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- EMDB-33028: lymphocytic choriomeningitis virus polymerase- Matrix Z Protein C... -

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Basic information

Entry
Database: EMDB / ID: EMD-33028
Titlelymphocytic choriomeningitis virus polymerase- Matrix Z Protein Complex (LCMV L-Z Complex)
Map dataEM map of LCMV L-Z complex
Sample
  • Complex: The complex of LCMV polymerase with matrix protein Z
    • Complex: matrix protein Z
      • Protein or peptide: RING finger protein Z
    • Complex: LCMV polymerase L protein
      • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: ZINC ION
  • Ligand: MANGANESE (II) ION
KeywordsL 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
RING finger protein Z, zinc finger / RING finger protein Z, arenaviridae / Protein Z, RING-type zinc finger superfamily / P-11 zinc finger / RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / : / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
RNA-directed RNA polymerase L / RING finger protein Z
Similarity search - Component
Biological speciesLymphocytic choriomeningitis virus (strain Armstrong)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLiu L / Lou Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: 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
DepositionMar 8, 2022-
Header (metadata) releaseSep 13, 2023-
Map releaseSep 13, 2023-
UpdateSep 27, 2023-
Current statusSep 27, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33028.png

Downloads & links

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Map

FileDownload / File: emd_33028.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of LCMV L-Z complex
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.243
Minimum - Maximum-1.59236 - 2.753838
Average (Standard dev.)0.005193738 (±0.08293075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 216.00002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33028_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33028_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The complex of LCMV polymerase with matrix protein Z

EntireName: The complex of LCMV polymerase with matrix protein Z
Components
  • Complex: The complex of LCMV polymerase with matrix protein Z
    • Complex: matrix protein Z
      • Protein or peptide: RING finger protein Z
    • Complex: LCMV polymerase L protein
      • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: ZINC ION
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: The complex of LCMV polymerase with matrix protein Z

SupramoleculeName: 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

SupramoleculeName: matrix protein Z / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Lymphocytic choriomeningitis virus (strain Armstrong)

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Supramolecule #3: LCMV polymerase L protein

SupramoleculeName: LCMV polymerase L protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Lymphocytic choriomeningitis virus (strain Armstrong)

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Macromolecule #1: RING finger protein Z

MacromoleculeName: RING finger protein Z / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lymphocytic choriomeningitis virus (strain Armstrong)
Strain: Armstrong
Molecular weightTheoretical: 10.198725 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MGQGKSREEK GTNSTNRAEI LPDTTYLGPL SCKSCWQKFD SLVRCHDHYL CRHCLNLLLS VSDRCPLCKY PLPTRLKIST APSSPPPYE E

UniProtKB: RING finger protein Z

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Macromolecule #2: RNA-directed RNA polymerase L

MacromoleculeName: RNA-directed RNA polymerase L / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lymphocytic choriomeningitis virus (strain Armstrong)
Strain: Armstrong
Molecular weightTheoretical: 254.894641 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: 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

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6klc


Details: 5I72
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98004
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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