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Yorodumi- EMDB-28891: cryo-EM structure of a structurally designed Human metapneumoviru... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28891 | |||||||||
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Title | cryo-EM structure of a structurally designed Human metapneumovirus F protein in complex with antibody MPE8 | |||||||||
Map data | cryo-EM map for HMPV F in complex with scFv MPE8 | |||||||||
Sample |
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Keywords | metapneumovirus / HMPV / F protein / antibody / MPE8 / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia phage T2 (virus) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.25 Å | |||||||||
Authors | Zhou T / Kwong PD / Morano NC / Ou L | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: cryo-EM structure of a structurally designed Human metapneumovirus F protein in complex with antibody MPE8 Authors: Ou L / Kwong PD | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28891.map.gz | 49.9 MB | EMDB map data format | |
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Header (meta data) | emd-28891-v30.xml emd-28891.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
Images | emd_28891.png | 93.5 KB | ||
Masks | emd_28891_msk_1.map | 103 MB | Mask map | |
Others | emd_28891_additional_1.map.gz emd_28891_half_map_1.map.gz emd_28891_half_map_2.map.gz | 97 MB 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28891 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28891 | HTTPS FTP |
-Related structure data
Related structure data | 8f6xMC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_28891.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | cryo-EM map for HMPV F in complex with scFv MPE8 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_28891_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Sharpened cryo-EM map for HMPV F in complex with scFv MPE8
File | emd_28891_additional_1.map | ||||||||||||
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Annotation | Sharpened cryo-EM map for HMPV F in complex with scFv MPE8 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryo-EM half map for HMPV F in complex with scFv MPE8
File | emd_28891_half_map_1.map | ||||||||||||
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Annotation | cryo-EM half map for HMPV F in complex with scFv MPE8 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryo-EM half map for HMPV F in complex with scFv MPE8
File | emd_28891_half_map_2.map | ||||||||||||
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Annotation | cryo-EM half map for HMPV F in complex with scFv MPE8 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Purified complex of HMPV F with single chain Fv MPE8
Entire | Name: Purified complex of HMPV F with single chain Fv MPE8 |
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Components |
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-Supramolecule #1: Purified complex of HMPV F with single chain Fv MPE8
Supramolecule | Name: Purified complex of HMPV F with single chain Fv MPE8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Molecular weight | Theoretical: 266 KDa |
-Macromolecule #1: Structurally designed HMPV F protein HMPV_v3B_D12_DS454,Fibritin
Macromolecule | Name: Structurally designed HMPV F protein HMPV_v3B_D12_DS454,Fibritin type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage T2 (virus) |
Molecular weight | Theoretical: 56.891637 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSWKVMIIIS LLITPQHGLK ESYLEESCST ITEGYLSVLR TGWYTNVFTL EVGDVENLTC TDGPSLIKTE LDLTKSALRE LKTCSADQG SGGSGATAAA VTAGIAIAKT IRLESEVNAI KGCLKTTNEC VSTLGNGVRV LATAVRELKE FVSKNLTSAI N KNKCDIPD ...String: MSWKVMIIIS LLITPQHGLK ESYLEESCST ITEGYLSVLR TGWYTNVFTL EVGDVENLTC TDGPSLIKTE LDLTKSALRE LKTCSADQG SGGSGATAAA VTAGIAIAKT IRLESEVNAI KGCLKTTNEC VSTLGNGVRV LATAVRELKE FVSKNLTSAI N KNKCDIPD LKMAVSFSQF NRRFLNVVRQ FSDNAGITPA ISLDLMTDAE LARAVSYMPT SAGQIKLMLE NRCMVRRKGF GI LIGVYGS SVIYMVQLPI FGVIDTPCWI IKAAPSCSEK DGNYACLLRE DQGWYCKNAG STVYYPNDKD CETRGDHVFC DTA AGINVA EQSRECNINI STTNYPCKVS TGRHPISMVA LSPLGALVAC YKGVSCSIGS NRVGIIKQLP KGCSYITNQD ADTV TIDNT VYQLSKVEGE QHVIKGRPVS SSFDPIKFPE CQFNCALDQV FESIENSQAL VDQSNKILNS AESAIGGYIP EAPRD GQAY VRKDGEWVLL STFLGGLVPR GSHHHHHHSA WSHPQFEK UniProtKB: Fusion glycoprotein F0, Fusion glycoprotein F0, Fibritin |
-Macromolecule #2: MPE8 Single chain variable fragment
Macromolecule | Name: MPE8 Single chain variable fragment / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 32.012062 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MELGLRWVFL VAILEGVQCE VQLVESGGGL VKPGGSLRLS CAASGFTFSS YSMNWVRQAP GKGLEWVSSI SASSSYSDYA DSAKGRFTI SRDNAKTSLF LQMNSLRAED TAIYFCARAR ATGYSSITPY FDIWGQGTLV TVSSGTGGSG GGGSGGGGSG G GASQSVVT ...String: MELGLRWVFL VAILEGVQCE VQLVESGGGL VKPGGSLRLS CAASGFTFSS YSMNWVRQAP GKGLEWVSSI SASSSYSDYA DSAKGRFTI SRDNAKTSLF LQMNSLRAED TAIYFCARAR ATGYSSITPY FDIWGQGTLV TVSSGTGGSG GGGSGGGGSG G GASQSVVT QTPSVSGAPG QRVTISCTGS SSNIGAGYDV HWYQQLPGTA PKLLIYDNNN RPSGVPDRFS ASKSGTSASL AI TGLQAED EADYYCQSYD RNLSGVFGTG TKVTVLGSGE NLYFQSGGSG GHHHHHHHHS AWSHPQFEK |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 3 / 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 | 0.5 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R2/2 / Material: GOLD / Mesh: 200 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.06 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Number classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 192259 |