components. On stress, cyanobacteria induced the formation of ghost cells, presenting thylakoid-anchored CISs to the environment. Functional assays suggest that these CISs may mediate ghost cell formation and/or interactions of ghost cells with other organisms. Collectively, these data provide a framework for understanding the evolutionary re-engineering of CISs and potential roles of these CISs in cyanobacterial programmed cell death.
History
DepositionDec 3, 2020-
Header (metadata) releaseFeb 23, 2022-
Map releaseFeb 23, 2022-
UpdateMar 16, 2022-
Current statusMar 16, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0275
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0275
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7b5h
  • Surface level: 0.0275
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7b5h
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12029.png

Downloads & links

-
Map

FileDownload / File: emd_12029.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.0275 / Movie #1: 0.0275
Minimum - Maximum-0.048076194 - 0.12496248
Average (Standard dev.)0.00085978355 (±0.006286565)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 563.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z563.200563.200563.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0480.1250.001

-
Supplemental data

-
Half map: #1

Fileemd_12029_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_12029_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Base plate and spike complex (C3) of the Anabaena PCC7120 contrac...

EntireName: Base plate and spike complex (C3) of the Anabaena PCC7120 contractile injection system
Components
  • Complex: Base plate and spike complex (C3) of the Anabaena PCC7120 contractile injection system
    • Protein or peptide: All3314 protein
    • Protein or peptide: All3315 protein
    • Protein or peptide: All3316 protein
    • Protein or peptide: All3317 protein
    • Protein or peptide: All3320 protein
    • Protein or peptide: Asl3322 protein
    • Protein or peptide: All3318 protein
    • Protein or peptide: All3321 protein
    • Protein or peptide: All3323 protein
    • Protein or peptide: All3324 protein
    • Protein or peptide: All3325 protein

+
Supramolecule #1: Base plate and spike complex (C3) of the Anabaena PCC7120 contrac...

SupramoleculeName: Base plate and spike complex (C3) of the Anabaena PCC7120 contractile injection system
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)

+
Macromolecule #1: All3314 protein

MacromoleculeName: All3314 protein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 166.114344 KDa
SequenceString: MTTTITIPNS YPIFTPNQVL TNKDLNRVVT YLDEQNRLTR VYLIGMGIVA GMEVSSIYQP GDVNIVVAPG CGITSEGYII SLAETKLTH YQSGVSVPSA LFAPSEEQTA ASTDQLVELF EQEGNNRLAL KNLPDENAFA RFLADQTLVV VYELQDQQRD S CLLDCDDT ...String:
MTTTITIPNS YPIFTPNQVL TNKDLNRVVT YLDEQNRLTR VYLIGMGIVA GMEVSSIYQP GDVNIVVAPG CGITSEGYII SLAETKLTH YQSGVSVPSA LFAPSEEQTA ASTDQLVELF EQEGNNRLAL KNLPDENAFA RFLADQTLVV VYELQDQQRD S CLLDCDDT GKDRNFRLRY FLLPRSVPEK LSAEALLQQG FSREPLPQQW RDFSINDIFQ AQSSFFQNFF PQVRRFGYTL ET PPVIRLS NIVDYDAFLK GYQQVCLQAI DEIDRTFPNL FRLFSPFFSS FNPAPSDFTG LKTLLNQRLS DIVSGSSAEN RRS PISQIE AQYALQYFYD YLSQLVSAFR ELAESAFDLM DDATPDTRRF PKFLMLGLVP LPNQKPEVYA LNSPYRSNFS QSPI YNGNQ LRVKQVRFLY DRLVRLCAAD SFYLLPFYDT PLKITPSKDR AATLSQQAIP YYLNYPQLYQ YWSYDTYRKG RSQSH PAYF YPNNANITPN SDLLHRLDDY SFYRIEGHIG EANATALQRI LDYQQRYNLA FDVITLKIGN LQSFQDINIS GQFDDL NAD FGRIKDTFAK LWQRYEESWS RNVFLYTLKR VFFDKTSLAE IKSDQLFNPI VARASVKEAY EFVKESGDSY RLYLRNA AG IRIARFETVI NFSGLSGDSL TQEQERIIGD LLACLPLGKI TYGVEPESAN NPLSYYLRFS LADELDLPAN RGTADISF I SLNFFTVNFE GNSPIINQPE FQDFETLYSL LRDVPESSIR VNRLELRMGD RLAADTLNYF ELKGLMTAYQ QRLAQIMEL QLFHKFAQNN PGMEHLGGVP KGGTFVLVYV DGRELVRNLL SADRDPTYQA RTEVIKKYAS LPPGSPQELA TSRELLNRED IVVGDFCLP YRFSSKTPTV SYVLTQPRPI VLLDRTTFCA GDETRYEFIL DPTGGTLKGE GSFFADGKYY FQPSRITDDI T SETAITFT YVVESSYDTL SVTVYPLPDA SFQIKTNFCS NENPVTLRAT QPGGNFRAFD SETDISASVI NNQEFNPSAV NL GGATEKV ITLVYTITSD QGCTNELSRD ITIFAVPNAT FQVGQGKTRF CSNDEPVDLI ARVPGGTFQV RDGAEDISAD VIN RLTTPP QFDPSAVNLG VAREKVITLE YSISNQGCSN KFTQELRIFA VPNANFRLST GNRDTFTNND PPVGLIATQL GGTF QAFDG EEDITADVIS PTTPPQFNPS AVNLGDEEEK VITLRYTISN QGCSNNTERR VTIVPPPEVP VRDVEDTSNP DSGDA PTEN PIPHPEVRAV NLLAISNNEV INSTNLDGDR TFNLSDFNPN NQYTFEAMTV PEKVNSVIFT YTKPNGSRQA LTANTA PYR MPDDWQPSIG IHEIQAQAIR EVNGDRLEGA TIKVIIRVID ADTDTSPSRS TNPDNLFTRI QNLFPLNRGE IITKIKL PQ LLAMSTAIFM LIVGWTYSSS KQVGSTPPSV IKPR

+
Macromolecule #2: All3315 protein

MacromoleculeName: All3315 protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 154.377031 KDa
SequenceString: MPEYLSISKQ KPDFPPYLNF QTLRDIGITH LQALSGKIWT DYNLHDPGVT ILEVLCYAIT DLGYRNNLDI ADLLALNPQD GNSRENNFF TPDAVLTCNP VTELDVRKRL IDIPGVRNAW LQKVTSYEPN IYVNFSDKRL QYNPPTAESK TLNPRGLYTV R LDLDQDYR ...String:
MPEYLSISKQ KPDFPPYLNF QTLRDIGITH LQALSGKIWT DYNLHDPGVT ILEVLCYAIT DLGYRNNLDI ADLLALNPQD GNSRENNFF TPDAVLTCNP VTELDVRKRL IDIPGVRNAW LQKVTSYEPN IYVNFSDKRL QYNPPTAESK TLNPRGLYTV R LDLDQDYR KNACGQIDRS WGDTLDEVKQ VLCDSRNLCE DFADIVILGE EEIGICADIQ LETNADAEDV LVNIYVRIQQ FL SPRLKFY TLQELLDKGK SPAEIFAGRP SVFDGENRLY KSHGFIDTDE LEALTLPTIL HTSDLYQEIL QVPGVSAIKK LSI ANYING LRQTQGHPWY LQLTDQYRPV LGVKTSKINF FKSELPIGVD EEEVERRYYE QQAAYIKTIR DRDELDIPVP KGSY YDLAD HYSIHHDFPT TYGISEDGLP PTVPALRKAQ ALQLKAYLVF FDQLLASYLA QLSHIRDLFS WEVDVTQPQQ NDYAT RLQE KQRTYFTQKL DFPEIEKIIP DNYLDVLDEA PETYRDRRNR FLDHLLARFS ESFSDYVLLN YQMFATRNNK ATQETE IIH DKAQFLQDYP TLSRDRFRAY NYYDCHAVWD TDNVAGFKKR VLRLLGIDDV RRRHLSHYRV DKDSRNLFLS IDFSSDD LT LTSKQRYATT EQAQADQDKL LLFALHPNFY KRLSYKYYYH YSWEILDTQN QSIVRSDRFF PSTKERAAAL EPLLQSLL T QLSQLDDTAL QNLVITQPTD EDLYSFRLQI PLNSGVITFT GVQRYFSRTE AVDAGVISLR LIQDVQNYRN ITLGQDQGT TPQKFTYYGY GLVDHQGSLL SEYTHHFPTE LERELSLQRW LTHIQANQNQ YKFAIETITN GYVFVINDIT NSQTLLRGIS SYATEYLAW QAASEFAENL RYLNRYLSPA KDHTGQTYSL GITDKTGKLL AVTTTESDRL LTFQRLNALE PFLVIEAATT P TSGYRYRL VDRQETTILQ SIQIYGDETT ARDRFYQDVL GTLFETGVIN PTTTNKEFGF RILSRPRDTN SVAAIHTQTY TS EAERDAA IEHLLLLVRT ARLRISTNSL DSLAYISQIY NPDNQLILQG TQRYTSEDIA WEQGNTLMEL AQDEENFRLI DSD DGVYGW ELTNEGKDEI FAAQYYNSRE ERTAAIAEIQ KYSNDEGFHL LEHILLRPRT KLPDLTAGDG FLPILVTPED VNTE PDDPY LLARTDPYSF WVTIVLPYWP QRFRDIPFRR FVERTLRLEA PAHIALKIAW VNVRQMRDFE LAYRHWLEQL ALESC ENAA CDLTGTLNRL LKILPQLRNV YPKATLHDCE ESSADNNPAI LNQTALGTAN D

+
Macromolecule #3: All3316 protein

MacromoleculeName: All3316 protein / type: protein_or_peptide / ID: 3 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 18.335021 KDa
SequenceString:
MNLRKRNELK SLFKNKSRLS ETYFVELIDS TLNKRDDRFH GIWKPGQTYQ KGDVVYYNHS LWEMQSENEI CAKEEQTPGI STDWKSLLK ELEQKVDKLQ HELETLHQEF TEYQKQMEIR LQLLARFIPI LFIGLGIMFF WLLGQSTVHI LAGTT

+
Macromolecule #4: All3317 protein

MacromoleculeName: All3317 protein / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 139.003422 KDa
SequenceString: MSNNRDLPKN PLIRDGVSQR QRQVSALSPA SIGVDERDLA DFLVLVYRLS AKVMYYRAEN QPWSPSDADG NWQNFFEGNT PIQIALISK VSPQVVKDIY SQKLAAFLAE RTVTSLSEVL SIWKTEILTK IQQWYLGIEA YTPLKSVIKG LVKTNLTEPL M RMQSFELG ...String:
MSNNRDLPKN PLIRDGVSQR QRQVSALSPA SIGVDERDLA DFLVLVYRLS AKVMYYRAEN QPWSPSDADG NWQNFFEGNT PIQIALISK VSPQVVKDIY SQKLAAFLAE RTVTSLSEVL SIWKTEILTK IQQWYLGIEA YTPLKSVIKG LVKTNLTEPL M RMQSFELG CGNVDEEFYR GFSGVFGLTI DAPLRSDRTP LMGTVKDART ELDTVFQVLL QTYRQIIQQA PNYLKASLSD RQ DHQPFLS LYFAFLEVLQ PARDDLNRLT QRHLDFFYRQ VLLLPDRPAQ ADQVHLLFEL AKSQREYKLT AGTSFKAGKD ATG VDLFYQ LDAETVIHKA QIASLKGLFL DSQERKTAAV PQNLTGLYAS PVANSVDGKG GAFPQEQIVK TWLPFGNEQR DHAR LGVAI ASDVLLLQEG RRVVEFKLSL GGFFPRLPDN QLHQAFVVYL SGEKAWIPAP ILPVGQLATN GQEQTRWDGS NLYLV VELA ADVAPILPYR PDAPIPYDPK ELNLPLQLER PIPVARLELN HQLLVNERSP YHYFRDAQIL DITVQTRVDE VRNLVV QND VSVLNPARPF EPFGFQPQDK ANLYIGSQEV LQKRLIALTI SLELATPKPN NWIEFYAGYD IPANFQPGKV KIQGLRQ KT WYPTTANVTA NLLDTPEISL TSKLANLKLD SFDQSAPVEM FTPQTKTGFL RLQLSGNFLH EQYPRVLAKQ VLAAATNQ T VVVSSNQKRQ AVIGAYYRRP DKSIFAATTY YVNLDDEPII PNEPYLPVVR SLSLKYTAQA GMSDCILFHL HPFGGFAKV NLAVNPPLLP YFNQEGELFI GLQNLDPPTA LPLLFQVAEE TADISLRRQE EYKLQWYYLK DNAWESLGDR IVNDASNGLV TSGIINLGI PADISRNQTT ILDPNFHWLK VTIPARSRTV CEIIGVHTQA ARVTFKDAGN DPNHLGSPLA GGTISKLAVP Q PEVKKIAQ PYTSFGGRVK EQPENFYIRI SERLRHKGRA VAIFDYERLV LEKFPQIYKV RCINHGQFDD AQEQLYELAP GS VTLAVIP DLSQRSTTND LEPKVNINLL QEIEKYLASV SSPWAMIKVV NPQYERIQVD FQVKLKAPYS SNFGYYRREL QQA IVGFLT PWTVDSGADI NFGGKVYRSS ILKFVEEQYY VDYVVNFKMN LNNQQDIREA IAITPRSVIT SVSPKTSNQD HMIE EFIEQ AIVFNNQKLE SGVLGYESLN DLELGE

+
Macromolecule #5: All3320 protein

MacromoleculeName: All3320 protein / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 63.636625 KDa
SequenceString: MNDRIIPRNS LYDVATFKLL SDGKDITNDY TVLSITVNQI VNRVPTARII LRDGAAADET FAASEGADLV PGQEVEIAAG YDGSDQKIF QGLIVKHALK VTANGDSMLM LDCRGLATKL TVGRHNRYFV DTKDSDAIAE IIAQHSLSAD VAATQVQHPE I VQYYATDW ...String:
MNDRIIPRNS LYDVATFKLL SDGKDITNDY TVLSITVNQI VNRVPTARII LRDGAAADET FAASEGADLV PGQEVEIAAG YDGSDQKIF QGLIVKHALK VTANGDSMLM LDCRGLATKL TVGRHNRYFV DTKDSDAIAE IIAQHSLSAD VAATQVQHPE I VQYYATDW DFILSRAEMN GQIVVAQDEK IKVKAPNTSG APQITLTYGV NLLELEAAMD ARHQYQAVKA TSWNYADQAL VE AEASEPT VNNQGNLSGR QLAQVIDLSA LELRHSGLVA EPELKAWADA QLLKSRLAKI QGRVKTKGYP DAKVDVLIQL AGV GDRFNG LAYVSGIRHE IVGGAWDTHI QMGLPPQWFY QEVDIIDKPA AGLLPGVNGL QIGVVVQLQD DPNGEDRILV KVPI IDAQA EGIWARIATL DAGNNRGSFF RPEVGDEVIL GFLNDDPRDP VVLGMLNSSA KPAPLRATAE NHRKGFFTRS QMQLT FDDD KKIITLQTPG GNKVTISDED KGITLTDQNG NTFAMSDRGI AMNSPKDITL EATGKLTLKA TQDVSIEGLN VNIAAN AQF KAQGNAGAEV SSSAIAVLKG SLVMIN

+
Macromolecule #6: Asl3322 protein

MacromoleculeName: Asl3322 protein / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 5.226893 KDa
SequenceString:
MPLEIRELVI KASVNEGGQN QGTGGAGDQS AIIAACVEQV LAILQEKSER

+
Macromolecule #7: All3318 protein

MacromoleculeName: All3318 protein / type: protein_or_peptide / ID: 7 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 16.764764 KDa
SequenceString:
MDDESNAYLG TGWGFPPTFE KKARSVRLVS AEDDIRESLQ ILLSTNLGER VMQPNYGCNL QDLLFESLSP TVASNIKELV RTAILYYEP RIRLNKLDIQ QGISDRQNPS AVNEADAQGL IQIIVDCTII STNSRFNFVY PFYLQEGSGN

+
Macromolecule #8: All3321 protein

MacromoleculeName: All3321 protein / type: protein_or_peptide / ID: 8 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 27.090568 KDa
SequenceString: MALTKVKLLA YQDKRFENKL GEFELPINPE QFSQSFKVEY NREQAQGSQR NDPEFKFTKP EELKLDFTFD GTGVVPVNNG KPGEFHQDV ADQVRVFLDL VYSMNSETHK PNFLRLIWGD FSFGEKNGFD CLLTDLQINY TLFDQTGKPL RAKLSTTFTS Y VEQNRRVR ...String:
MALTKVKLLA YQDKRFENKL GEFELPINPE QFSQSFKVEY NREQAQGSQR NDPEFKFTKP EELKLDFTFD GTGVVPVNNG KPGEFHQDV ADQVRVFLDL VYSMNSETHK PNFLRLIWGD FSFGEKNGFD CLLTDLQINY TLFDQTGKPL RAKLSTTFTS Y VEQNRRVR EEGKQSPDVT HQRKVKAGDT LPLMTHRIYG DPAYYLQIAK VNGLINFRKL ATNTDLRFPP LEKTQS

+
Macromolecule #9: All3323 protein

MacromoleculeName: All3323 protein / type: protein_or_peptide / ID: 9 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 19.204932 KDa
SequenceString:
MIRTYPPVSF FFEVVFQGEN LDKDVVETRF QSVTGLSVDM QTETLKEGGE NRFEHILPVR TKYDPLVLKR GLVNDSQMVK WCMDAILNF DIRPMNLLVR LLHIERSDPN QPPEAIATGG SSTIAPLMTW KVINAWPKKW SVSEFNAEQN SIAVESLELN Y SYFETLK

+
Macromolecule #10: All3324 protein

MacromoleculeName: All3324 protein / type: protein_or_peptide / ID: 10 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 16.459543 KDa
SequenceString:
MAEYPLPKFH FQVDWGGSRL GFTEVSGLDV ETEVIEYREG NLPQYHKLKM PGMQKFSNIT MKRGTFQGDN DFYKWWNTVA LNTIERRDL TISLLNEKHE PVVVWKVNRA WPTKVQSTDL KGDGNEVAIE SIEVAHEGLT IQNG

+
Macromolecule #11: All3325 protein

MacromoleculeName: All3325 protein / type: protein_or_peptide / ID: 11 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 53.23616 KDa
SequenceString: MPSTYKTPGV YIEEISKFPP SIAQVETAIP AFIGYTQIAK VGVENFHTDA DNLILRPVRI TSLLEYEQFF GKAINETTIQ VVIQDTTDS RGNLTERKAS ARITSPSPHN LYYSMQAYFA NGGGPCYIVS VGPMSNTGTI QLEALQNGLA EVAKEDEVTL L VFPESQSL ...String:
MPSTYKTPGV YIEEISKFPP SIAQVETAIP AFIGYTQIAK VGVENFHTDA DNLILRPVRI TSLLEYEQFF GKAINETTIQ VVIQDTTDS RGNLTERKAS ARITSPSPHN LYYSMQAYFA NGGGPCYIVS VGPMSNTGTI QLEALQNGLA EVAKEDEVTL L VFPESQSL SDENYAALMS AALEQCANLQ DRFTVMDLKL PATRPIPANA IVGASNAFRD LSLPQDNLKY GACYAPDIET IF NYFYQED AVTIFRSVNG GAEEQDTLTM AGYNPANGGD GIQYALIESA IDQLPLILPP SPLVVGQYAR TDNTRGVWKA PAN VALSSV IKPVLKITNE QQNNLNVHPT GKSINAIRAF TGKGTLIWGA RTLAGNDNEW RYVSVRRFFN MAEESIKKGS EPFV FEPND ANTWTKVKAM IENFLTLQWR AGALAGAKPE QAFYVKIGLN ETMTALDILE GRMIVEIGMA VVRPAEFIIL KFSHK MQES

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 1.5 µm / Calibrated defocus min: 0.9 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 4 / Number real images: 19000 / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 228163
CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER / Details: related structure
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 36909
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more