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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 data
SampleHuman Rhinovirus 2 in complex with its cellular receptor, VLDL-R:
virus / Cellular Receptor
Biological speciesHuman rhinovirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 16 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

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)
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
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
Number of components: 2

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Component #1: virus, Human rhinovirus 2

VirusName: Human rhinovirus 2 / Class: VIRION / Enveloped: No / Empty: No / Isolate: SEROTYPE
SpeciesSpecies: Human rhinovirus 2
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES

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Component #2: cellular-component, Cellular Receptor

Cellular-componentName: 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
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pMALTM-c2x
Source (natural)Organ or tissue: muscle

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen 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
pH: 7.4
Support film300 mesh copper grid
VitrificationCryogen name: ETHANE / Method: Blot with filter paper for 1-2 seconds

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Electron microscopy imaging

ImagingMicroscope: JEOL 2010F
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 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 HolderHolder: Oxford cryo-holder CT3200 / Model: OTHER
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 33 / Scanner: OTHER / Sampling size: 7 µm / Details: Zeiss PhotoScan TD scanner

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 912
Details: HRV2 and receptor fragment were incubated for 1 hour at 4 degree Celcius.
Applied symmetry: I (正20面体型対称)
3D reconstructionAlgorithm: 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.)

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Atomic model buiding

Modeling #1Software: 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.

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