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- EMDB-12373: 1918 H1N1 Viral influenza polymerase heterotrimer with Nb8199 core -

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Basic information

Entry
Database: EMDB / ID: EMD-12373
Title1918 H1N1 Viral influenza polymerase heterotrimer with Nb8199 core
Map data
Sample
  • Complex: 1918 Influenza virus polymerase heterotirmer in complex with vRNA promoters and Nb8199
    • Complex: Nb8199 Core
      • Protein or peptide: Nb8199 Core
    • Complex: Polymerase acidic protein, RNA-directed RNA polymerase catalytic subunit, Polymerase basic protein 2
      • Protein or peptide: Polymerase acidic protein
      • Protein or peptide: RNA-directed RNA polymerase catalytic subunit
      • Protein or peptide: Polymerase basic protein 2,Immunoglobulin G-binding protein A
    • Complex: RNA
      • RNA: RNA (5'-R(P*GP*GP*CP*CP*UP*GP*CP*U)-3')
      • RNA: RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*CP*C)-3')
Function / homology
Function and homology information


IgG binding / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / viral transcription / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / endonuclease activity / host cell cytoplasm ...IgG binding / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / viral transcription / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / host cell nucleus / RNA binding / extracellular region / metal ion binding
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / Influenza RNA-dependent RNA polymerase subunit PB1 / LysM domain superfamily / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal ...Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / Influenza RNA-dependent RNA polymerase subunit PB1 / LysM domain superfamily / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / LysM domain / LysM domain profile. / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / Influenza RNA polymerase PB2 middle domain / Influenza RNA polymerase PB2 6th domain / Influenza RNA polymerase PB2 C-terminal domain / : / : / Influenza RNA polymerase PB2 helical domain / LysM domain / Influenza RNA polymerase PB2 CAP binding domain / Immunoglobulin/albumin-binding domain superfamily / Polymerase acidic protein / YSIRK type signal peptide / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Immunoglobulin G-binding protein A / Polymerase acidic protein / RNA-directed RNA polymerase catalytic subunit / Polymerase basic protein 2
Similarity search - Component
Biological speciesCamelidae mixed library (mammal) / Influenza A virus (A/Brevig Mission/1/1918(H1N1)) / Staphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.63 Å
AuthorsKeown JR / Carrique L / Fodor E / Grimes JM
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust200835/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/R009945/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/K000241/1 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Mapping inhibitory sites on the RNA polymerase of the 1918 pandemic influenza virus using nanobodies.
Authors: Jeremy R Keown / Zihan Zhu / Loïc Carrique / Haitian Fan / Alexander P Walker / Itziar Serna Martin / Els Pardon / Jan Steyaert / Ervin Fodor / Jonathan M Grimes /
Abstract: Influenza A viruses cause seasonal epidemics and global pandemics, representing a considerable burden to healthcare systems. Central to the replication cycle of influenza viruses is the viral RNA- ...Influenza A viruses cause seasonal epidemics and global pandemics, representing a considerable burden to healthcare systems. Central to the replication cycle of influenza viruses is the viral RNA-dependent RNA polymerase which transcribes and replicates the viral RNA genome. The polymerase undergoes conformational rearrangements and interacts with viral and host proteins to perform these functions. Here we determine the structure of the 1918 influenza virus polymerase in transcriptase and replicase conformations using cryo-electron microscopy (cryo-EM). We then structurally and functionally characterise the binding of single-domain nanobodies to the polymerase of the 1918 pandemic influenza virus. Combining these functional and structural data we identify five sites on the polymerase which are sensitive to inhibition by nanobodies. We propose that the binding of nanobodies at these sites either prevents the polymerase from assuming particular functional conformations or interactions with viral or host factors. The polymerase is highly conserved across the influenza A subtypes, suggesting these sites as effective targets for potential influenza antiviral development.
History
DepositionFeb 16, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateFeb 9, 2022-
Current statusFeb 9, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.43
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.43
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7nj5
  • Surface level: 1.43
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12373.png

Downloads & links

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Map

FileDownload / File: emd_12373.map.gz / Format: CCP4 / Size: 8.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 130 pix.
= 260. Å		2 Å/pix.
x 130 pix.
= 260. Å		2 Å/pix.
x 130 pix.
= 260. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.43 / Movie #1: 1.43
Minimum - Maximum-3.8395407 - 6.9438634
Average (Standard dev.)0.032418728 (±0.27504438)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions130130130
Spacing130130130
CellA=B=C: 260.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z260.000260.000260.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS130130130
D min/max/mean-3.8406.9440.032

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Supplemental data

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Sample components

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Entire : 1918 Influenza virus polymerase heterotirmer in complex with vRNA...

EntireName: 1918 Influenza virus polymerase heterotirmer in complex with vRNA promoters and Nb8199
Components
  • Complex: 1918 Influenza virus polymerase heterotirmer in complex with vRNA promoters and Nb8199
    • Complex: Nb8199 Core
      • Protein or peptide: Nb8199 Core
    • Complex: Polymerase acidic protein, RNA-directed RNA polymerase catalytic subunit, Polymerase basic protein 2
      • Protein or peptide: Polymerase acidic protein
      • Protein or peptide: RNA-directed RNA polymerase catalytic subunit
      • Protein or peptide: Polymerase basic protein 2,Immunoglobulin G-binding protein A
    • Complex: RNA
      • RNA: RNA (5'-R(P*GP*GP*CP*CP*UP*GP*CP*U)-3')
      • RNA: RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*CP*C)-3')

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Supramolecule #1: 1918 Influenza virus polymerase heterotirmer in complex with vRNA...

SupramoleculeName: 1918 Influenza virus polymerase heterotirmer in complex with vRNA promoters and Nb8199
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: Nb8199 Core

SupramoleculeName: Nb8199 Core / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Camelidae mixed library (mammal)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: Polymerase acidic protein, RNA-directed RNA polymerase catalytic ...

SupramoleculeName: Polymerase acidic protein, RNA-directed RNA polymerase catalytic subunit, Polymerase basic protein 2
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Influenza A virus (A/Brevig Mission/1/1918(H1N1))
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #4: RNA

SupramoleculeName: RNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Influenza A virus (A/Brevig Mission/1/1918(H1N1))
Recombinant expressionOrganism: synthetic construct (others)

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Macromolecule #1: Polymerase acidic protein

MacromoleculeName: Polymerase acidic protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Influenza A virus (A/Brevig Mission/1/1918(H1N1)) / Strain: A/Brevig Mission/1/1918(H1N1)
Molecular weightTheoretical: 82.707391 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEDFVRQCFN PMIVELAEKA MKEYGEDLKI ETNKFAAICT HLEVCFMYSD FHFINERGES IIVESGDPNA LLKHRFEIIE GRDRTMAWT VVNSICNTTG AEKPKFLPDL YDYKENRFIE IGVTRREVHI YYLEKANKIK SEKTHIHIFS FTGEEMATKA D YTLDEESR ...String:
MEDFVRQCFN PMIVELAEKA MKEYGEDLKI ETNKFAAICT HLEVCFMYSD FHFINERGES IIVESGDPNA LLKHRFEIIE GRDRTMAWT VVNSICNTTG AEKPKFLPDL YDYKENRFIE IGVTRREVHI YYLEKANKIK SEKTHIHIFS FTGEEMATKA D YTLDEESR ARIKTRLFTI RQEMASRGLW DSFRQSERGE ETIEERFEIT GTMRRLADQS LPPNFSSLEN FRAYVDGFEP NG YIEGKLS QMSKEVNARI EPFLKTTPRP LRLPDGPPCS QRSKFLLMDA LKLSIEDPSH EGEGIPLYDA IKCMRTFFGW KEP NVVKPH EKGINPNYLL AWKQVLAELQ DIENEEKIPK TKNMKKTSQL KWALGENMAP EKVDFDDCKD VSDLKQYDSD EPEL RSLAS WIQSEFNKAC ELTDSSWIEL DEIGEDVAPI EHIASMRRNY FTAEVSHCRA TEYIMKGVYI NTALLNASCA AMDDF QLIP MISKCRTKEG RRKTNLYGFI IKGRSHLRND TDVVNFVSME FSLTDPRLEP HKWEKYCVLE IGDMLLRSAI GQVSRP MFL YVRTNGTSKI KMKWGMEMRR CLLQSLQQIE SMIEAESSVK EKDMTKEFFE NKSETWPIGE SPKGVEEGSI GKVCRTL LA KSVFNSLYAS PQLEGFSAES RKLLLIVQAL RDNLEPGTFD LGGLYEAIEE CLINDPWVLL NASWFNSFLT HALR

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Macromolecule #2: RNA-directed RNA polymerase catalytic subunit

MacromoleculeName: RNA-directed RNA polymerase catalytic subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Influenza A virus (A/Brevig Mission/1/1918(H1N1)) / Strain: A/Brevig Mission/1/1918(H1N1)
Molecular weightTheoretical: 86.625211 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDVNPTLLFL KVPAQNAIST TFPYTGDPPY SHGTGTGYTM DTVNRTHQYS EKGRWTTNTE TGAPQLNPID GPLPEDNEPS GYAQTDCVL EAMAFLEESH PGIFENSCLE TMEVVQQTRV DKLTQGRQTY DWTLNRNQPA ATALANTIEV FRSNGLTANE S GRLIDFLK ...String:
MDVNPTLLFL KVPAQNAIST TFPYTGDPPY SHGTGTGYTM DTVNRTHQYS EKGRWTTNTE TGAPQLNPID GPLPEDNEPS GYAQTDCVL EAMAFLEESH PGIFENSCLE TMEVVQQTRV DKLTQGRQTY DWTLNRNQPA ATALANTIEV FRSNGLTANE S GRLIDFLK DVMESMDKEE MEITTHFQRK RRVRDNMTKK MVTQRTIGKK KQRLNKRSYL IRALTLNTMT KDAERGKLKR RA IATPGMQ IRGFVYFVET LARSICEKLE QSGLPVGGNE KKAKLANVVR KMMTNSQDTE LSFTITGDNT KWNENQNPRM FLA MITYIT RNQPEWFRNV LSIAPIMFSN KMARLGKGYM FESKSMKLRT QIPAEMLASI DLKYFNDSTR KKIEKIRPLL IDGT ASLSP GMMMGMFNML STVLGVSILN LGQKRYTKTT YWWDGLQSSD DFALIVNAPN HEGIQAGVDR FYRTCKLLGI NMSKK KSYI NRTGTFEFTS FFYRYGFVAN FSMELPSFGV SGINESADMS IGVTVIKNNM INNDLGPATA QMALQLFIKD YRYTYR CHR GDTQIQTRRS FEIKKLWEQT RSKAGLLVSD GGPNLYNIRN LHIPEVCLKW ELMDEDYQGR LCNPLNPFVS HKEIESV NN AVMMPAHGPA KNMEYDAVAT THSWIPKRNR SILNTSQRGI LEDEQMYQKC CNLFEKFFPS SSYRRPVGIS SMVEAMVS R ARIDARIDFE SGRIKKEEFA EIMKICSTIE ELRRQK

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Macromolecule #3: Polymerase basic protein 2,Immunoglobulin G-binding protein A

MacromoleculeName: Polymerase basic protein 2,Immunoglobulin G-binding protein A
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 102.377219 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MERIKELRDL MSQSRTREIL TKTTVDHMAI IKKYTSGRQE KNPALRMKWM MAMKYPITAD KRIMEMIPER NEQGQTLWSK TNDAGSDRV MVSPLAVTWW NRNGPTTSAV HYPKIYKTYF EKVERLKHGT FGPVHFRNQV KIRRRVDINP GHADLSAKEA Q DVIMEVVF ...String:
MERIKELRDL MSQSRTREIL TKTTVDHMAI IKKYTSGRQE KNPALRMKWM MAMKYPITAD KRIMEMIPER NEQGQTLWSK TNDAGSDRV MVSPLAVTWW NRNGPTTSAV HYPKIYKTYF EKVERLKHGT FGPVHFRNQV KIRRRVDINP GHADLSAKEA Q DVIMEVVF PNEVGARILT SESQLTITKE KKEELQDCKI SPLMVAYMLE RELVRKTRFL PVAGGTSSVY IEVLHLTQGT CW EQMYTPG GEVRNDDVDQ SLIIAARNIV RRATVSADPL ASLLEMCHST QIGGIRMVDI LRQNPTEEQA VDICKAAMGL RIS SSFSFG GFTFKRTSGS SVKREEEVLT GNLQTLKIRV HEGYEEFTMV GRRATAILRK ATRRLIQLIV SGRDEQSIAE AIIV AMVFS QEDCMIKAVR GDLNFVNRAN QRLNPMHQLL RHFQKDAKVL FQNWGIEPID NVMGMIGILP DMTPSTEMSM RGVRV SKMG VDEYSSTERV VVSIDRFLRV RDQRGNVLLS PEEVSETQGT EKLTITYSSS MMWEVNGPES VLVNTYQWII RNWETV KIQ WSQNPTMLYN KMEFEPFQSL VPKAARGQYS GFVRTLFQQM RDVLGTFDTV QIIKLLPFAA APPKQSRMQF SSLTVNV RG SGMRILVRGN SPVFNYNKAT KRLTVLGKDA GALTEDPDEG TAGVESAVLR GFLILGKEDR RYGPALSINE LSNLAKGE K ANVLIGQGDV VLVMKRKRDS SILTDSQTAT KRIRMAINEN LYFQGELKTA ALAQHDEAVD NKFNKEQQNA FYEILHLPN LNEEQRNAFI QSLKDDPSQS ANLLAEAKKL NDAQAPKVDN KFNKEQQNAF YEILHLPNLN EEQRNAFIQS LKADPSQSAN LLAEAKKLN GAQAPKVDAN SAGKST

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Macromolecule #6: Nb8199 Core

MacromoleculeName: Nb8199 Core / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Camelidae mixed library (mammal)
Molecular weightTheoretical: 14.804354 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LVQAGGSLRL SCAASGRTFS SYAMGWFRQA PGKEREFVGA IDLSGLYKHY GDSVKGRFTI SRDNAKNTVY LQMSSLKPE DTAVYYCAAA GIYYAGSYSP LLYDYWGQGT QVTVSSHHHH HHEPEA

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Macromolecule #4: RNA (5'-R(P*GP*GP*CP*CP*UP*GP*CP*U)-3')

MacromoleculeName: RNA (5'-R(P*GP*GP*CP*CP*UP*GP*CP*U)-3') / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Influenza A virus (A/Brevig Mission/1/1918(H1N1))
Molecular weightTheoretical: 5.335125 KDa
SequenceString:
GGCCUGCUUU UGCUAUU

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Macromolecule #5: RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*CP*C)-3')

MacromoleculeName: RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*CP*C)-3')
type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Influenza A virus (A/Brevig Mission/1/1918(H1N1))
Molecular weightTheoretical: 4.862017 KDa
SequenceString:
AGUAGAAACA AGGCC

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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

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
166.0 mMNaClSodium chloridesodium chloride
25.0 mMNaSCNsodium thiocynate
20.0 mMHEPES-NaHepes
0.005 %Tween-20Tween20
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 69.5 e/Å2

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Image processing

Particle selectionNumber selected: 1874000
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 2.15)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.15)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 216500

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Atomic model buiding 1

Initial modelPDB ID:

7hna

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7nj5:
1918 H1N1 Viral influenza polymerase heterotrimer with Nb8199 core

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