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Yorodumi- EMDB-31569: Cryo-EM structure of VEEV VLP-LDLRAD3-D1 complex at the 5-fold axes -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31569 | |||||||||
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Title | Cryo-EM structure of VEEV VLP-LDLRAD3-D1 complex at the 5-fold axes | |||||||||
Map data | Cryo-EM structure of VEEV VLP-LDLRAD3-D1 complex at the 5-fold axes | |||||||||
Sample |
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Function / homology | Function and homology information regulation of protein processing / receptor-mediated endocytosis / amyloid-beta binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Venezuelan equine encephalitis virus (strain TC-83) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Zhang X / Xiang Y / Ma J / Ma B / Huang C | |||||||||
Citation | Journal: Nature / Year: 2021 Title: Structure of Venezuelan equine encephalitis virus with its receptor LDLRAD3. Authors: Bingting Ma / Cuiqing Huang / Jun Ma / Ye Xiang / Xinzheng Zhang / Abstract: Venezuelan equine encephalitis virus (VEEV) is an enveloped RNA virus that causes encephalitis and potentially mortality in infected humans and equines. At present, no vaccines or drugs are available ...Venezuelan equine encephalitis virus (VEEV) is an enveloped RNA virus that causes encephalitis and potentially mortality in infected humans and equines. At present, no vaccines or drugs are available that prevent or cure diseases caused by VEEV. Low-density lipoprotein receptor class A domain-containing 3 (LDLRAD3) was recently identified as a receptor for the entry of VEEV into host cells. Here we present the cryo-electron microscopy structure of the LDLRAD3 extracellular domain 1 (LDLRAD3-D1) in complex with VEEV virus-like particles at a resolution of 3.0 Å. LDLRAD3-D1 has a cork-like structure and is inserted into clefts formed between adjacent VEEV E2-E1 heterodimers in the viral-surface trimer spikes through hydrophobic and polar contacts. Mutagenesis studies of LDLRAD3-D1 identified residues that are involved in the key interactions with VEEV. Of note, some of the LDLRAD3-D1 mutants showed a significantly increased binding affinity for VEEV, suggesting that LDLRAD3-D1 may serve as a potential scaffold for the development of inhibitors of VEEV entry. Our structures provide insights into alphavirus assembly and the binding of receptors to alphaviruses, which may guide the development of therapeutic countermeasures against alphaviruses. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31569.map.gz | 59.8 MB | EMDB map data format | |
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Header (meta data) | emd-31569-v30.xml emd-31569.xml | 16.5 KB 16.5 KB | Display Display | EMDB header |
Images | emd_31569.png | 199.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31569 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31569 | HTTPS FTP |
-Validation report
Summary document | emd_31569_validation.pdf.gz | 572.9 KB | Display | EMDB validaton report |
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Full document | emd_31569_full_validation.pdf.gz | 572.4 KB | Display | |
Data in XML | emd_31569_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_31569_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31569 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31569 | HTTPS FTP |
-Related structure data
Related structure data | 7ffnMC 7ffeC 7fffC 7fflC 7ffoC 7ffqC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31569.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of VEEV VLP-LDLRAD3-D1 complex at the 5-fold axes | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Venezuelan equine encephalitis virus (strain TC-83)
Entire | Name: Venezuelan equine encephalitis virus (strain TC-83) |
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Components |
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-Supramolecule #1: Venezuelan equine encephalitis virus (strain TC-83)
Supramolecule | Name: Venezuelan equine encephalitis virus (strain TC-83) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Venezuelan equine encephalitis virus (strain TC-83) |
-Supramolecule #2: Venezuelan equine encephalitis virus (strain TC-83)
Supramolecule | Name: Venezuelan equine encephalitis virus (strain TC-83) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #4-#5 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: LDLRAD3
Supramolecule | Name: LDLRAD3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: togavirin |
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Source (natural) | Organism: Venezuelan equine encephalitis virus (strain TC-83) Strain: TC-83 |
Molecular weight | Theoretical: 30.980801 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFPFQPMYPM QPMPYRNPFA APRRPWFPRT DPFLAMQVQE LTRSMANLTF KQRRDAPPEG PSANKPKKEA SQKQKGGGQG KKKKNQGKK KAKTGPPNPK AQNGNKKKTN KKPGKRQRMV MKLESDKTFP IMLEGKINGY ACVVGGKLFR PMHVEGKIDN D VLAALKTK ...String: MFPFQPMYPM QPMPYRNPFA APRRPWFPRT DPFLAMQVQE LTRSMANLTF KQRRDAPPEG PSANKPKKEA SQKQKGGGQG KKKKNQGKK KAKTGPPNPK AQNGNKKKTN KKPGKRQRMV MKLESDKTFP IMLEGKINGY ACVVGGKLFR PMHVEGKIDN D VLAALKTK KASKYDLEYA DVPQNMRADT FKYTHEKPQG YYSWHHGAVQ YENGRFTVPK GVGAKGDSGR PILDNQGRVV AI VLGGVNE GSRTALSVVM WNEKGVTVKY TPENCEQW |
-Macromolecule #2: assembly protein E3
Macromolecule | Name: assembly protein E3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Venezuelan equine encephalitis virus (strain TC-83) Strain: TC-83 |
Molecular weight | Theoretical: 6.488601 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SLVTTMCLLA NVTFPCAQPP ICYDRKPAET LAMLSVNVDN PGYDELLEAA VKCPGRKRR |
-Macromolecule #3: Low-density lipoprotein receptor class A domain-containing protein 3
Macromolecule | Name: Low-density lipoprotein receptor class A domain-containing protein 3 type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 8.652934 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MWLLGPLCLL LSSAAESQLL PGNNFTNECN IPGNFMCSNG RCIPGAWQCD GLPDCFDKSD EKECPKAKSK GPLEVLFQGP |
-Macromolecule #4: Spike glycoprotein E2
Macromolecule | Name: Spike glycoprotein E2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Venezuelan equine encephalitis virus (strain TC-83) Strain: TC-83 |
Molecular weight | Theoretical: 47.113746 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: STEELFNEYK LTRPYMARCI RCAVGSCHSP IAIEAVKSDG HDGYVRLQTS SQYGLDSSGN LKGRTMRYDM HGTIKEIPLH QVSLYTSRP CHIVDGHGYF LLARCPAGDS ITMEFKKDSV RHSCSVPYEV KFNPVGRELY THPPEHGVEQ ACQVYAHDAQ N RGAYVEMH ...String: STEELFNEYK LTRPYMARCI RCAVGSCHSP IAIEAVKSDG HDGYVRLQTS SQYGLDSSGN LKGRTMRYDM HGTIKEIPLH QVSLYTSRP CHIVDGHGYF LLARCPAGDS ITMEFKKDSV RHSCSVPYEV KFNPVGRELY THPPEHGVEQ ACQVYAHDAQ N RGAYVEMH LPGSEVDSSL VSLSGSSVTV TPPDGTSALV ECECGGTKIS ETINKTKQFS QCTKKEQCRA YRLQNDKWVY NS DKLPKAA GATLKGKLHV PFLLADGKCT VPLAPEPMIT FGFRSVSLKL HPKNPTYLIT RQLADEPHYT HELISEPAVR NFT VTEKGW EFVWGNHPPK RFWAQETAPG NPHGLPHEVI THYYHRYPMS TILGLSICAA IATVSVAAST WLFCRSRVAC LTPY RLTPN ARIPFCLAVL CCARTARA |
-Macromolecule #5: Spike glycoprotein E1
Macromolecule | Name: Spike glycoprotein E1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Venezuelan equine encephalitis virus (strain TC-83) Strain: TC-83 |
Molecular weight | Theoretical: 47.952066 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: YEHATTMPSQ AGISYNTIVN RAGYAPLPIS ITPTKIKLIP TVNLEYVTCH YKTGMDSPAI KCCGSQECTP TYRPDEQCKV FTGVYPFMW GGAYCFCDTE NTQVSKAYVM KSDDCLADHA EAYKAHTASV QAFLNITVGE HSIVTTVYVN GETPVNFNGV K ITAGPLST ...String: YEHATTMPSQ AGISYNTIVN RAGYAPLPIS ITPTKIKLIP TVNLEYVTCH YKTGMDSPAI KCCGSQECTP TYRPDEQCKV FTGVYPFMW GGAYCFCDTE NTQVSKAYVM KSDDCLADHA EAYKAHTASV QAFLNITVGE HSIVTTVYVN GETPVNFNGV K ITAGPLST AWTPFDRKIV QYAGEIYNYD FPEYGAGQPG AFGDIQSRTV SSSDLYANTN LVLQRPKAGA IHVPYTQAPS GF EQWKKDK APSLKFTAPF GCEIYTNPIR AENCAVGSIP LAFDIPDALF TRVSETPTLS AAECTLNECV YSSDFGGIAT VKY SASKSG KCAVHVPSGT ATLKEAAVEL TEQGSATIHF STANIHPEFR LQICTSYVTC KGDCHPPKDH IVTHPQYHAQ TFTA AVSKT AWTWLTSLLG GSAVIIIIGL VLATIVAMYV LTNQKHN |
-Macromolecule #6: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 726076 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |