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- EMDB-44347: GP38-GnH-DS-Gc in the pre-fusion conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-44347
TitleGP38-GnH-DS-Gc in the pre-fusion conformation
Map dataFinal locally refined, DeepEMhanced map
Sample
  • Complex: GP38-GnH-DS-Gc in complex with ADI-46152 and ADI-36125 Fabs
    • Protein or peptide: GP38
    • Protein or peptide: Glycoprotein N
    • Protein or peptide: Glycoprotein C
    • Protein or peptide: ADI-46152 heavy chain
    • Protein or peptide: ADI-46152 light chain
    • Protein or peptide: ADI-36125 heavy chain
    • Protein or peptide: ADI-36125 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsGP38 / Gn / Gc / CCHFV / pre-fusion / heterotrimer / GP38-Gn-Gc / Gn-Gc / GP38/Gn/Gc / Gn/Gc / GP38-Gn / GP38/Gn / VIRAL PROTEIN
Function / homology
Function and homology information


host cell Golgi membrane / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Nairovirus M polyprotein-like / : / : / : / : / Nairovirus GP38 / Nairovirus, structural glycoprotein Gn / Nairovirus, mucin-like domain / Nairovirus NSm / Hantavirus glycoprotein Gc ...Nairovirus M polyprotein-like / : / : / : / : / Nairovirus GP38 / Nairovirus, structural glycoprotein Gn / Nairovirus, mucin-like domain / Nairovirus NSm / Hantavirus glycoprotein Gc / : / Hantavirus glycoprotein Gc, N-terminal / Hantavirus glycoprotein Gc, C-terminal
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesOrthonairovirus haemorrhagiae / Crimean-Congo hemorrhagic fever virus strain IbAr10200 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsMcFadden E / McLellan JS
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI152246 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI142777 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 30, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44347.png

Downloads & links

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Map

FileDownload / File: emd_44347.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal locally refined, DeepEMhanced map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 399.936 Å		0.83 Å/pix.
x 480 pix.
= 399.936 Å		0.83 Å/pix.
x 480 pix.
= 399.936 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.112
Minimum - Maximum-0.03763542 - 2.0221426
Average (Standard dev.)0.00035125873 (±0.011155043)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 399.93597 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_44347_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A local refinement

Fileemd_44347_half_map_1.map
AnnotationHalf map A local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B local refinement

Fileemd_44347_half_map_2.map
AnnotationHalf map B local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GP38-GnH-DS-Gc in complex with ADI-46152 and ADI-36125 Fabs

EntireName: GP38-GnH-DS-Gc in complex with ADI-46152 and ADI-36125 Fabs
Components
  • Complex: GP38-GnH-DS-Gc in complex with ADI-46152 and ADI-36125 Fabs
    • Protein or peptide: GP38
    • Protein or peptide: Glycoprotein N
    • Protein or peptide: Glycoprotein C
    • Protein or peptide: ADI-46152 heavy chain
    • Protein or peptide: ADI-46152 light chain
    • Protein or peptide: ADI-36125 heavy chain
    • Protein or peptide: ADI-36125 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: GP38-GnH-DS-Gc in complex with ADI-46152 and ADI-36125 Fabs

SupramoleculeName: GP38-GnH-DS-Gc in complex with ADI-46152 and ADI-36125 Fabs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: Fab fragment generated by HRV3C cleavage of IgG, GP38-GnH-DS-Gc in a single chain polypeptide
Source (natural)Organism: Orthonairovirus haemorrhagiae

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Macromolecule #1: GP38

MacromoleculeName: GP38 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Crimean-Congo hemorrhagic fever virus strain IbAr10200
Strain: IbAr10200
Molecular weightTheoretical: 30.216844 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NLKMEIILTL SQGLKKYYGK ILRLLQLTLE EDTEGLLEWC KRNLGLDCDD TFFQKRIEEF FITGEGHFNE VLQFRTPGTL STTESTPAG LPTAEPFKSY FAKGFLSIDS GYYSAKCYSG TSNSGLQLIN ITRHSTRIVD TPGPKITNLK TINCINLKAS I FKEHREVE ...String:
NLKMEIILTL SQGLKKYYGK ILRLLQLTLE EDTEGLLEWC KRNLGLDCDD TFFQKRIEEF FITGEGHFNE VLQFRTPGTL STTESTPAG LPTAEPFKSY FAKGFLSIDS GYYSAKCYSG TSNSGLQLIN ITRHSTRIVD TPGPKITNLK TINCINLKAS I FKEHREVE INVLLPQVAV NLSNCHVVIK SHVCDYSLDI DGAVRLPHIY HEGVFIPGTY KIVIDKKNKL NDRCTLFTDC VI KGREVRK GCSVLRQYKT EIRIGKASTG S

UniProtKB: Envelopment polyprotein

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Macromolecule #2: Glycoprotein N

MacromoleculeName: Glycoprotein N / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Crimean-Congo hemorrhagic fever virus strain IbAr10200
Strain: IbAr10200
Molecular weightTheoretical: 10.426316 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SRLLSEEPSD DCISRTQLLR TETAEIHGDN YGGPGDKITI CNGSTICDQR LGSELGCYTI NRVRSFKLCE NSENLYFQGG GGSGGGSGG GSENLYFQG

UniProtKB: Envelopment polyprotein

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Macromolecule #3: Glycoprotein C

MacromoleculeName: Glycoprotein C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Crimean-Congo hemorrhagic fever virus strain IbAr10200
Strain: IbAr10200
Molecular weightTheoretical: 59.474047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SLSIEAPWGA INVQSTYKPT VSTANIALSW SSVEHRGNKI LVSGRSESIM KLEERTGISW DLGVEDASES KLLTVSVMDL SQMYSPVFE YLSGDRQVGE WPKATCTGDC PERCGCTSST CLHKEWPHSR NWRCNPTWCW GVGTGCTCCG LDVKDLFTDY M FVKWKVEY ...String:
SLSIEAPWGA INVQSTYKPT VSTANIALSW SSVEHRGNKI LVSGRSESIM KLEERTGISW DLGVEDASES KLLTVSVMDL SQMYSPVFE YLSGDRQVGE WPKATCTGDC PERCGCTSST CLHKEWPHSR NWRCNPTWCW GVGTGCTCCG LDVKDLFTDY M FVKWKVEY IKTEAIVCVE LTSQERQCSL IEAGTRFNLG PVTITLSEPR NIQQKLPPEI ITLHPRIEEG FFDLMHVQKV LS ASTVCKL QSCTHGVPGD LQVYHIGNLL KGDKVNGHLI HKIEPHFNTS WMSWDGCDLD YYCNMGDWPS CTYTGVTQHN HAS FVNLLN IETDYTKNFH FHSKRVTAHG DTPQLDLKAR PTYGAGEITV LVEVADMELH TKKIEISGLK FASLACTGCY ACSS GISCK VRIHVDEPDE LTVHVKSDDP DVVAASSSLM ARKLEFGTDS TFKAFSAMPK TSLCFYIVER EHCKSCSEED TKKCV NTKL EGSLEVLFQG PGHHHHHHHH SAWSHPQFEK GGGSGGGGSG GSAWSHPQFE K

UniProtKB: Envelopment polyprotein

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Macromolecule #4: ADI-46152 heavy chain

MacromoleculeName: ADI-46152 heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.562246 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSE VQLVESGGVL VQPGGSLRLS CAASGFTVNS NYMTWVRQAP GKGLEWVSVI YSGGYTYYAD SVKGRFAIS RDNSKNTVYL QMNSLRVEDT AVYYCARLRL SSSWYPEAFD YWGQGTLVTV SSASTKGPSV FPLAPSSKST S GGTAALGC ...String:
MGWSCIILFL VATATGVHSE VQLVESGGVL VQPGGSLRLS CAASGFTVNS NYMTWVRQAP GKGLEWVSVI YSGGYTYYAD SVKGRFAIS RDNSKNTVYL QMNSLRVEDT AVYYCARLRL SSSWYPEAFD YWGQGTLVTV SSASTKGPSV FPLAPSSKST S GGTAALGC LVKDYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VE PKSCDKG LEVLFQGPTH TCPPCPAPEL LGGPSVFLFP PKPKDTLMIS RTPEVTCVVV DVSHEDPEVK FNWYVDGVEV HNA KTKPRE EQYNSTYRVV SVLTVLHQDW LNGKEYKCKV SNKALPAPIE KTISKAKGQP REPQVYTLPP SRDELTKNQV SLTC LVKGF YPSDIAVEWE SNGQPENNYK TTPPVLDSDG SFFLYSKLTV DKSRWQQGNV FSCSVMHEAL HNHYTQKSLS LSPGK

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Macromolecule #5: ADI-46152 light chain

MacromoleculeName: ADI-46152 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.709848 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRPTWAWWLF LVLLLALWAP ARGAILLTQS PSSLSASVGD RVTITCRASQ GISSALAWYQ QKPGRAPKVL IYDASSLANG VPSRFSGSG SGTDFTLTIN SLQPEDFATY YCQQFNYYPL TFGGGTKVEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL N NFYPREAK ...String:
MRPTWAWWLF LVLLLALWAP ARGAILLTQS PSSLSASVGD RVTITCRASQ GISSALAWYQ QKPGRAPKVL IYDASSLANG VPSRFSGSG SGTDFTLTIN SLQPEDFATY YCQQFNYYPL TFGGGTKVEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL N NFYPREAK VQWKVDNALQ SGNSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTQGTTSVTK SFNRGEC

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Macromolecule #6: ADI-36125 heavy chain

MacromoleculeName: ADI-36125 heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.377969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSQ VQLVQSGGGL VKPGGSLRLS CAASGFSLSS YSMNWVRQAP GKGLEWVSSI SNTGSYKYYA DSVKGRFTI SRDNAKNSVY LQMNSLRAED RAVYYCARDH VHWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
MGWSCIILFL VATATGVHSQ VQLVQSGGGL VKPGGSLRLS CAASGFSLSS YSMNWVRQAP GKGLEWVSSI SNTGSYKYYA DSVKGRFTI SRDNAKNSVY LQMNSLRAED RAVYYCARDH VHWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKG LE VLFQGPT HTCPPCPAPE LLGGPSVFLF PPKPKDTLMI SRTPEVTCVV VDVSHEDPEV KFNWYVDGVE VHNAKTKPRE EQY NSTYRV VSVLTVLHQD WLNGKEYKCK VSNKALPAPI EKTISKAKGQ PREPQVYTLP PSRDELTKNQ VSLTCLVKGF YPSD IAVEW ESNGQPENNY KTTPPVLDSD GSFFLYSKLT VDKSRWQQGN VFSCSVMHEA LHNHYTQKSL SLSPGK

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Macromolecule #7: ADI-36125 light chain

MacromoleculeName: ADI-36125 light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.091293 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRPTWAWWLF LVLLLALWAP ARGETTLTQS PSSLSASVGD RVTITCRASQ GISNFLAWYQ QKPGKVPKLL IYTTSTLQSG VPSRFSGSG SGTDFTLTIS SLQPEDVATY YCLYYNSAPW TFGQGTKVEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL N NFYPREAK ...String:
MRPTWAWWLF LVLLLALWAP ARGETTLTQS PSSLSASVGD RVTITCRASQ GISNFLAWYQ QKPGKVPKLL IYTTSTLQSG VPSRFSGSG SGTDFTLTIS SLQPEDVATY YCLYYNSAPW TFGQGTKVEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL N NFYPREAK VQWKVDNALQ SGNSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGEC

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration0.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 69.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 728031
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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