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Yorodumi- EMDB-33028: lymphocytic choriomeningitis virus polymerase- Matrix Z Protein C... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33028 | |||||||||
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Title | lymphocytic choriomeningitis virus polymerase- Matrix Z Protein Complex (LCMV L-Z Complex) | |||||||||
Map data | EM map of LCMV L-Z complex | |||||||||
Sample |
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Keywords | L protein / RING finger protein / METAL BINDING PROTEIN-TRANSFERASE complex | |||||||||
Function / homology | Function and homology information negative stranded viral RNA replication / viral budding via host ESCRT complex / cap snatching / viral budding from plasma membrane / virion component / host cell cytoplasm / Hydrolases; Acting on ester bonds / host cell perinuclear region of cytoplasm / hydrolase activity / RNA-directed RNA polymerase ...negative stranded viral RNA replication / viral budding via host ESCRT complex / cap snatching / viral budding from plasma membrane / virion component / host cell cytoplasm / Hydrolases; Acting on ester bonds / host cell perinuclear region of cytoplasm / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / host cell plasma membrane / RNA binding / zinc ion binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Lymphocytic choriomeningitis virus (strain Armstrong) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Liu L / Lou Z | |||||||||
Funding support | China, 1 items
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Citation | Journal: Protein Cell / Year: 2023 Title: Structure basis for allosteric regulation of lymphocytic choriomeningitis virus polymerase function by Z matrix protein. Authors: Lu Liu / Panpan Wang / Aijun Liu / Leike Zhang / Liming Yan / Yu Guo / Gengfu Xiao / Zihe Rao / Zhiyong Lou / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33028.map.gz | 28.8 MB | EMDB map data format | |
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Header (meta data) | emd-33028-v30.xml emd-33028.xml | 18.3 KB 18.3 KB | Display Display | EMDB header |
Images | emd_33028.png | 75.7 KB | ||
Others | emd_33028_half_map_1.map.gz emd_33028_half_map_2.map.gz | 28.4 MB 28.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33028 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33028 | HTTPS FTP |
-Validation report
Summary document | emd_33028_validation.pdf.gz | 974.9 KB | Display | EMDB validaton report |
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Full document | emd_33028_full_validation.pdf.gz | 974.5 KB | Display | |
Data in XML | emd_33028_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | emd_33028_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33028 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33028 | HTTPS FTP |
-Related structure data
Related structure data | 7x6vMC 7x6sC 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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-Map
File | Download / File: emd_33028.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | EM map of LCMV L-Z complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33028_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33028_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The complex of LCMV polymerase with matrix protein Z
Entire | Name: The complex of LCMV polymerase with matrix protein Z |
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Components |
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-Supramolecule #1: The complex of LCMV polymerase with matrix protein Z
Supramolecule | Name: The complex of LCMV polymerase with matrix protein Z / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: matrix protein Z
Supramolecule | Name: matrix protein Z / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Lymphocytic choriomeningitis virus (strain Armstrong) |
-Supramolecule #3: LCMV polymerase L protein
Supramolecule | Name: LCMV polymerase L protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Lymphocytic choriomeningitis virus (strain Armstrong) |
-Macromolecule #1: RING finger protein Z
Macromolecule | Name: RING finger protein Z / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lymphocytic choriomeningitis virus (strain Armstrong) Strain: Armstrong |
Molecular weight | Theoretical: 10.198725 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MGQGKSREEK GTNSTNRAEI LPDTTYLGPL SCKSCWQKFD SLVRCHDHYL CRHCLNLLLS VSDRCPLCKY PLPTRLKIST APSSPPPYE E UniProtKB: RING finger protein Z |
-Macromolecule #2: RNA-directed RNA polymerase L
Macromolecule | Name: RNA-directed RNA polymerase L / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lymphocytic choriomeningitis virus (strain Armstrong) Strain: Armstrong |
Molecular weight | Theoretical: 254.894641 KDa |
Recombinant expression | Organism: unidentified baculovirus |
Sequence | String: MDEIISELRE LCLNYIEQDE RLSRQKLNFL GQREPRMVLI EGLKLLSRCI EIDSADKSGC THNHDDKSVE TILVESGIVC PGLPLIIPD GYKLIDNSLI LLECFVRSTP ASFEKKFIED TNKLACIRED LAVAGVTLVP IVDGRCDYDN SFMPEWANFK F RDLLFKLL ...String: MDEIISELRE LCLNYIEQDE RLSRQKLNFL GQREPRMVLI EGLKLLSRCI EIDSADKSGC THNHDDKSVE TILVESGIVC PGLPLIIPD GYKLIDNSLI LLECFVRSTP ASFEKKFIED TNKLACIRED LAVAGVTLVP IVDGRCDYDN SFMPEWANFK F RDLLFKLL EYSNQNEKVF EESEYFRLCE SLKTTIDKRS GMDSMKILKD ARSTHNDEIM RMCHEGINPN MSCDDVVFGI NS LFSRFRR DLESGKLKRN FQKVNPEGLI KEFSELYENL ADSDDILTLS REAVESCPLM RFITAETHGH ERGSETSTEY ERL LSMLNK VKSLKLLNTR RRQLLNLDVL CLSSLIKQSK FKGLKNDKHW VGCCYSSVND RLVSFHSTKE EFIRLLRNRK KSKV FRKVS FEELFRASIS EFIAKIQKCL LVVGLSFEHY GLSEHLEQEC HIPFTEFENF MKIGAHPIMY YTKFEDYNFQ PSTEQ LKNI QSLRRLSSVC LALTNSMKTS SVARLRQNQI GSVRYQVVEC KEVFCQVIKL DSEEYHLLYQ KTGESSRCYS IQGPDG HLI SFYADPKRFF LPIFSDEVLY NMIDIMISWI RSCPDLKDCL TDIEVALRTL LLLMLTNPTK RNQKQVQSVR YLVMAIV SD FSSTSLMDKL REDLITPAEK VVYKLLRFLI KTIFGTGEKV LLSAKFKFML NVSYLCHLIT KETPDRLTDQ IKCFEKFF E PKSQFGFFVN PKEAITPEEE CVFYEQMKRF TSKEIDCQHT TPGVNLEAFS LMVSSFNNGT LIFKGEKKLN SLDPMTNSG CATALDLASN KSVVVNKHLN GERLLEYDFN KLLVSAVSQI TESFVRKQKY KLSHSDYEYK VSKLVSRLVI GSKGEETGRS EDNLAEICF DGEEETSFFK SLEEKVNTTI ARYRRGRRAN DKGDGEKLTN TKGLHHLQLI LTGKMAHLRK VILSEISFHL V EDFDPSCL TNDDMKFICE AVEGSTELSP LYFTSVIKDQ CGLDEMAKNL CRKFFSENDW FSCMKMILLQ MNANAYSGKY RH MQRQGLN FKFDWDKLEE DVRISERESN SESLSKALSL TKCMSAALKN LCFYSEESPT SYTSVGPDSG RLKFALSYKE QVG GNRELY IGDLRTKMFT RLIEDYFESF SSFFSGSCLN NDKEFENAIL SMTINVREGF LNYSMDHSKW GPMMCPFLFL MFLQ NLKLG DDQYVRSGKD HVSTLLTWHM HKLVEVPFPV VNAMMKSYVK SKLKLLRGSE TTVTERIFRQ YFEMGIVPSH ISSLI DMGQ GILHNASDFY GLLSERFINY CIGVIFGERP EAYTSSDDQI TLFDRRLSDL VVSDPEEVLV LLEFQSHLSG LLNKFI SPK SVAGRFAAEF KSRFYVWGEE VPLLTKFVSA ALHNVKCKEP HQLCETIDTI ADQAIANGVP VSLVNSIQRR TLDLLKY AN FPLDPFLLNT NTDVKDWLDG SRGYRIQRLI EELCPNETKV VRKLVRKLHH KLKNGEFNEE FFLDLFNRDK KEAILQLG D LLGLEEDLNQ LADVNWLNLN EMFPLRMVLR QKVVYPSVMT FQEERIPSLI KTLQNKLCSK FTRGAQKLLS EAINKSAFQ SCISSGFIGL CKTLGSRCVR NKNRENLYIK KLLEDLTTDD HVTRVCNRDG ITLYICDKQS HPEAHRDHIC LLRPLLWDYI CISLSNSFE LGVWVLAEPT KGKNNSENLT LKHLNPCDYV ARKPESSRLL EDKVNLNQVI QSVRRLYPKI FEDQLLPFMS D MSSKNMRW SPRIKFLDLC VLIDINSESL SLISHVVKWK RDEHYTVLFS DLANSHQRSD SSLVDEFVVS TRDVCKNFLK QV YFESFVR EFVATTRTLG NFSWFPHKEM MPSEDGAEAL GPFQSFVSKV VNKNVERPMF RNDLQFGFGW FSYRMGDVVC NAA MLIRQG LTNPKAFKSL KDLWDYMLNY TKGVLEFSIS VDFTHNQNNT DCLRKFSLIF LVRCQLQNPG VAELLSCSHL FKGE IDRRM LDECLHLLRT DSVFKVNDGV FDIRSEEFED YMEDPLILGD SLELELLGSK RILDGIRSID FERVGPEWEP VPLTV KMGA LFEGRNLVQN IIVKLETKDM KVFLAGLEGY EKISDVLGNL FLHRFRTGEH LLGSEISVIL QELCIDRSIL LIPLSL LPD WFAFKDCRLC FSKSRSTLMY ETVGGRFRLK GRSCDDWLGG SVAEDID UniProtKB: RNA-directed RNA polymerase L |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #4: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MN |
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Molecular weight | Theoretical: 54.938 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: Details: 5I72 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98004 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |