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- EMDB-35865: Structure of the Mumps Virus L Protein (state2) Bound by Phosphop... -

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Basic information

Entry
Database: EMDB / ID: EMD-35865
TitleStructure of the Mumps Virus L Protein (state2) Bound by Phosphoprotein Tetramer
Map data
Sample
  • Complex: The MuV polymerase complex of RNA-directed RNA polymerase L with tetrameric phosphoproteins
    • Protein or peptide: Phosphoprotein
    • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: ZINC ION
KeywordsMumps virus polymerase complex / RNA-dependent RNA synthesis / Large protein / phosphoprotein. / VIRAL PROTEIN
Function / homology
Function and homology information


NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / hydrolase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / ATP binding
Similarity search - Function
RNA-directed RNA polymerase, paramyxovirus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirales mRNA-capping domain V / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile.
Similarity search - Domain/homology
RNA-directed RNA polymerase L / Phosphoprotein
Similarity search - Component
Biological speciesMumps orthorubulavirus / Mumps virus strain Jeryl Lynn
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsLi TH / Shen QT
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Structural insights into mumps virus polymerase complex for coordinating replication and transcription
Authors: Li TL / Shen QT
History
DepositionApr 7, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35865.png

Downloads & links

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Map

FileDownload / File: emd_35865.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.53 Å/pix.
x 440 pix.
= 233.2 Å		0.53 Å/pix.
x 440 pix.
= 233.2 Å		0.53 Å/pix.
x 440 pix.
= 233.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.53 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.0060957377 - 2.6822536
Average (Standard dev.)0.00048069545 (±0.052936915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 233.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35865_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35865_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 MuV polymerase complex of RNA-directed RNA polymerase L with ...

EntireName: The MuV polymerase complex of RNA-directed RNA polymerase L with tetrameric phosphoproteins
Components
  • Complex: The MuV polymerase complex of RNA-directed RNA polymerase L with tetrameric phosphoproteins
    • Protein or peptide: Phosphoprotein
    • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: ZINC ION

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Supramolecule #1: The MuV polymerase complex of RNA-directed RNA polymerase L with ...

SupramoleculeName: The MuV polymerase complex of RNA-directed RNA polymerase L with tetrameric phosphoproteins
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: The MuV polymerase complex expressed in Sf9 cells and purified by affinity chromatography and size-exlusive chromatography sequentially.
Source (natural)Organism: Mumps orthorubulavirus / Strain: Jeryl-Lynn

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Macromolecule #1: Phosphoprotein

MacromoleculeName: Phosphoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mumps virus strain Jeryl Lynn / Strain: Jeryl-Lynn
Molecular weightTheoretical: 41.651066 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDQFIKQDET GDLIETGMNV ANHFLSTPIQ GTNSLSKASI LPGVAPVLIG NPEQKNIQHP TASHQGSKTK GRGSGVRSII VSPSEAGNG GTQIPEPLFA QTGQGGIVTT VYQDPTIQPT GSYRSVELAK IGKERMINRF VEKPRTSTPV TEFKRGGPGA A AQGQTIQE ...String:
MDQFIKQDET GDLIETGMNV ANHFLSTPIQ GTNSLSKASI LPGVAPVLIG NPEQKNIQHP TASHQGSKTK GRGSGVRSII VSPSEAGNG GTQIPEPLFA QTGQGGIVTT VYQDPTIQPT GSYRSVELAK IGKERMINRF VEKPRTSTPV TEFKRGGPGA A AQGQTIQE EGIDGNGASA GSKERSGSLS GATLYAHLSL PQQDSTPANV GIAPQSAISA NEIMDLLRGM DARLQHLEQK VD KVLAQGS MVTQIKNELS TVKTTLATIE GMMATVKIMD PGNPTGVPVD ELRRSFSDHV TIVSGPGDVS FSSSEKPTLY LDE LARPVS KPRPAKQTKS QPVKDLAGQK VMITKMITDC VANPQMKQAF EQRLAKASTE DALNDIKRDI IRSAI

UniProtKB: Phosphoprotein

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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 / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Mumps virus strain Jeryl Lynn / Strain: Jeryl-Lynn
Molecular weightTheoretical: 256.833094 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAGLNEILLP EVHLNSPIVR YKLFYYILHG QLPNDLEPDD LGPLANQNWK AIRAEESQVH ARLKQIRVEL IARIPSLRWT RSQREIAIL IWPRILPILQ AYDLRQSMQL PTVWEKLTQS TVNLISDGLE RVVLHISNQL TGKPNLFTRS RAGQDTKDYS I PSTRELSQ ...String:
MAGLNEILLP EVHLNSPIVR YKLFYYILHG QLPNDLEPDD LGPLANQNWK AIRAEESQVH ARLKQIRVEL IARIPSLRWT RSQREIAIL IWPRILPILQ AYDLRQSMQL PTVWEKLTQS TVNLISDGLE RVVLHISNQL TGKPNLFTRS RAGQDTKDYS I PSTRELSQ IWFNNEWSGS VKTWLMIKYR MRQLITNQKT GELTDLVTIV DTRSTLCIIT PELVALYSSE HKALTYLTFE MV LMVTDML EGRLNVSSLC TASHYLSPLK KRIEVLLTLV DDLALLMGDK VYGIVSSLES FVYAQLQYGD PVIDIKGTFY GFI CNEILD LLTEDNIFTE EEANKVLLDL TSQFDNLSPD LTAELLCIMR LWGHPTLTAS QAASKVRESM CAPKVLDFQT IMKT LAFFH AILINGYRRS HNGIWPPTTL HGNAPKSLIE MRHDNSELKY EYVLKNWKSI SMLRIHKCFD ASPDEDLSIF MKDKA ISCP RQDWMGVFRR SLIKQRYRDA NRPLPQPFNR RLLLNFLEDD RFDPIKELEY VTSGEYLRDP EFCASYSLKE KEIKAT GRI FAKMTKRMRS CQVIAESLLA NHAGKLMREN GVVLDQLKLT KSLLTMNQIG IISEHSRRST ADNMTLAHSG SNKHRIN NS QFKKNKDNKH EMPDDGFEIA ACFLTTDLTK YCLNWRYQVI IPFARTLNSM YGIPHLFEWI HLRLMRSTLY VGDPFNPP S DPTQLDLDTA LNDDIFIVSP RGGIEGLCQK LWTMISISTI ILSATEANTR VMSMVQGDNQ AIAITTRVVR SLSHSEKKE QAYKASKLFF ERLRANNHGI GHHLKEQETI LSSDFFIYSK RVFYKGRILT QALKNVSKMC LTADILGDCS QASCSNLATT VMRLTENGV EKDLCYFLNA FMTIRQLCYD LVFPQTKSLS QDITNAYLNH PILISRLCLL PSQLGGLNFL SCSRLFNRNI G DPLVSAIA DVKRLIKAGC LDIWVLYNIL GRRPGKGKWS TLAADPYTLN IDYLVPSTTF LKKHAQYTLM ERSVNPMLRG VF SENAAEE EEELAQYLLD REVVMPRVAH VILAQSSCGR RKQIQGYLDS TRTIIRYSLE VRPLSAKKLN TVIEYNLLYL SYN LEIIEK PNIVQPFLNA INVDTCSIDI ARSLRKLSWA TLLNGRPIEG LETPDPIELV HGCLIIGSDE CEHCSSGDDK FTWF FLPKG IRLDDDPASN PPIRVPYIGS KTDERRVASM AYIKGASVSL KSALRLAGVY IWAFGDTEES WQDAYELAST RVNLT LEQL QSLTPLPTSA NLVHRLDDGT TQLKFTPASS YAFSSFVHIS NDCQILEIDD QVTDSNLIYQ QVMITGLALI ETWNNP PIN FSVYETTLHL HTGSSCCIRP VESCVVNPPL LPVPLINVPQ MNKFVYDPEP LSLLEMEKIE DIAYQTRIGG LDQIPLL EK IPLLAHLTAK QMVNSITGLD EATSIMNDAV VQADYTSNWI SECCYTYIDS VFVYSGWALL LELSYQMYYL RIQGIQGI L DYVYMTLRRI PGMAITGISS TISHPRILRR CINLDVIAPI NSPHIASLDY TKLSIDAVMW GTKQVLTNIS QGIDYEIVV PSESQLTLSD RVLNLVARKL SLLAIIWANY NYPPKVKGMS PEDKCQALTT HLLQTVEYVE YIQIEKTNIR RMIIEPKLTA YPSNLFYLS RKLLNAIRDS EEGQFLIASY YNSFGYLEPI LMESKIFNLS SSESASLTEF DFILNLELSD ASLEKYSLPS L LMTAENMD NPFPQPPLHH VLRPLGLSST SWYKTISVLN YISHMKISDG AHLYLAEGSG ASMSLIETFL PGETIWYNSL FN SGENPPQ RNFAPLPTQF IESVPYRLIQ AGIAAGNGIV QSFYPLWNGN SDITDLSTKT SVEYIIHKVG ADTCALVHVD LEG VPGSMN SMLERAQVHA LLITVTVLKP GGLLILKASW EPFNRFSFLL TVLWQFFSTI RILRSSYSDP NNHEVYIIAT LAVD PTTSS FTTALNRART LNEQGFSLIP PELVSEYWRK RVEQGQIIQD CIDKVISECV RDQYLADNNI ILQAGGTPST RKWLD LPDY SSFNELQSEM ARLITIHLKE VIEILKGQAS DHDTLLFTSY NVGPLGKINT ILRLIVERIL MYTVRNWCIL PTQTRL TLR QSIELGEFRL RDVITPMEIL KLSPNRKYLK SALNQSTFNH LMGETSDILL NRAYQKRIWK AIGCVIYCFG LLTPDVE GS ERIDVDNDIP DYDIHGDII

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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMTris-HClTRIS hydrochloride
6.0 mMMgCl2magnesium chloride
1.0 mMTCEPTris(2-carboxyethyl)phosphine
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.75 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 477568
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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