+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41048 | |||||||||
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Title | Lassa GPC Trimer in complex with Fab 8.11G and nanobody D5 | |||||||||
Map data | Sharpened map | |||||||||
Sample |
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Keywords | vaccine / GPC / GP1 / GP2 / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information host cell Golgi membrane / receptor-mediated 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 / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Lassa virus Josiah / Camelus bactrianus (Bactrian camel) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||
Authors | Gorman J / Kwong PD | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Cleavage-intermediate Lassa virus trimer elicits neutralizing responses, identifies neutralizing nanobodies, and reveals an apex-situated site-of-vulnerability. Authors: Jason Gorman / Crystal Sao-Fong Cheung / Zhijian Duan / Li Ou / Maple Wang / Xuejun Chen / Cheng Cheng / Andrea Biju / Yaping Sun / Pengfei Wang / Yongping Yang / Baoshan Zhang / Jeffrey C ...Authors: Jason Gorman / Crystal Sao-Fong Cheung / Zhijian Duan / Li Ou / Maple Wang / Xuejun Chen / Cheng Cheng / Andrea Biju / Yaping Sun / Pengfei Wang / Yongping Yang / Baoshan Zhang / Jeffrey C Boyington / Tatsiana Bylund / Sam Charaf / Steven J Chen / Haijuan Du / Amy R Henry / Tracy Liu / Edward K Sarfo / Chaim A Schramm / Chen-Hsiang Shen / Tyler Stephens / I-Ting Teng / John-Paul Todd / Yaroslav Tsybovsky / Raffaello Verardi / Danyi Wang / Shuishu Wang / Zhantong Wang / Cheng-Yan Zheng / Tongqing Zhou / Daniel C Douek / John R Mascola / David D Ho / Mitchell Ho / Peter D Kwong / Abstract: Lassa virus (LASV) infection is expanding outside its traditionally endemic areas in West Africa, posing a pandemic biothreat. LASV-neutralizing antibodies, moreover, have proven difficult to elicit. ...Lassa virus (LASV) infection is expanding outside its traditionally endemic areas in West Africa, posing a pandemic biothreat. LASV-neutralizing antibodies, moreover, have proven difficult to elicit. To gain insight into LASV neutralization, here we develop a prefusion-stabilized LASV glycoprotein trimer (GPC), pan it against phage libraries comprising single-domain antibodies (nanobodies) from shark and camel, and identify one, D5, which neutralizes LASV. Cryo-EM analyses reveal D5 to recognize a cleavage-dependent site-of-vulnerability at the trimer apex. The recognized site appears specific to GPC intermediates, with protomers lacking full cleavage between GP1 and GP2 subunits. Guinea pig immunizations with the prefusion-stabilized cleavage-intermediate LASV GPC, first as trimer and then as a nanoparticle, induce neutralizing responses, targeting multiple epitopes including that of D5; we identify a neutralizing antibody (GP23) from the immunized guinea pigs. Collectively, our findings define a prefusion-stabilized GPC trimer, reveal an apex-situated site-of-vulnerability, and demonstrate elicitation of LASV-neutralizing responses by a cleavage-intermediate LASV trimer. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41048.map.gz | 97.1 MB | EMDB map data format | |
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Header (meta data) | emd-41048-v30.xml emd-41048.xml | 26.3 KB 26.3 KB | Display Display | EMDB header |
Images | emd_41048.png | 72.2 KB | ||
Masks | emd_41048_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-41048.cif.gz | 7.2 KB | ||
Others | emd_41048_additional_1.map.gz emd_41048_additional_2.map.gz emd_41048_half_map_1.map.gz emd_41048_half_map_2.map.gz | 51.2 MB 7.1 MB 95.7 MB 95.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41048 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41048 | HTTPS FTP |
-Validation report
Summary document | emd_41048_validation.pdf.gz | 843.5 KB | Display | EMDB validaton report |
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Full document | emd_41048_full_validation.pdf.gz | 843 KB | Display | |
Data in XML | emd_41048_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | emd_41048_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41048 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41048 | HTTPS FTP |
-Related structure data
Related structure data | 8t5cMC 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_41048.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.076 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41048_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: unsharpened map
File | emd_41048_additional_1.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: density modified (resolve)
File | emd_41048_additional_2.map | ||||||||||||
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Annotation | density modified (resolve) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_41048_half_map_1.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_41048_half_map_2.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Lassa GPC Trimer in complex with Fab 8.11G and nanobody D5
Entire | Name: Lassa GPC Trimer in complex with Fab 8.11G and nanobody D5 |
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Components |
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-Supramolecule #1: Lassa GPC Trimer in complex with Fab 8.11G and nanobody D5
Supramolecule | Name: Lassa GPC Trimer in complex with Fab 8.11G and nanobody D5 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Lassa virus Josiah |
-Macromolecule #1: Glycoprotein G1
Macromolecule | Name: Glycoprotein G1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Lassa virus Josiah |
Molecular weight | Theoretical: 22.884879 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: TSLYKGVYEL QTLELNMETL NMTMPLSCTK NNSHHYIMVG NETGLELTLT NTSIINHKFC NLSDAHKKNL YDHALMSIIS TFHLSIPNF NQYEAMSCDF NGGKISVQYN LSHSYAGDAA NHCGTVANGV LQTFMRMAWG GSYIALDSGG CGNWDCIMTS Y QYLIIQNT ...String: TSLYKGVYEL QTLELNMETL NMTMPLSCTK NNSHHYIMVG NETGLELTLT NTSIINHKFC NLSDAHKKNL YDHALMSIIS TFHLSIPNF NQYEAMSCDF NGGKISVQYN LSHSYAGDAA NHCGTVANGV LQTFMRMAWG GSYIALDSGG CGNWDCIMTS Y QYLIIQNT TWEDHCQFSR PSPIGYLGLL SQRTRDIYIS RRRR UniProtKB: Pre-glycoprotein polyprotein GP complex |
-Macromolecule #2: Glycoprotein G2
Macromolecule | Name: Glycoprotein G2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Lassa virus Josiah |
Molecular weight | Theoretical: 22.14317 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GTFTWTLSDS EGKDTPGGYC LTRWMLIEAE LKCFGNTAVA KCNEKHDEEF CDMLRLFDFN KQAIQRCKAP AQMSIQLINK AVNALINDQ LIMKNHLRDI MGIPYCNYSK YWYLNHTTTG RTSLPKCWLV SNGSYLNETH FSDDIEQQAD NMITEMLQKE G GGYIPEAP ...String: GTFTWTLSDS EGKDTPGGYC LTRWMLIEAE LKCFGNTAVA KCNEKHDEEF CDMLRLFDFN KQAIQRCKAP AQMSIQLINK AVNALINDQ LIMKNHLRDI MGIPYCNYSK YWYLNHTTTG RTSLPKCWLV SNGSYLNETH FSDDIEQQAD NMITEMLQKE G GGYIPEAP RDGQAYVRKD GEWVLLSTFL GGLVPR UniProtKB: Pre-glycoprotein polyprotein GP complex |
-Macromolecule #3: D5 nanobody
Macromolecule | Name: D5 nanobody / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Camelus bactrianus (Bactrian camel) |
Molecular weight | Theoretical: 13.228544 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AWQLVESGGG SVQPGGSLTL TCQASKSTFS TSGMRWERQA QGKGVEFVAD ISSDSTRKWY SDSVKGRFTI SRSNWWRTVT LQMNDLKPE DTARYYCKDL ESHHLRGQGT QVTVSSSGQA G |
-Macromolecule #4: 8.11G Heavy Chain
Macromolecule | Name: 8.11G Heavy Chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.257604 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DQVQLQESGP GLVKPSETLS LTCSISGVST RNYYWSWIRQ SPGKGLEWIG YIFNIGTTNY NPSLKSRLTI SVDTSKNQFS LKITSVTAA DTAVYYCASG FEYGDYTFDY WGQGTPVTVS S |
-Macromolecule #5: 8.11G Light Chain
Macromolecule | Name: 8.11G Light Chain / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.101508 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DEIVLTQSPA TLSVSPGGRA SLSCRASQSI GDKLSWYQQK PGQAPRLVIY GAYTRATDIS PRFSGSRSGT DFNLTISRMQ SGDFAVYFC QQYENWPRTF GQGTKLEIKR |
-Macromolecule #14: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 14 / Number of copies: 23 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.4 / Details: PBS |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 2.0 sec. / Average electron dose: 51.15 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |