|Entry||Database: EMDB / ID: EMD-1049|
|Title||A cellular receptor of human rhinovirus type 2, the very-low-density lipoprotein receptor, binds to two neighboring proteins of the viral capsid.|
|Sample||Human Rhinovirus 2 in complex with its cellular receptor, VLDL-R:|
virus / Cellular Receptor
|Biological species||Human rhinovirus 2 / Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / Resolution: 16 Å|
|Authors||Neumann E / Moser R / Snyers L / Blaas D / Hewat EA|
|Citation||Journal: J Virol / Year: 2003|
Title: A cellular receptor of human rhinovirus type 2, the very-low-density lipoprotein receptor, binds to two neighboring proteins of the viral capsid.
Authors: Emmanuelle Neumann / Rosita Moser / Luc Snyers / Dieter Blaas / Elizabeth A Hewat /
Abstract: The very-low-density lipoprotein receptor (VLDL-R) is a receptor for the minor-group human rhinoviruses (HRVs). Only two of the eight binding repeats of the VLDL-R bind to HRV2, and their footprints ...The very-low-density lipoprotein receptor (VLDL-R) is a receptor for the minor-group human rhinoviruses (HRVs). Only two of the eight binding repeats of the VLDL-R bind to HRV2, and their footprints describe an annulus on the dome at each fivefold axis. By studying the complex formed between a selection of soluble fragments of the VLDL-R and HRV2, we demonstrate that it is the second and third repeats that bind. We also show that artificial concatemers of the same repeat can bind to HRV2 with the same footprint as that for the native receptor. In a 16-A-resolution cryoelectron microscopy map of HRV2 in complex with the VLDL-R, the individual repeats are defined. The third repeat is strongly bound to charged and polar residues of the HI and BC loops of viral protein 1 (VP1), while the second repeat is more weakly bound to the neighboring VP1. The footprint of the strongly bound third repeat extends down the north side of the canyon. Since the receptor molecule can bind to two adjacent copies of VP1, we suggest that the bound receptor "staples" the VP1s together and must be detached before release of the RNA can occur. When the receptor is bound to neighboring sites on HRV2, steric hindrance prevents binding of the second repeat.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_1049.map.gz / Format: CCP4 / Size: 30.9 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.76 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Human Rhinovirus 2 in complex with its cellular receptor, VLDL-R
|Entire||Name: Human Rhinovirus 2 in complex with its cellular receptor, VLDL-R|
Number of Components: 2
-Component #1: virus, Human rhinovirus 2
|Virus||Name: Human rhinovirus 2 / Class: VIRION / Enveloped: No / Empty: No / Isolate: SEROTYPE|
|Species||Species: Human rhinovirus 2|
|Source (natural)||Host Species: Homo sapiens (human) / Host Category: VERTEBRATES|
-Component #2: cellular-component, Cellular Receptor
|Cellular-component||Name: Cellular Receptor / a.k.a: Very Low Density Lipoprotein - Receptor|
Details: The VLDL-R consists of eight imperfect ligand-binding repeats of approximately 40 amino acids at its N-terminus. Recombinant VLDL-minireceptors encompassing different ligand-binding repeats ...Details: The VLDL-R consists of eight imperfect ligand-binding repeats of approximately 40 amino acids at its N-terminus. Recombinant VLDL-minireceptors encompassing different ligand-binding repeats are here expressed with the first three repeats + a Maltose Binding Protein fused to the N-terminus + a Hexa-his-tag fused to the C-terminus.
Recombinant expression: Yes
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Escherichia coli (E. coli) / Vector: pMALTM-c2x|
|Source (natural)||Organ Or Tissue: muscle|
|Specimen||Specimen State: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.82 mg/mL|
Buffer solution: 50 mM Tris-HCl for the virus 2 mM CaCl2, 20 mM Tris-HCL for the receptor fragment
|Support film||300 mesh copper grid|
|Vitrification||Cryogen Name: ETHANE / Method: Blot with filter paper for 1-2 seconds|
-Electron microscopy imaging
|Imaging||Microscope: JEOL 2010F|
|Electron gun||Electron Source: FIELD EMISSION GUN / Accelerating Voltage: 200 kV / Electron Dose: 15 e/Å2 / Illumination Mode: SPOT SCAN|
|Lens||Magnification: 40000 X (nominal), 39700 X (calibrated)|
Astigmatism: objective lens astigmatism was corrected at 300,000 times magnification
Cs: 1.4 mm / Imaging Mode: BRIGHT FIELD / Defocus: 1180 - 2900 nm
|Specimen Holder||Holder: Oxford cryo-holder CT3200 / Model: OTHER|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of Digital Images: 33 / Scanner: OTHER / Sampling Size: 7 µm / Details: Zeiss PhotoScan TD scanner|
|Processing||Method: single particle reconstruction / Number of Projections: 912 |
Details: HRV2 and receptor fragment were incubated for 1 hour at 4 degree Celcius.
Applied Symmetry: I (icosahedral)
|3D reconstruction||Algorithm: Model Based - PFT / CTF correction: CTFMIX / Resolution: 16 Å / Resolution Method: FSC 0.5|
Details: Methods for reconstructing density maps of "single" particles from cryoelectron micrographs to subnanometer resolution (Conway et al.,J Struct Biol. 1999 Dec 1;128(1):106-18.)
-Atomic model buiding
|Modeling #1||Software: O / Refinement protocol: rigid body / Refinement space: REAL|
Details: Protocol: Manual docking. Fitting the X-RAY structures of HRV2 and the VLDL-R repeats to the cryo-electron microscope reconstructed density. Determination of the residues included in the footprints.
-Aug 12, 2020. Covid-19 info
New page: Covid-19 featured information page in EM Navigator.
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
- This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
- Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
- The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi