[English] 日本語
Yorodumi
- PDB-3j9f: Poliovirus complexed with soluble, deglycosylated poliovirus rece... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3j9f
TitlePoliovirus complexed with soluble, deglycosylated poliovirus receptor (Pvr) at 4 degrees C
Components
  • (Poliovirus receptorCD155) x 3
  • Protein VP1
  • Protein VP2
  • Protein VP3
  • Protein VP4
KeywordsVIRUS/CELL ADHESION / deglycosylated receptor / picornavirus / PVR / CD155 / enterovirus / cell entry / VIRUS-CELL ADHESION complex
Function / homology
Function and homology information


susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / symbiont-mediated suppression of host translation initiation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of natural killer cell mediated cytotoxicity / homophilic cell adhesion via plasma membrane adhesion molecules / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity ...susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / symbiont-mediated suppression of host translation initiation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of natural killer cell mediated cytotoxicity / homophilic cell adhesion via plasma membrane adhesion molecules / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / cell adhesion molecule binding / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / adherens junction / endocytosis involved in viral entry into host cell / : / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / virus receptor activity / signaling receptor activity / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / 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 / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
CD80-like, immunoglobulin C2-set / CD80-like C2-set 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 ...CD80-like, immunoglobulin C2-set / CD80-like C2-set 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Viral coat protein subunit / Immunoglobulin V-set domain / 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. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PALMITIC ACID / Genome polyprotein / Poliovirus receptor
Similarity search - Component
Biological speciesHuman poliovirus 1 Mahoney
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å
AuthorsStrauss, M. / Filman, D.J. / Belnap, D.M. / Cheng, N. / Noel, R.T. / Hogle, J.M.
CitationJournal: J Virol / Year: 2015
Title: Nectin-like interactions between poliovirus and its receptor trigger conformational changes associated with cell entry.
Authors: Mike Strauss / David J Filman / David M Belnap / Naiqian Cheng / Roane T Noel / James M Hogle /
Abstract: Poliovirus infection is initiated by attachment to a receptor on the cell surface called Pvr or CD155. At physiological temperatures, the receptor catalyzes an irreversible expansion of the virus to ...Poliovirus infection is initiated by attachment to a receptor on the cell surface called Pvr or CD155. At physiological temperatures, the receptor catalyzes an irreversible expansion of the virus to form an expanded form of the capsid called the 135S particle. This expansion results in the externalization of the myristoylated capsid protein VP4 and the N-terminal extension of the capsid protein VP1, both of which become inserted into the cell membrane. Structures of the expanded forms of poliovirus and of several related viruses have recently been reported. However, until now, it has been unclear how receptor binding triggers viral expansion at physiological temperature. Here, we report poliovirus in complex with an enzymatically partially deglycosylated form of the 3-domain ectodomain of Pvr at a 4-Å resolution, as determined by cryo-electron microscopy. The interaction of the receptor with the virus in this structure is reminiscent of the interactions of Pvr with its natural ligands. At a low temperature, the receptor induces very few changes in the structure of the virus, with the largest changes occurring within the footprint of the receptor, and in a loop of the internal protein VP4. Changes in the vicinity of the receptor include the displacement of a natural lipid ligand (called "pocket factor"), demonstrating that the loss of this ligand, alone, is not sufficient to induce particle expansion. Finally, analogies with naturally occurring ligand binding in the nectin family suggest which specific structural rearrangements in the virus-receptor complex could help to trigger the irreversible expansion of the capsid.
IMPORTANCE: The cell-surface receptor (Pvr) catalyzes a large structural change in the virus that exposes membrane-binding protein chains. We fitted known atomic models of the virus and Pvr into ...IMPORTANCE: The cell-surface receptor (Pvr) catalyzes a large structural change in the virus that exposes membrane-binding protein chains. We fitted known atomic models of the virus and Pvr into three-dimensional experimental maps of the receptor-virus complex. The molecular interactions we see between poliovirus and its receptor are reminiscent of the nectin family, by involving the burying of otherwise-exposed hydrophobic groups. Importantly, poliovirus expansion is regulated by the binding of a lipid molecule within the viral capsid. We show that receptor binding either causes this molecule to be expelled or requires it, but that its loss is not sufficient to trigger irreversible expansion. Based on our model, we propose testable hypotheses to explain how the viral shell becomes destabilized, leading to RNA uncoating. These findings give us a better understanding of how poliovirus has evolved to exploit a natural process of its host to penetrate the membrane barrier.
History
DepositionJan 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / em_image_scans / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 21, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-6243
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6243
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-6243
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Protein VP1
2: Protein VP2
3: Protein VP3
4: Protein VP4
7: Poliovirus receptor
8: Poliovirus receptor
9: Poliovirus receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,66315
Polymers131,5367
Non-polymers4,1278
Water0
1
1: Protein VP1
2: Protein VP2
3: Protein VP3
4: Protein VP4
7: Poliovirus receptor
8: Poliovirus receptor
9: Poliovirus receptor
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,139,808900
Polymers7,892,187420
Non-polymers247,621480
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
1: Protein VP1
2: Protein VP2
3: Protein VP3
4: Protein VP4
7: Poliovirus receptor
8: Poliovirus receptor
9: Poliovirus receptor
hetero molecules
x 5


  • icosahedral pentamer
  • 678 kDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)678,31775
Polymers657,68235
Non-polymers20,63540
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: Protein VP1
2: Protein VP2
3: Protein VP3
4: Protein VP4
7: Poliovirus receptor
8: Poliovirus receptor
9: Poliovirus receptor
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 814 kDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)813,98190
Polymers789,21942
Non-polymers24,76248
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

-
Components

-
Protein , 7 types, 7 molecules 1234789

#1: Protein Protein VP1 / P1D / Virion protein 1


Mass: 33488.613 Da / Num. of mol.: 1 / Fragment: UNP residues 580-881 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 Mahoney / References: UniProt: P03300
#2: Protein Protein VP2 / P1B / Virion protein 2


Mass: 30075.783 Da / Num. of mol.: 1 / Fragment: UNP residues 70-341 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 Mahoney / References: UniProt: P03300
#3: Protein Protein VP3 / P1C / Virion protein 3


Mass: 26547.482 Da / Num. of mol.: 1 / Fragment: UNP residues 342-579 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 Mahoney / References: UniProt: P03300
#4: Protein Protein VP4 / P1A / Virion protein 4


Mass: 7603.405 Da / Num. of mol.: 1 / Fragment: UNP residues 2-69 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 Mahoney / References: UniProt: P03300
#5: Protein Poliovirus receptor / CD155 / Nectin-like protein 5 / NECL-5 / PVR / CD155


Mass: 12869.564 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15151
#6: Protein Poliovirus receptor / CD155 / Nectin-like protein 5 / NECL-5 / PVR / CD155


Mass: 10999.521 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15151
#7: Protein Poliovirus receptor / CD155 / Nectin-like protein 5 / NECL-5 / PVR / CD155


Mass: 9952.081 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15151

-
Sugars , 5 types, 7 molecules

#8: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#9: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#10: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#11: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#13: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 1 types, 1 molecules

#12: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2

-
Details

Nonpolymer detailsGLYCOSYLATION IN THIS ENTRY IS DERIVED FROM STARTING STRUCTURE PDB ENTRY 4FQP AND DOES NOT ...GLYCOSYLATION IN THIS ENTRY IS DERIVED FROM STARTING STRUCTURE PDB ENTRY 4FQP AND DOES NOT REPRESENT THE ACTUAL GLYCOSYLATION PRESENT IN A FULLY GLYCOSYLATED RECEPTOR. THIS ENTRY IS A MODEL OF POLIVIRUS BOUND TO ENZYMATICALLY DEGLYCOSYLATED RECEPTOR - THE GLYCOSYLATION IN THIS ENTRY IS INCLUDED ONLY AS A MARKER OF THE GLYCOSYLATION SITES IN THE FULLY GLYCOSYLATED RECEPTOR.
Sequence detailsTHE RECEPTOR HAS BEEN MODELED AS THREE INDIVIDUAL DOMAINS WITH DUPLICATED, CLASHING LINKER SEGMENTS ...THE RECEPTOR HAS BEEN MODELED AS THREE INDIVIDUAL DOMAINS WITH DUPLICATED, CLASHING LINKER SEGMENTS (CHAIN 7: UNP RESIDUES 28-143, CHAIN 8: UNP RESIDUES 142-243, CHAIN 9: UNP RESIDUES 242-333). THE EXPERIMENTAL PROTEIN CONSTRUCT COMPRISES THE COMPLETE, UNBROKEN RECEPTOR SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeDetailsParent-ID
1Poliovirus type 1 (Mahoney strain) bound to soluble, deglycosylated poliovirus receptor (Pvr)COMPLEX60 Pvr bind to one poliovirus0
2Human poliovirus 1 MahoneyVIRUS1
3Poliovirus receptorCD1551
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG / Date: Nov 1, 1999
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
Image recordingFilm or detector model: KODAK SO-163 FILM

-
Processing

SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 9 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 3822 / Nominal pixel size: 1.77182 Å / Actual pixel size: 1.77182 Å / Details: (Single particle--Applied symmetry: I) / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL / Details: REFINEMENT PROTOCOL--rigid body
Atomic model buildingPDB-ID: 1HXS

1hxs

Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms9038 0 275 0 9313

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

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

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

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

Read more