+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38242 | |||||||||
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Title | Tail tip complex of bacteriophage lambda in the open state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Bacteriophage / caudovirales / siphoviridae / phage lambda / host recognition / LamB / cryo-EM / VIRUS | |||||||||
Function / homology | Function and homology information symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / 4 iron, 4 sulfur cluster binding / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / virion attachment to host cell / metal ion binding Similarity search - Function | |||||||||
Biological species | Escherichia phage Lambda (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.46 Å | |||||||||
Authors | Ge XF / Wang JW | |||||||||
Funding support | China, 2 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of lambda tail with LamB Authors: Ge XF / Wang JW | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38242.map.gz | 118 MB | EMDB map data format | |
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Header (meta data) | emd-38242-v30.xml emd-38242.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38242_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_38242.png | 193.8 KB | ||
Filedesc metadata | emd-38242.cif.gz | 6.3 KB | ||
Others | emd_38242_half_map_1.map.gz emd_38242_half_map_2.map.gz | 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38242 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38242 | HTTPS FTP |
-Related structure data
Related structure data | 8xcgMC 8xciC 8xcjC 8xckC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_38242.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.0742 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_38242_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38242_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Bacteriophage lambda tail with LamB
Entire | Name: Bacteriophage lambda tail with LamB |
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Components |
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-Supramolecule #1: Bacteriophage lambda tail with LamB
Supramolecule | Name: Bacteriophage lambda tail with LamB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Escherichia phage Lambda (virus) |
-Macromolecule #1: Tail tip protein M
Macromolecule | Name: Tail tip protein M / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage Lambda (virus) |
Molecular weight | Theoretical: 12.547373 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKTFRWKVKP GMDVASVPSV RKVRFGDGYS QRAPAGLNAN LKTYSVTLSV PREEATVLES FLEEHGGWKS FLWTPPYEWR QIKVTCAKW SSRVSMLRVE FSAEFEQVVN UniProtKB: Tail tip protein M |
-Macromolecule #2: Tip attachment protein J
Macromolecule | Name: Tip attachment protein J / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage Lambda (virus) |
Molecular weight | Theoretical: 124.550625 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGKGSSKGHT PREAKDNLKS TQLLSVIDAI SEGPIEGPVD GLKSVLLNST PVLDTEGNTN ISGVTVVFRA GEQEQTPPEG FESSGSETV LGTEVKYDTP ITRTITSANI DRLRFTFGVQ ALVETTSKGD RNPSEVRLLV QIQRNGGWVT EKDITIKGKT T SQYLASVV ...String: MGKGSSKGHT PREAKDNLKS TQLLSVIDAI SEGPIEGPVD GLKSVLLNST PVLDTEGNTN ISGVTVVFRA GEQEQTPPEG FESSGSETV LGTEVKYDTP ITRTITSANI DRLRFTFGVQ ALVETTSKGD RNPSEVRLLV QIQRNGGWVT EKDITIKGKT T SQYLASVV MGNLPPRPFN IRMRRMTPDS TTDQLQNKTL WSSYTEIIDV KQCYPNTALV GVQVDSEQFG SQQVSRNYHL RG RILQVPS NYNPQTRQYS GIWDGTFKPA YSNNMAWCLW DMLTHPRYGM GKRLGAADVD KWALYVIGQY CDQSVPDGFG GTE PRITCN AYLTTQRKAW DVLSDFCSAM RCMPVWNGQT LTFVQDRPSD KTWTYNRSNV VMPDDGAPFR YSFSALKDRH NAVE VNWID PNNGWETATE LVEDTQAIAR YGRNVTKMDA FGCTSRGQAH RAGLWLIKTE LLETQTVDFS VGAEGLRHVP GDVIE ICDD DYAGISTGGR VLAVNSQTRT LTLDREITLP SSGTALISLV DGSGNPVSVE VQSVTDGVKV KVSRVPDGVA EYSVWE LKL PTLRQRLFRC VSIRENDDGT YAITAVQHVP EKEAIVDNGA HFDGEQSGTV NGVTPPAVQH LTAEVTADSG EYQVLAR WD TPKVVKGVSF LLRLTVTADD GSERLVSTAR TTETTYRFTQ LALGNYRLTV RAVNAWGQQG DPASVSFRIA APAAPSRI E LTPGYFQITA TPHLAVYDPT VQFEFWFSEK QIADIRQVET STRYLGTALY WIAASINIKP GHDYYFYIRS VNTVGKSAF VEAVGRASDD AEGYLDFFKG KITESHLGKE LLEKVELTED NASRLEEFSK EWKDASDKWN AMWAVKIEQT KDGKHYVAGI GLSMEDTEE GKLSQFLVAA NRIAFIDPAN GNETPMFVAQ GNQIFMNDVF LKRLTAPTIT SGGNPPAFSL TPDGKLTAKN A DISGSVNA NSGTLSNVTI AENCTINGTL RAEKIVGDIV KAASAAFPRQ RESSVDWPSG TRTVTVTDDH PFDRQIVVLP LT FRGSKRT VSGRTTYSMC YLKVLMNGAV IYDGAANEAV QVFSRIVDMP AGRGNVILTF TLTSTRHSAD IPPYTFASDV QVM VIKKQA LGISVV UniProtKB: Tip attachment protein J |
-Macromolecule #3: Tail tip assembly protein I
Macromolecule | Name: Tail tip assembly protein I / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage Lambda (virus) |
Molecular weight | Theoretical: 23.14659 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAATHTLPLA SPGMARICLY GDLQRFGRRI DLRVKTGAEA IRALATQLPA FRQKLSDGWY QVRIAGRDVS TSGLTAQLHE TLPDGAVIH IVPRVAGAKS GGVFQIVLGA AAIAGSFFTA GATLAAWGAA IGAGGMTGIL FSLGASMVLG GVAQMLAPKA R TPRIQTTD ...String: MAATHTLPLA SPGMARICLY GDLQRFGRRI DLRVKTGAEA IRALATQLPA FRQKLSDGWY QVRIAGRDVS TSGLTAQLHE TLPDGAVIH IVPRVAGAKS GGVFQIVLGA AAIAGSFFTA GATLAAWGAA IGAGGMTGIL FSLGASMVLG GVAQMLAPKA R TPRIQTTD NGKQNTYFSS LDNMVAQGNV LPVLYGEMRV GSRVVSQEIS TADEGDGGQV VVIGR UniProtKB: Tail tip assembly protein I |
-Macromolecule #4: Tail tip protein L
Macromolecule | Name: Tail tip protein L / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage Lambda (virus) |
Molecular weight | Theoretical: 25.730578 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MQDIRQETLN ECTRAEQSAS VVLWEIDLTE VGGERYFFCN EQNEKGEPVT WQGRQYQPYP IQGSGFELNG KGTSTRPTLT VSNLYGMVT GMAEDMQSLV GGTVVRRKVY ARFLDAVNFV NGNSYADPEQ EVISRWRIEQ CSELSAVSAS FVLSTPTETD G AVFPGRIM ...String: MQDIRQETLN ECTRAEQSAS VVLWEIDLTE VGGERYFFCN EQNEKGEPVT WQGRQYQPYP IQGSGFELNG KGTSTRPTLT VSNLYGMVT GMAEDMQSLV GGTVVRRKVY ARFLDAVNFV NGNSYADPEQ EVISRWRIEQ CSELSAVSAS FVLSTPTETD G AVFPGRIM LANTCTWTYR GDECGYSGPA VADEYDQPTS DITKDKCSKC LSGCKFRNNV GNFGGFLSIN KLSQ UniProtKB: Tail tip protein L |
-Macromolecule #5: IRON/SULFUR CLUSTER
Macromolecule | Name: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 3 / Formula: SF4 |
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Molecular weight | Theoretical: 351.64 Da |
Chemical component information | ChemComp-FS1: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |