[English] 日本語
Yorodumi
- PDB-1vba: POLIOVIRUS (TYPE 3, SABIN STRAIN) (P3/SABIN, P3/LEON/12A(1)B) COM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vba
TitlePOLIOVIRUS (TYPE 3, SABIN STRAIN) (P3/SABIN, P3/LEON/12A(1)B) COMPLEXED WITH R78206
Components(POLIOVIRUS TYPE ...) x 5
KeywordsVIRUS / VIRUS COAT PROTEIN / HYDROLASE / THIOL PROTEASE / Icosahedral virus
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / 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 MAVS activity / 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 ...caveolin-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / 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 MAVS activity / 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 / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / 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 / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / 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 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / 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 / Few Secondary Structures / Irregular / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chem-J78 / MYRISTIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesPoliovirus type 3
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsGrant, R.A. / Hiremath, C.N. / Filman, D.J. / Syed, R. / Andries, K. / Hogle, J.M.
Citation
Journal: Curr.Biol. / Year: 1994
Title: Structures of poliovirus complexes with anti-viral drugs: implications for viral stability and drug design.
Authors: Grant, R.A. / Hiremath, C.N. / Filman, D.J. / Syed, R. / Andries, K. / Hogle, J.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Binding of the Antiviral Drug Win51711 to the Sabin Strain of Type 3 Poliovirus: Structural Comparison with Drug Binding in Rhinovirus 14
Authors: Hiremath, C.N. / Grant, R.A. / Filman, D.J. / Hogle, J.M.
#2: Journal: New Aspects of Positive-Strand RNA Viruses / Year: 1990
Title: Role of Conformational Transitions in Poliovirus Assembly and Cell Entry
Authors: Hogle, J.M. / Syed, R. / Fricks, C.E. / Icenogle, J.P. / Flore, O. / Filman, D.J.
#3: Journal: Embo J. / Year: 1989
Title: Structural Factors that Control Conformational Transitions and Serotype Specificity in Type 3 Poliovirus
Authors: Filman, D.J. / Syed, R. / Chow, M. / Macadam, A.J. / Minor, P.D. / Hogle, J.M.
#4: Journal: Nature / Year: 1987
Title: Myristylation of Picornavirus Capsid Protein Vp4 and its Structural Significance
Authors: Chow, M. / Newman, J.F. / Filman, D. / Hogle, J.M. / Rowlands, D.J. / Brown, F.
#5: Journal: Science / Year: 1985
Title: Three-Dimensional Structure of Poliovirus at 2.9 A Resolution
Authors: Hogle, J.M. / Chow, M. / Filman, D.J.
#6: Journal: Nucleic Acids Res. / Year: 1983
Title: The Nucleotide Sequence of Poliovirus Type 3 Leon 12 A1B: Comparison with Poliovirus Type 1
Authors: Stanway, G. / Cann, A.J. / Hauptmann, R. / Hughes, P. / Clarke, L.D. / Mountford, R.C. / Minor, P.D. / Schild, G.C. / Almond, J.W.
History
DepositionJan 2, 1996-
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: POLIOVIRUS TYPE 3
1: POLIOVIRUS TYPE 3
2: POLIOVIRUS TYPE 3
3: POLIOVIRUS TYPE 3
4: POLIOVIRUS TYPE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0247
Polymers97,4125
Non-polymers6122
Water0
1
0: POLIOVIRUS TYPE 3
1: POLIOVIRUS TYPE 3
2: POLIOVIRUS TYPE 3
3: POLIOVIRUS TYPE 3
4: POLIOVIRUS TYPE 3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,881,415420
Polymers5,844,704300
Non-polymers36,711120
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
0: POLIOVIRUS TYPE 3
1: POLIOVIRUS TYPE 3
2: POLIOVIRUS TYPE 3
3: POLIOVIRUS TYPE 3
4: POLIOVIRUS TYPE 3
hetero molecules
x 5


  • icosahedral pentamer
  • 490 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)490,11835
Polymers487,05925
Non-polymers3,05910
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
0: POLIOVIRUS TYPE 3
1: POLIOVIRUS TYPE 3
2: POLIOVIRUS TYPE 3
3: POLIOVIRUS TYPE 3
4: POLIOVIRUS TYPE 3
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 588 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)588,14142
Polymers584,47030
Non-polymers3,67112
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
0: POLIOVIRUS TYPE 3
1: POLIOVIRUS TYPE 3
2: POLIOVIRUS TYPE 3
3: POLIOVIRUS TYPE 3
4: POLIOVIRUS TYPE 3
hetero molecules
x 15


  • crystal asymmetric unit, crystal frame
  • 1.47 MDa, 75 polymers
Theoretical massNumber of molelcules
Total (without water)1,470,354105
Polymers1,461,17675
Non-polymers9,17830
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation15
Unit cell
Length a, b, c (Å)321.060, 358.620, 381.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699)
3generate(-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5)
4generate(-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5)
5generate(0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699)
6generate(1), (1), (1)
7generate(-0.5, 0.30901699, 0.80901699), (0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699)
8generate(-0.30901699, 0.80901699, 0.5), (-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699)
9generate(0.30901699, 0.80901699, 0.5), (-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699)
10generate(0.5, 0.30901699, 0.80901699), (0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699)
11generate(1), (1), (1)
12generate(0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699), (0.30901699, -0.80901699, 0.5)
13generate(0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5), (-0.80901699, -0.5, 0.30901699)
14generate(-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5), (-0.80901699, 0.5, -0.30901699)
15generate(-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699), (0.30901699, 0.80901699, -0.5)

-
Components

-
POLIOVIRUS TYPE ... , 5 types, 5 molecules 01234

#1: Protein/peptide POLIOVIRUS TYPE 3


Mass: 446.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: P3/SABIN PREPARED FROM A LOW-PASSAGE SEED STOCK OF A PLAQUE ISOLATE (P3/LEON/12A(1)B PLACQUE 411) OBTAINED FROM P.D.MINOR (NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS CONTROL, LONDON)
Source: (natural) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B)
Genus: Enterovirus / Species: Poliovirus / Strain: P3-SABIN
#2: Protein POLIOVIRUS TYPE 3


Mass: 33523.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: P3/SABIN PREPARED FROM A LOW-PASSAGE SEED STOCK OF A PLAQUE ISOLATE (P3/LEON/12A(1)B PLACQUE 411) OBTAINED FROM P.D.MINOR (NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS CONTROL, LONDON)
Source: (natural) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B)
Genus: Enterovirus / Organ: SEED / Species: Poliovirus / Strain: P3-SABIN / References: UniProt: P03302
#3: Protein POLIOVIRUS TYPE 3


Mass: 30169.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: P3/SABIN PREPARED FROM A LOW-PASSAGE SEED STOCK OF A PLAQUE ISOLATE (P3/LEON/12A(1)B PLACQUE 411) OBTAINED FROM P.D.MINOR (NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS CONTROL, LONDON)
Source: (natural) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B)
Genus: Enterovirus / Organ: SEED / Species: Poliovirus / Strain: P3-SABIN / References: UniProt: P03302
#4: Protein POLIOVIRUS TYPE 3


Mass: 25950.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: P3/SABIN PREPARED FROM A LOW-PASSAGE SEED STOCK OF A PLAQUE ISOLATE (P3/LEON/12A(1)B PLACQUE 411) OBTAINED FROM P.D.MINOR (NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS CONTROL, LONDON)
Source: (natural) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B)
Genus: Enterovirus / Organ: SEED / Species: Poliovirus / Strain: P3-SABIN / References: UniProt: P03302
#5: Protein POLIOVIRUS TYPE 3


Mass: 7320.917 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: P3/SABIN PREPARED FROM A LOW-PASSAGE SEED STOCK OF A PLAQUE ISOLATE (P3/LEON/12A(1)B PLACQUE 411) OBTAINED FROM P.D.MINOR (NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS CONTROL, LONDON)
Source: (natural) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B)
Genus: Enterovirus / Organ: SEED / Species: Poliovirus / Strain: P3-SABIN / References: UniProt: P03302

-
Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-J78 / (METHYLPYRIDAZINE PIPERIDINE PROPYLOXYPHENYL)ETHYLACETATE / R78206


Mass: 383.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H29N3O3
#7: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2

-
Details

Sequence detailsTHE APPROPRIATE SEQUENCE FOR THIS VIRUS CORRESPONDS TO THE STANWAY ET AL. REFERENCE ABOVE. THE ...THE APPROPRIATE SEQUENCE FOR THIS VIRUS CORRESPONDS TO THE STANWAY ET AL. REFERENCE ABOVE. THE NUMBERING OF THE VP1 RESIDUES HAS BEEN ALTERED TO FACILITATE COMPARISON WITH THE STRUCTURE OF THE MAHONEY STRAIN OF TYPE 1 POLIOVIRUS (PDB ENTRY 2PLV). MAHONEY HAS A TWO RESIDUE INSERTION, RELATIVE TO P3/SABIN, LOCATED IN THE DISORDERED N-TERMINUS OF VP1. THUS THE RESIDUES NUMBERED 24 - 302 IN THIS ENTRY ARE ACTUALLY RESIDUES 22 - 300. VP4 HAS A MYRISTATE MOIETY COVALENTLY LINKED TO ITS N-TERMINUS. THIS MYRISTATE HAS BEEN DESIGNATED RESIDUE 1 OF VP4 AND THE AMINO ACID RESIDUES OF VP4 ARE NUMBERED 2 - 69.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 30 %
Crystal grow
*PLUS
Method: other / Details: Filman, D.J., (1989) EMBO, J., 8, 1567.

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 157185 / % possible obs: 32 % / Observed criterion σ(I): 0
Reflection
*PLUS
Num. measured all: 412714

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.297 / Highest resolution: 2.9 Å
Details: STEREOCHEMICAL CONSTRAINTS BASED ON PARAM19 AND TOP19 FILES USED IN X-PLOR VERSIONS PREVIOUS TO VERSION 3.1 ATOMIC MODELS FOR THE VIRUS AND THE DRUG WERE BUILT TO FIT ICOSAHEDRALLY ...Details: STEREOCHEMICAL CONSTRAINTS BASED ON PARAM19 AND TOP19 FILES USED IN X-PLOR VERSIONS PREVIOUS TO VERSION 3.1 ATOMIC MODELS FOR THE VIRUS AND THE DRUG WERE BUILT TO FIT ICOSAHEDRALLY CONSTRAINED 'FO' MAP USING THE GRAPHICS PROGRAM FRODO (JONES, 1978) MODIFIED TO INCORPORATE T = 1 ICOSAHEDRAL SYMMETRY. ATOMIC MODELS WERE OPTIMIZED WITH RESPECT TO THIS MAP BY A PSEUDO-REAL-SPACE REFINEMENT PROCEDURE, MINIMIZING A RESIDUAL WITH A STEREOCHEMICAL AND A CRYSTALLOGRAPHIC COMPONENT. THE GRADIENT OF THE STEREOCHEMICAL COMPONENT WAS PROVIDED BY THE X-PLOR PROGRAM (A. BRUNGER, X-PLOR VERSION 2.1 YALE UNIVERSITY 1990). THE CRYSTALLOGRAPHIC COMPONENT AND ITS GRADIENT WERE EVALUATED OVER THE VOLUME OF AN ARBITRARY PSEUDO-CELL (THE PROTOMER BOX) WHICH IS SUFFICIENTLY LARGE TO COMFORTABLY ENCLOSE A COMPLETE CHEMICALLY CONTINUOUS POLIOVIRUS PROTOMER, TOGETHER WITH WHATEVER FRAGMENTS OF SYMMETRY-RELATED PROTOMERS HAPPEN TO LIE SUFFICIENTLY CLOSE TO THE BOX TO CONTRIBUTE TO IT. THIS REFINEMENT SEEKS TO MINIMIZE THE DISCREPANCY BETWEEN THE 'PHASED' FOURIER TRANSFORMS OF MODEL-BASED ELECTRON DENSITY AND AUTHENTIC SYMMETRY-CONSTRAINED ELECTRON DENSITY, WHEN EACH TRANSFORM IS CALCULATED IN THE ARBITRARY PROTOMER BOX VOLUME, SCALED IN A RESOLUTION-DEPENDENT FASHION. SEE JRNL REFERENCE FOR MORE DETAILS. THE DISORDERED RESIDUES ABSENT FROM THE MODEL INCLUDE THE AMINO TERMINUS OF VP1 PRIOR TO THE RESIDUE LABELED GLN 24, 1 - 5 IN VP2, 236 - 238 IN VP3, AND THE RESIDUES LABELED 17 - 22 IN VP4. THE POLYPEPTIDE DESIGNATED IN THIS FILE AS RESIDUES 6 - 9 OF CHAIN 0 REPRESENTS A FEATURE IN THE ELECTRON DENSITY MAP WHICH APPEARS TO BE A BETA STRAND. ALTHOUGH THE SIDE CHAINS OF THIS STRAND CANNOT BE CORRELATED RELIABLY WITH THE SEQUENCE OF THE PROTEIN, THE FEATURE IS BELIEVED LIKELY TO CORRESPOND TO SOME PORTION OF THE AMINO TERMINAL EXTENSION OF VP1. THE POLYPEPTIDE DESIGNATED IN THIS FILE AS RESIDUES 6 - 9 OF CHAIN 0 REPRESENTS A FEATURE IN THE ELECTRON DENSITY MAP WHICH APPEARS TO BE A BETA STRAND. ALTHOUGH THE SIDE CHAINS OF THIS STRAND CANNOT BE CORRELATED RELIABLY WITH THE SEQUENCE OF THE PROTEIN, THE FEATURE IS BELIEVED LIKELY TO CORRESPOND TO SOME PORTION OF THE AMINO TERMINAL EXTENSION OF VP1.
Refinement stepCycle: LAST / Highest resolution: 2.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6603 0 43 0 6646
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.013
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.583
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: 'PSEUDO-REAL SPACE PROCEDURE' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.297
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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