[English] 日本語
Yorodumi
- PDB-7jlt: Crystal Structure of SARS-CoV-2 NSP7-NSP8 complex. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jlt
TitleCrystal Structure of SARS-CoV-2 NSP7-NSP8 complex.
Components
  • Non-structural protein 7
  • Non-structural protein 8
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Peptidase family C16 domain profile. / : / : / Coronavirus replicase NSP7 / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile.
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBiswal, M. / Hai, R. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI147057 United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Two conserved oligomer interfaces of NSP7 and NSP8 underpin the dynamic assembly of SARS-CoV-2 RdRP.
Authors: Biswal, M. / Diggs, S. / Xu, D. / Khudaverdyan, N. / Lu, J. / Fang, J. / Blaha, G. / Hai, R. / Song, J.
History
DepositionJul 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-structural protein 7
B: Non-structural protein 8
C: Non-structural protein 7
D: Non-structural protein 8


Theoretical massNumber of molelcules
Total (without water)62,4784
Polymers62,4784
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-83 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.828, 110.566, 42.904
Angle α, β, γ (deg.)90.000, 105.730, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Non-structural protein 7 / nsp7


Mass: 9335.882 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTD1
#2: Protein Non-structural protein 8 / nsp8


Mass: 21903.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTD1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Magnesium Chloride Hexahydrate, 0.1 M Bis-Tris pH 6.5, 25% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 10428 / % possible obs: 99.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.073 / Rrim(I) all: 0.149 / Χ2: 0.631 / Net I/σ(I): 4.8 / Num. measured all: 41299
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.83.90.82710370.6270.4690.9550.44799.8
2.8-2.913.80.64610230.6930.3730.7490.46798.8
2.91-3.043.70.51610490.7150.3070.6030.52698.6
3.04-3.23.90.37910240.8590.2160.4380.52899.6
3.2-3.43.80.25310440.9350.1450.2920.56398.8
3.4-3.6640.1710450.9690.0960.1960.65699.5
3.66-4.033.80.13110340.9760.0760.1520.7198.5
4.03-4.6240.08610320.9880.0480.0990.77299
4.62-5.814.30.07410590.9930.040.0840.79899.9
5.81-504.40.06210810.9950.0340.0710.773100

-
Processing

Software
NameVersionClassification
PHENIXdev_3908refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AHM

2ahm


Resolution: 2.7→41.3 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 30.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.283 1041 10 %
Rwork0.2365 9364 -
obs0.2411 10405 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.05 Å2 / Biso mean: 57.8091 Å2 / Biso min: 27.98 Å2
Refinement stepCycle: final / Resolution: 2.7→41.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 0 50 2985
Biso mean---50.63 -
Num. residues----393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.850.35551440.29811289143395
2.85-3.020.33931480.28751337148599
3.02-3.260.32891500.28621351150199
3.26-3.580.31521480.23551330147899
3.58-4.10.32211460.23351313145999
4.1-5.170.23341510.20391364151599
5.17-41.30.23631540.223413801534100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.5779-0.5308-1.2317.98852.82353.103-1.1160.82420.3495-0.79480.11430.3239-0.0585-0.50420.70020.3931-0.25980.21960.51070.06760.372932.71154.595415.9052
22.67950.38982.0590.07480.34292.4421-0.5452-0.1410.8831.40670.59170.1545-0.2826-0.3322-0.02530.7229-0.0558-0.26071.00250.54771.159547.28732.672624.6763
32.0955-2.09812.82975.733-0.25245.8313-0.0894-1.22891.1717-0.06890.1134-0.39-0.3024-0.39-0.46390.4391-0.08780.08740.4531-0.02030.499536.01712.499721.3384
46.9227-4.5161.09275.1281.00843.64740.4423-0.2944-0.8297-0.49920.00840.54670.33-0.4806-0.53680.40740.0741-0.01330.52550.15360.376536.564712.184811.7891
51.6927-1.31130.07631.67770.76411.64770.8398-0.31550.23040.6049-0.67240.28480.3969-0.3987-0.82110.81850.09270.08270.60560.2250.540743.648-4.0974.3681
63.17251.0364-0.90445.4004-0.25344.1320.05711.2701-0.3645-0.61020.2272-0.65480.15480.2543-0.22360.386-0.10740.00180.45750.03560.551437.7838-4.806511.5689
77.48123.1308-1.7085.80930.69965.1820.2760.20830.6822-0.1152-0.46430.49640.1752-0.63370.62120.3073-0.09-0.02950.54710.06750.353142.217512.64865.3378
86.3266-0.1304-0.25256.61662.24530.7631-0.45050.52461.03741.4279-1.2977-1.23990.1336-0.32560.7380.73390.0465-0.19790.46010.13220.477951.270316.51136.1014
93.21711.7894-1.9685.4614-1.48663.05840.27750.27940.29490.334-0.1533-0.2879-0.2550.0094-0.33090.44160.0152-0.00910.39150.09550.482352.259119.6999-1.1451
102.3848-1.05242.27495.14980.87323.4049-0.04660.70570.0914-0.55390.0045-0.0267-0.580.26370.27940.4349-0.08870.07490.49750.04870.538956.94318.5248-3.3912
115.45721.2331-0.84866.05811.65871.33570.28470.2897-0.77060.9412-0.0769-0.06181.1570.45480.04140.51840.034-0.08080.51670.01560.485329.3478-4.053522.7532
124.5054-1.5214-0.67978.59853.43941.2915-0.3624-0.004-0.42760.3380.69850.42280.90770.8666-0.58890.4693-0.00210.07860.45660.12770.377332.8338-12.375223.8579
135.4098-1.41011.87674.4430.32070.7067-0.0510.559-0.30960.8279-0.34330.09140.371-0.9409-0.09470.5187-0.03480.07150.46560.0970.3922.4897-9.506724.8472
149.2831-5.33792.92855.09010.54683.3006-0.9014-0.63050.8148-0.84620.7499-1.7067-0.1075-0.8234-0.7020.7414-0.0646-0.08140.55950.11310.708312.436.928423.2881
153.94241.17610.95764.8481-0.96743.0460.08420.53340.47080.13810.12920.41350.10970.3593-0.35450.3953-0.0488-0.09410.59090.12090.357819.2958-0.348422.2971
164.20641.986-2.26266.0608-0.69522.90780.0888-0.136-0.46780.5095-0.06560.3330.0991-0.2799-0.09880.3736-0.0709-0.0740.50260.04630.36297.7991-18.171334.0363
174.46352.89142.35934.1044-0.58483.43630.55011.40090.50650.58380.8059-1.7912.04481.4474-0.39340.3715-0.03210.10880.45090.16220.61713.8658-21.994931.0084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )A1 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 25 )A21 - 25
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 44 )A26 - 44
4X-RAY DIFFRACTION4chain 'A' and (resid 45 through 60 )A45 - 60
5X-RAY DIFFRACTION5chain 'A' and (resid 61 through 79 )A61 - 79
6X-RAY DIFFRACTION6chain 'B' and (resid 77 through 98 )B77 - 98
7X-RAY DIFFRACTION7chain 'B' and (resid 99 through 126 )B99 - 126
8X-RAY DIFFRACTION8chain 'B' and (resid 127 through 132 )B127 - 132
9X-RAY DIFFRACTION9chain 'B' and (resid 133 through 170 )B133 - 170
10X-RAY DIFFRACTION10chain 'B' and (resid 171 through 191 )B171 - 191
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 25 )C1 - 25
12X-RAY DIFFRACTION12chain 'C' and (resid 26 through 44 )C26 - 44
13X-RAY DIFFRACTION13chain 'C' and (resid 45 through 67 )C45 - 67
14X-RAY DIFFRACTION14chain 'C' and (resid 68 through 79 )C68 - 79
15X-RAY DIFFRACTION15chain 'D' and (resid 77 through 111 )D77 - 111
16X-RAY DIFFRACTION16chain 'D' and (resid 112 through 183 )D112 - 183
17X-RAY DIFFRACTION17chain 'D' and (resid 184 through 193 )D184 - 193

+
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