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- EMDB-1049: A cellular receptor of human rhinovirus type 2, the very-low-dens... -

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Basic information

Entry
Database: EMDB / ID: EMD-1049
TitleA cellular receptor of human rhinovirus type 2, the very-low-density lipoprotein receptor, binds to two neighboring proteins of the viral capsid.
Map dataThis is a 3D reconstruction of HRV2/MBP-VLDLR(-123)
Sample
  • Sample: Human Rhinovirus 2 in complex with its cellular receptor, VLDL-R
  • Virus: Human rhinovirus 2
  • Organelle or cellular component: Cellular Receptor
Biological speciesHomo sapiens (human) / Human rhinovirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 16.0 Å
AuthorsNeumann E / Moser R / Snyers L / Blaas D / Hewat EA
CitationJournal: 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.
History
Header (metadata) releaseMay 19, 2003-
DepositionMay 29, 2003-
Map releaseJun 3, 2003-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4380
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4380
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1049.gif

Downloads & links

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Map

FileDownload / File: emd_1049.map.gz / Format: CCP4 / Size: 30.9 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationThis is a 3D reconstruction of HRV2/MBP-VLDLR(-123)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.76 Å/pix.
x 255 pix.
= 448.8 Å		1.76 Å/pix.
x 255 pix.
= 448.8 Å		1.76 Å/pix.
x 255 pix.
= 448.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4380.0 / Movie #1: 4380
Minimum - Maximum-17360.0 - 25708.0
Average (Standard dev.)312.54598999000001 (±3491.530029300000024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-127-127-127
Dimensions255255255
Spacing255255255
CellA=B=C: 448.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z1.761.761.76
M x/y/z255255255
origin x/y/z0.0000.0000.000
length x/y/z448.800448.800448.800
α/β/γ90.00090.00090.000
start NX/NY/NZ0052
NX/NY/NZ12812855
MAP C/R/S123
start NC/NR/NS-127-127-127
NC/NR/NS255255255
D min/max/mean-17360.00025708.000312.546

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Supplemental data

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Sample components

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Entire : Human Rhinovirus 2 in complex with its cellular receptor, VLDL-R

EntireName: Human Rhinovirus 2 in complex with its cellular receptor, VLDL-R
Components
  • Sample: Human Rhinovirus 2 in complex with its cellular receptor, VLDL-R
  • Virus: Human rhinovirus 2
  • Organelle or cellular component: Cellular Receptor

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Supramolecule #1000: Human Rhinovirus 2 in complex with its cellular receptor, VLDL-R

SupramoleculeName: Human Rhinovirus 2 in complex with its cellular receptor, VLDL-R
type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: Human rhinovirus 2

SupramoleculeName: Human rhinovirus 2 / type: virus / ID: 1 / NCBI-ID: 12130 / Sci species name: Human rhinovirus 2 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Diameter: 300 Å

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Supramolecule #2: Cellular Receptor

SupramoleculeName: Cellular Receptor / type: organelle_or_cellular_component / ID: 2 / Name.synonym: 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 (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: muscle
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pMALTM-c2x

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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

Concentration0.82 mg/mL
BufferpH: 7.4
Details: 50 mM Tris-HCl for the virus 2 mM CaCl2, 20 mM Tris-HCL for the receptor fragment
GridDetails: 300 mesh copper grid
VitrificationCryogen name: ETHANE / Method: Blot with filter paper for 1-2 seconds

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Electron microscopy

MicroscopeJEOL 2010F
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 300,000 times magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 7 µm / Number real images: 33 / Average electron dose: 15 e/Å2 / Details: Zeiss PhotoScan TD scanner
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 39700 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 1.4 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.18 µm / Nominal magnification: 40000
Sample stageSpecimen holder: Oxford cryo-holder CT3200 / Specimen holder model: OTHER

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Image processing

DetailsHRV2 and receptor fragment were incubated for 1 hour at 4 degree Celcius.
CTF correctionDetails: CTFMIX
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF
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.)
Number images used: 912

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Atomic model buiding 1

SoftwareName: O
DetailsProtocol: 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.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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