[English] 日本語
Yorodumi- PDB-1d3e: CRYO-EM STRUCTURE OF HUMAN RHINOVIRUS 16 (HRV16) COMPLEXED WITH A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d3e | ||||||
---|---|---|---|---|---|---|---|
Title | CRYO-EM STRUCTURE OF HUMAN RHINOVIRUS 16 (HRV16) COMPLEXED WITH A TWO-DOMAIN FRAGMENT OF ITS CELLULAR RECEPTOR, INTERCELLULAR ADHESION MOLECULE-1 (D1D2-ICAM-1). IMPLICATIONS FOR VIRUS-RECEPTOR INTERACTIONS. ALPHA CARBONS ONLY | ||||||
Components |
| ||||||
Keywords | Virus/Receptor / HUMAN RHINOVIRUS / HRV16 / ICAM-1 / FITTING OF X-RAY STRUCTURES INTO CRYO-EM RECONSTRUCTIONS / COMMON COLD / VIRUS UNCOATING / VIRUS/ VIRAL PROTEIN / RHINOVIRUS-RECEPTOR COMPLEX / Icosahedral virus / Virus-Receptor COMPLEX | ||||||
Function / homology | Function and homology information regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / membrane to membrane docking / adhesion of symbiont to host / establishment of endothelial barrier / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ...regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / membrane to membrane docking / adhesion of symbiont to host / establishment of endothelial barrier / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cell adhesion mediated by integrin / leukocyte cell-cell adhesion / leukocyte migration / Interleukin-10 signaling / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / immunological synapse / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / cellular response to leukemia inhibitory factor / cellular response to glucose stimulus / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / transmembrane signaling receptor activity / integrin binding / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / virus receptor activity / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / signaling receptor activity / DNA replication / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / positive regulation of ERK1 and ERK2 cascade / RNA helicase activity / receptor-mediated virion attachment to host cell / cell adhesion / membrane raft / induction by virus of host autophagy / external side of plasma membrane / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / focal adhesion / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / cell surface / proteolysis / RNA binding / extracellular space / extracellular exosome / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human rhinovirus sp. | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 28 Å | ||||||
Authors | Bella, J. / Rossmann, M.G. | ||||||
Citation | Journal: EMBO J / Year: 1999 Title: Structural studies of two rhinovirus serotypes complexed with fragments of their cellular receptor. Authors: P R Kolatkar / J Bella / N H Olson / C M Bator / T S Baker / M G Rossmann / Abstract: Two human rhinovirus serotypes complexed with two- and five-domain soluble fragments of the cellular receptor, intercellular adhesion molecule-1, have been investigated by X-ray crystallographic ...Two human rhinovirus serotypes complexed with two- and five-domain soluble fragments of the cellular receptor, intercellular adhesion molecule-1, have been investigated by X-ray crystallographic analyses of the individual components and by cryo-electron microscopy of the complexes. The three-dimensional image reconstructions provide a molecular envelope within which the crystal structures of the viruses and the receptor fragments can be positioned with accuracy. The N-terminal domain of the receptor binds to the rhinovirus 'canyon' surrounding the icosahedral 5-fold axes. Fitting of molecular models into the image reconstruction density identified the residues on the virus that interact with those on the receptor surface, demonstrating complementarity of the electrostatic patterns for the tip of the N-terminal receptor domain and the floor of the canyon. The complexes seen in the image reconstructions probably represent the first stage of a multistep binding process. A mechanism is proposed for the subsequent viral uncoating process. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: The Structure of the Two Amino-Terminal Domains of Human Icam-1 Suggests How It Functions as a Rhinovirus Receptor and as an Lfa-1 Integrin Ligand. Authors: Bella, J. / Kolatkar, P.R. / Marlor, C.W. / Greve, J.M. / Rossmann, M.G. #2: Journal: Structure / Year: 1997 Title: The Refined Structure of Human Rhinovirus 16 at 2.15 Angstroms Resolution: Implications for the Viral Life Cycle Authors: Hadfield, A.T. / Lee, W.M. / Zhao, R. / Oliveira, M.A. / Minor, I. / Rueckert, R.R. / Rossmann, M.G. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: Structure of a Human Rhinovirus Complexed with its Receptor Molecule Authors: Olson, N.H. / Kolatkar, P.R. / Oliveira, M.A. / Cheng, R.H. / Greve, J.M. / Mcclelland, A. / Baker, T.S. / Rossmann, M.G. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: A Dimeric Crystal Structure for the N-Terminal Two Domains of Intercellular Adhesion Molecule-1 Authors: Casasnovas, J.M. / Stehle, T. / Liu, J.H. / Wang, J.H. / Springer, T.A. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 1d3e.cif.gz | 49.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1d3e.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 1d3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d3e_validation.pdf.gz | 343.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1d3e_full_validation.pdf.gz | 343 KB | Display | |
Data in XML | 1d3e_validation.xml.gz | 999 B | Display | |
Data in CIF | 1d3e_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/1d3e ftp://data.pdbj.org/pub/pdb/validation_reports/d3/1d3e | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 60
2 |
|
3 |
| x 5
4 |
| x 6
5 |
|
Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 20438.260 Da / Num. of mol.: 1 / Fragment: FIRST TWO DOMAINS, RESIDUES 1-185 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Fragment: 1 - 185 / References: UniProt: P05362*PLUS |
---|---|
#2: Protein | Mass: 32314.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus sp. / Genus: Rhinovirus / Strain: SEROTYPE 16 / References: UniProt: P05362, UniProt: Q82122 |
#3: Protein | Mass: 27910.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus sp. / Genus: Rhinovirus / Strain: SEROTYPE 16 / References: UniProt: Q82122 |
#4: Protein | Mass: 26314.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus sp. / Genus: Rhinovirus / Strain: SEROTYPE 16 / References: UniProt: Q82122 |
#5: Protein | Mass: 7374.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus sp. / Genus: Rhinovirus / Strain: SEROTYPE 16 / References: UniProt: Q82122 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: HUMAN RHINOVIRUS 16 COMPLEXED WITH INTERCELLULAR ADHESION MOLECULE-1 Type: COMPLEX | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||||
Vitrification | Details: HRV16 WAS INCUBATED WITH D1D2-ICAM-1 FOR 16 HOURS AT 34 DEGREES CELSIUS (307 KELVIN) USING A SIXTEEN-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER ...Details: HRV16 WAS INCUBATED WITH D1D2-ICAM-1 FOR 16 HOURS AT 34 DEGREES CELSIUS (307 KELVIN) USING A SIXTEEN-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS EM420 / Date: Oct 1, 1991 |
---|---|
Electron gun | Accelerating voltage: 80 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 47500 X / Nominal defocus max: 1000 nm |
Specimen holder | Temperature: 120 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3D reconstruction | Method: COMMON-LINES AND POLAR-FOURIER-TRANSFORM FULLER ET AL. 1996, J.STRUC.BIOL.c 116, 48-55; BAKER AND CHENG, 1996, J.STRUC.BIOL. 116, 120-130 Resolution: 28 Å / Resolution method: OTHER / Num. of particles: 44 / Nominal pixel size: 5.1 Å / Actual pixel size: 4.95 Å Magnification calibration: THE PIXEL SIZE OF THE CRYO-EM MAP WAS CALIBRATED AGAINST A LOW RESOLUTION DENSITY MAP CALCULATED FROM THE CRYSTAL STRUCTURE OF HRV16. DENSITIES WERE COMPARED BY CROSS- ...Magnification calibration: THE PIXEL SIZE OF THE CRYO-EM MAP WAS CALIBRATED AGAINST A LOW RESOLUTION DENSITY MAP CALCULATED FROM THE CRYSTAL STRUCTURE OF HRV16. DENSITIES WERE COMPARED BY CROSS- CORRELATION WITHIN A SPHERICAL SHELL OF INTERNAL RADIUS 110 ANGSTROMS AND EXTERNAL RADIUS OF 145 ANGSTROMS. Details: THE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS DETERMINED TO BE AT LEAST 28 ANGSTROMS, AS MEASURED BY RANDOMLY SPLITTING THE PARTICLES INTO TWO SETS AND COMPARING STRUCTURE FACTORS ...Details: THE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS DETERMINED TO BE AT LEAST 28 ANGSTROMS, AS MEASURED BY RANDOMLY SPLITTING THE PARTICLES INTO TWO SETS AND COMPARING STRUCTURE FACTORS OBTAINED FROM SEPARATE RECONSTRUCTIONS (BAKER ET AL. 1991, BIOPHYS.J. 60, 1445-1456). THE EIGENVALUE SPECTRUM GAVE AN INDICATION OF THE RANDOMNESS OF THE DATA THAT WAS INCLUDED IN THE RECONSTRUCTION. THE COMPLETENESS OF THE DATA WAS VERIFIED IN THAT ALL EIGENVALUES EXCEEDED 1.0. Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: VECTOR R-FACTOR Details: REFINEMENT PROTOCOL--RIGID BODY REFINEMENT DETAILS--THE CRYSTAL STRUCTURE OF HRV16 WAS PLACED INTO THE CALIBRATED CRYO-EM DENSITY MAP BY ALIGNING THE ICOSAHEDRAL SYMMETRY AXES. APPROPRIATELY ...Details: REFINEMENT PROTOCOL--RIGID BODY REFINEMENT DETAILS--THE CRYSTAL STRUCTURE OF HRV16 WAS PLACED INTO THE CALIBRATED CRYO-EM DENSITY MAP BY ALIGNING THE ICOSAHEDRAL SYMMETRY AXES. APPROPRIATELY GLYCOSYLATED MODELS OF D1D2-ICAM-1 WITH VARIOUS INTERDOMAIN ANGLES (AS SEEN IN DIFFERENT CRYSTAL STRUCTURES OF D1D2-ICAM-1), WERE FIRST MANUALLY FITTED INTO THE CRYO-EM DENSITY CORRESPONDING TO THE ICAM-1 FRAGMENT, AND SUBSEQUENTLY REFINED AS RIGID BODIES IN RECIPROCAL SPACE. OBSERVED STRUCTURE FACTORS WERE OBTAINED BY INVERSE FOURIER TRANSFORM OF CRYO-EM DIFFERENCE MAPS CALCULATED BY 1) SUBSTRACTION OF THE HRV16 AND RNA CONTRIBUTION FROM THE CRYO-EM RECONSTRUCTED DENSITY OF THE COMPLEXES; 2) REDUCTION OF THE DIFFERENCE MAPS TO AN ICOSAHEDRAL ASYMMETRIC UNIT. THE COORDINATES ARE IN THE P, Q, R FRAME IN ANGSTROM UNITS AND CORRESPOND TO ICOSAHEDRAL SYMMETRY AXES. THE ORIGIN IS CHOSEN AT THE CENTER OF THE VIRUS WITH P, Q AND R ALONG MUTUALLY PERPENDICULAR TWO-FOLD AXES OF THE ICOSAHEDRON. THEY SHOULD REMAIN IN THAT FRAME FOR THE EASE OF THE USER IN CREATING THE BIOLOGICALLY SIGNIFICANT VIRAL COMPLEX PARTICLE USING THE 60 ICOSAHEDRAL SYMMETRY OPERATORS. RESIDUES NOT VISIBLE IN THE ORIGINAL CRYSTAL STRUCTURES ARE NOT INCLUDED IN THE CRYO-EM STRUCTURE MODEL. FOR EXAMPLE, HRV16 RESIDUES 2001-2009, 4008-4022 AND 4045-4068 ARE NOT VISIBLE IN THE CRYSTAL STRUCTURE (PDB ENTRY 1AYM) AND THEREFORE ARE NOT INCLUDED IN THE COORDINATES BELOW. | ||||||||||||||||||||
Refinement | Highest resolution: 28 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 28 Å
| ||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||
Refine LS restraints | *PLUS
|