[English] 日本語
Yorodumi
- PDB-7vmv: Crystal structure of Dengue NS2B-NS3 Protease after secondary cleavage -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vmv
TitleCrystal structure of Dengue NS2B-NS3 Protease after secondary cleavage
Components(Core proteinCapsid) x 2
KeywordsVIRAL PROTEIN / NS3 Protease
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / double-stranded RNA binding / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / double-stranded RNA binding / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / membrane => GO:0016020 / protein dimerization activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / ATP hydrolysis activity / extracellular region / ATP binding / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.351 Å
AuthorsQuek, J.P.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF2016NRF-CRP001-063 Singapore
CitationJournal: Viruses / Year: 2022
Title: Dynamic Interactions of Post Cleaved NS2B Cofactor and NS3 Protease Identified by Integrative Structural Approaches.
Authors: Quek, J.P. / Ser, Z. / Chew, B.L.A. / Li, X. / Wang, L. / Sobota, R.M. / Luo, D. / Phoo, W.W.
History
DepositionOct 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Core protein
B: Core protein
C: Core protein
D: Core protein
E: Core protein
F: Core protein
G: Core protein
H: Core protein


Theoretical massNumber of molelcules
Total (without water)116,1148
Polymers116,1148
Non-polymers00
Water0
1
A: Core protein
B: Core protein


Theoretical massNumber of molelcules
Total (without water)29,0282
Polymers29,0282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-20 kcal/mol
Surface area12520 Å2
MethodPISA
2
C: Core protein
D: Core protein


Theoretical massNumber of molelcules
Total (without water)29,0282
Polymers29,0282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-22 kcal/mol
Surface area10890 Å2
MethodPISA
3
E: Core protein
F: Core protein


Theoretical massNumber of molelcules
Total (without water)29,0282
Polymers29,0282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-20 kcal/mol
Surface area11120 Å2
MethodPISA
4
G: Core protein
H: Core protein


Theoretical massNumber of molelcules
Total (without water)29,0282
Polymers29,0282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-22 kcal/mol
Surface area12520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)259.984, 259.984, 259.984
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 49 through 54 or (resid 55...
21(chain C and (resid 49 through 66 or (resid 67...
31(chain E and (resid 49 through 76 or resid 78...
41(chain G and (resid 49 through 54 or (resid 55...
12(chain B and ((resid 18 and (name N or name...
22(chain D and ((resid 18 and (name N or name...
32(chain F and (resid 18 through 23 or (resid 24...
42(chain H and ((resid 18 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAGLUGLU(chain A and (resid 49 through 54 or (resid 55...AA49 - 5429 - 34
121LYSLYSALAALA(chain A and (resid 49 through 54 or (resid 55...AA55 - 5735 - 37
131METMETLYSLYS(chain A and (resid 49 through 54 or (resid 55...AA46 - 9926 - 79
141METMETLYSLYS(chain A and (resid 49 through 54 or (resid 55...AA46 - 9926 - 79
151METMETLYSLYS(chain A and (resid 49 through 54 or (resid 55...AA46 - 9926 - 79
161METMETLYSLYS(chain A and (resid 49 through 54 or (resid 55...AA46 - 9926 - 79
211ALAALAASPASP(chain C and (resid 49 through 66 or (resid 67...CC49 - 6629 - 46
221ILEILEILEILE(chain C and (resid 49 through 66 or (resid 67...CC6747
231ALAALALYSLYS(chain C and (resid 49 through 66 or (resid 67...CC49 - 9929 - 79
241ALAALALYSLYS(chain C and (resid 49 through 66 or (resid 67...CC49 - 9929 - 79
251ALAALALYSLYS(chain C and (resid 49 through 66 or (resid 67...CC49 - 9929 - 79
261ALAALALYSLYS(chain C and (resid 49 through 66 or (resid 67...CC49 - 9929 - 79
311ALAALAVALVAL(chain E and (resid 49 through 76 or resid 78...EE49 - 7629 - 56
321GLNGLNGLUGLU(chain E and (resid 49 through 76 or resid 78...EE78 - 8058 - 60
331ASPASPASPASP(chain E and (resid 49 through 76 or resid 78...EE8161
341SERSERLYSLYS(chain E and (resid 49 through 76 or resid 78...EE48 - 9928 - 79
351SERSERLYSLYS(chain E and (resid 49 through 76 or resid 78...EE48 - 9928 - 79
361SERSERLYSLYS(chain E and (resid 49 through 76 or resid 78...EE48 - 9928 - 79
371SERSERLYSLYS(chain E and (resid 49 through 76 or resid 78...EE48 - 9928 - 79
411ALAALAGLUGLU(chain G and (resid 49 through 54 or (resid 55...GG49 - 5429 - 34
421LYSLYSALAALA(chain G and (resid 49 through 54 or (resid 55...GG55 - 5735 - 37
431GLYGLYLYSLYS(chain G and (resid 49 through 54 or (resid 55...GG47 - 9927 - 79
441GLYGLYLYSLYS(chain G and (resid 49 through 54 or (resid 55...GG47 - 9927 - 79
451GLYGLYLYSLYS(chain G and (resid 49 through 54 or (resid 55...GG47 - 9927 - 79
461GLYGLYLYSLYS(chain G and (resid 49 through 54 or (resid 55...GG47 - 9927 - 79
112LEULEULEULEU(chain B and ((resid 18 and (name N or name...BB1818
122LEULEUGLUGLU(chain B and ((resid 18 and (name N or name...BB18 - 18018 - 180
132LEULEUGLUGLU(chain B and ((resid 18 and (name N or name...BB18 - 18018 - 180
142LEULEUGLUGLU(chain B and ((resid 18 and (name N or name...BB18 - 18018 - 180
152LEULEUGLUGLU(chain B and ((resid 18 and (name N or name...BB18 - 18018 - 180
212LEULEULEULEU(chain D and ((resid 18 and (name N or name...DD1818
222THRTHRGLUGLU(chain D and ((resid 18 and (name N or name...DD17 - 16917 - 169
232THRTHRGLUGLU(chain D and ((resid 18 and (name N or name...DD17 - 16917 - 169
242THRTHRGLUGLU(chain D and ((resid 18 and (name N or name...DD17 - 16917 - 169
252THRTHRGLUGLU(chain D and ((resid 18 and (name N or name...DD17 - 16917 - 169
312LEULEUTYRTYR(chain F and (resid 18 through 23 or (resid 24...FF18 - 2318 - 23
322ARGARGARGARG(chain F and (resid 18 through 23 or (resid 24...FF2424
332THRTHRILEILE(chain F and (resid 18 through 23 or (resid 24...FF17 - 17117 - 171
342THRTHRILEILE(chain F and (resid 18 through 23 or (resid 24...FF17 - 17117 - 171
352THRTHRILEILE(chain F and (resid 18 through 23 or (resid 24...FF17 - 17117 - 171
362THRTHRILEILE(chain F and (resid 18 through 23 or (resid 24...FF17 - 17117 - 171
412LEULEULEULEU(chain H and ((resid 18 and (name N or name...HH1818
422ALAALAGLUGLU(chain H and ((resid 18 and (name N or name...HH3 - 1733 - 173
432ALAALAGLUGLU(chain H and ((resid 18 and (name N or name...HH3 - 1733 - 173
442ALAALAGLUGLU(chain H and ((resid 18 and (name N or name...HH3 - 1733 - 173
452ALAALAGLUGLU(chain H and ((resid 18 and (name N or name...HH3 - 1733 - 173

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Core protein / Capsid / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 9407.243 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 4 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0M4C4I5, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#2: Protein
Core protein / Capsid / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 19621.170 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5I3B6, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 1.7 M Sodium malonate, pH 5.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.04
ReflectionResolution: 3.351→43.33 Å / Num. obs: 20533 / % possible obs: 97.65 % / Redundancy: 1.8 % / CC1/2: 0.998 / Net I/σ(I): 10
Reflection shellResolution: 3.351→3.471 Å / Num. unique obs: 2084 / CC1/2: 0.512

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VBC
Resolution: 3.351→43.33 Å / Cross valid method: THROUGHOUT / σ(F): 585.55 / Phase error: 28.92 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2628 988 -
Rwork0.2258 19517 -
obs-20504 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 267.75 Å2 / Biso mean: 138.6228 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.351→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6021 0 0 0 6021
Num. residues----852
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A736X-RAY DIFFRACTION15.827TORSIONAL
12C736X-RAY DIFFRACTION15.827TORSIONAL
13E736X-RAY DIFFRACTION15.827TORSIONAL
14G736X-RAY DIFFRACTION15.827TORSIONAL
21B2384X-RAY DIFFRACTION15.827TORSIONAL
22D2384X-RAY DIFFRACTION15.827TORSIONAL
23F2384X-RAY DIFFRACTION15.827TORSIONAL
24H2384X-RAY DIFFRACTION15.827TORSIONAL
LS refinement shellResolution: 3.3511→3.471 Å / Rfactor Rfree error: 0 /
RfactorNum. reflection
Rfree0.3576 121
Rwork0.3606 2079
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.14860.04130.12156.9749-0.0713-0.0783-0.14070.22750.45450.28790.5272-1.00950.08550.1946-0.40380.99770.0931-0.09651.2113-0.06381.122818.763144.262577.1836
24.8342-1.19421.84025.77132.43526.83090.34250.3880.2853-0.3323-0.018-0.58030.32220.8381-0.33360.56710.12920.06810.80470.12740.770215.067155.527876.4436
35.14184.6155-3.8065.6697-3.17312.24690.56980.43390.78880.55130.08090.87590.08870.2836-0.58741.5011-0.3591-0.0791.6482-0.0391.336733.1151-11.215743.8934
48.05310.3445-1.12955.45291.87354.7407-0.08191.8780.3347-0.9164-0.14690.94860.2556-1.02030.25610.9975-0.1407-0.22061.3236-0.04640.827541.7839-1.004438.3146
53.0018-5.3692-0.92857.7464-0.9221.385-0.13660.1297-0.7347-0.1039-0.12060.76730.1621-0.1330.190.8759-0.0098-0.16661.1365-0.11171.247422.6217.189279.0085
67.6545-2.45362.38183.37140.32875.7708-0.3967-0.8658-0.36380.2024-0.02751.36270.2611-1.29470.37270.7074-0.05080.18960.9572-0.12451.19728.3184.153777.8788
75.50557.3311-1.99778.4797-4.32171.7186-0.1074-0.8958-0.2701-0.1445-0.2559-0.2825-0.27630.55370.3561.0481-0.0960.09351.2022-0.18751.185125.0792-31.447658.1298
85.89741.5786-0.89165.67390.29892.98460.1327-0.378-0.227-0.2043-0.1538-0.8692-0.41810.77950.02830.77410.01310.1330.96890.02310.781415.5028-42.382464.9787
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 46 through 99)A46 - 99
2X-RAY DIFFRACTION2(chain 'B' and resid 18 through 180)B18 - 180
3X-RAY DIFFRACTION3(chain 'C' and resid 49 through 99)C49 - 99
4X-RAY DIFFRACTION4(chain 'D' and resid 17 through 169)D17 - 169
5X-RAY DIFFRACTION5(chain 'E' and resid 48 through 99)E48 - 99
6X-RAY DIFFRACTION6(chain 'F' and resid 17 through 171)F17 - 171
7X-RAY DIFFRACTION7(chain 'G' and resid 47 through 99)G47 - 99
8X-RAY DIFFRACTION8(chain 'H' and resid 3 through 173)H3 - 173

+
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