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- PDB-1d3e: CRYO-EM STRUCTURE OF HUMAN RHINOVIRUS 16 (HRV16) COMPLEXED WITH A... -

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Entry
Database: PDB / ID: 1d3e
TitleCRYO-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
  • PROTEIN (INTERCELLULAR ADHESION MOLECULE-1)
  • PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP1)
  • PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP2)
  • PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP3)
  • PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP4)
KeywordsVirus/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 / cell adhesion mediated by integrin ...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 / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / 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 / symbiont genome entry into host cell via pore formation in plasma membrane / cellular response to leukemia inhibitory factor / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cellular response to glucose stimulus / endocytosis involved in viral entry into host cell / : / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / nucleoside-triphosphate phosphatase / transmembrane signaling receptor activity / integrin binding / protein complex oligomerization / virus receptor activity / signaling receptor activity / monoatomic ion channel activity / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / DNA replication / RNA helicase activity / receptor-mediated virion attachment to host cell / positive regulation of ERK1 and ERK2 cascade / cell adhesion / induction by virus of host autophagy / RNA-directed RNA polymerase / membrane raft / symbiont-mediated suppression of host gene expression / viral RNA genome replication / external side of plasma membrane / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / focal adhesion / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / cell surface / proteolysis / extracellular space / RNA binding / extracellular exosome / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / ICAM-1/3/5, D2 domain / Intercellular adhesion molecule / Intercellular adhesion molecule, N-terminal / : / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / Immunoglobulin domain / Poliovirus 3A protein-like / Poliovirus 3A protein like ...: / ICAM-1/3/5, D2 domain / Intercellular adhesion molecule / Intercellular adhesion molecule, N-terminal / : / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / Immunoglobulin domain / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulin subtype / Immunoglobulin / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Immunoglobulin-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Intercellular adhesion molecule 1 / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human rhinovirus sp.
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 28 Å
AuthorsBella, 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
DepositionSep 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 18, 2019Group: Data collection / Other / Category: atom_sites / cell / em_image_scans
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_oper_list ...database_2 / pdbx_struct_oper_list / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.5Apr 17, 2024Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.status_code_sf

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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Assembly

Deposited unit
I: PROTEIN (INTERCELLULAR ADHESION MOLECULE-1)
1: PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP1)
2: PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP2)
3: PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP3)
4: PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP4)


Theoretical massNumber of molelcules
Total (without water)114,3515
Polymers114,3515
Non-polymers00
Water0
1
I: PROTEIN (INTERCELLULAR ADHESION MOLECULE-1)
1: PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP1)
2: PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP2)
3: PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP3)
4: PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP4)
x 60


Theoretical massNumber of molelcules
Total (without water)6,861,068300
Polymers6,861,068300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: PROTEIN (INTERCELLULAR ADHESION MOLECULE-1)
1: PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP1)
2: PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP2)
3: PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP3)
4: PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP4)
x 5


  • icosahedral pentamer
  • 572 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)571,75625
Polymers571,75625
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
I: PROTEIN (INTERCELLULAR ADHESION MOLECULE-1)
1: PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP1)
2: PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP2)
3: PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP3)
4: PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP4)
x 6


  • icosahedral 23 hexamer
  • 686 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)686,10730
Polymers686,10730
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

#1: Protein PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) / D1D2-ICAM-1 / Coordinate model: Cα atoms only


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 PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP1) / HRV16 VP1 / Coordinate model: Cα atoms only


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 PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP2) / HRV16 VP2 / Coordinate model: Cα atoms only


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 PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP3) / HRV16 VP3 / Coordinate model: Cα atoms only


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 PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP4) / HRV16 VP4 / Coordinate model: Cα atoms only


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HUMAN RHINOVIRUS 16 COMPLEXED WITH INTERCELLULAR ADHESION MOLECULE-1
Type: COMPLEX
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationDetails: 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
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 mg/mlprotein1drop
224-27 %PEG33501reservoir
310 mMTris1reservoir
425 mM1reservoirNaCl
51 mM1reservoirMgCl2
61 mM1reservoirCaCl2

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS EM420 / Date: Oct 1, 1991
Electron gunAccelerating voltage: 80 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 47500 X / Nominal defocus max: 1000 nm
Specimen holderTemperature: 120 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: 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 buildingProtocol: 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.
RefinementHighest resolution: 28 Å
Refinement stepCycle: LAST / Highest resolution: 28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms989 0 0 0 989
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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