[English] 日本語
Yorodumi
- PDB-9d9p: Crystal structure of CVB3 replication-linked RNA in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9d9p
TitleCrystal structure of CVB3 replication-linked RNA in complex with 3C protein
Components
  • Protease 3C
  • RNA (90-MER)
KeywordsVIRAL PROTEIN/RNA / Cloverleaf RNA-3C protein complex / Viral replication / enterovirus / Coxsackievirus / Viral RNA / 3C proteinase / RNA / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host transcription / 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 / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane ...symbiont-mediated perturbation of host transcription / 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 / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host NF-kappaB cascade / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / 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 / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
Picornavirus coat protein VP4 superfamily / : / Picornavirus coat protein / 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 superfamily / : / Picornavirus coat protein / 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) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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
PHOSPHATE ION / RNA / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus B3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsDas, N.K. / Koirala, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-2236996 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for 3C and 3CD recruitment by enteroviral genomes during negative-strand RNA synthesis.
Authors: Das, N.K. / Patel, A. / Abdelghani, R. / Koirala, D.
History
DepositionAug 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
R: RNA (90-MER)
A: Protease 3C
B: Protease 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2018
Polymers71,7263
Non-polymers4755
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-56 kcal/mol
Surface area29370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.406, 95.251, 113.637
Angle α, β, γ (deg.)90.000, 98.630, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 4 or resid 7...
d_2ens_1(chain "B" and (resid 1 through 4 or resid 7...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETALAALAAB0 - 31 - 4
d_12PHEPHETHRTHRAB6 - 207 - 21
d_13TYRTYRASPASPAB22 - 3223 - 33
d_14TRPTRPPROPROAB34 - 3835 - 39
d_15HISHISALAALAAB40 - 5941 - 60
d_16GLUGLUALAALAAB61 - 9162 - 92
d_17GLUGLUSERSERAB93 - 10794 - 108
d_18PHEPHEASNASNAB109 - 139110 - 140
d_19PROPROGLYGLYAB141 - 166142 - 167
d_110GLNGLNASNASNAB168 - 180169 - 181
d_21METMETALAALABC0 - 31 - 4
d_22PHEPHETHRTHRBC6 - 207 - 21
d_23TYRTYRASPASPBC22 - 3223 - 33
d_24TRPTRPPROPROBC34 - 3835 - 39
d_25HISHISALAALABC40 - 5941 - 60
d_26GLUGLUALAALABC61 - 9162 - 92
d_27GLUGLUSERSERBC93 - 10794 - 108
d_28PHEPHEASNASNBC109 - 139110 - 140
d_29PROPROGLYGLYBC141 - 166142 - 167
d_210GLNGLNASNASNBC168 - 180169 - 181

NCS oper: (Code: givenMatrix: (-0.397738039858, -0.668119017018, -0.628825437421), (-0.663414702273, -0.264013454116, 0.700127009087), (-0.633786544869, 0.695639184595, -0.338231785022)Vector: 21. ...NCS oper: (Code: given
Matrix: (-0.397738039858, -0.668119017018, -0.628825437421), (-0.663414702273, -0.264013454116, 0.700127009087), (-0.633786544869, 0.695639184595, -0.338231785022)
Vector: 21.7497447233, -19.1810008852, 41.4770575386)

-
Components

#1: RNA chain RNA (90-MER)


Mass: 28789.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Coxsackievirus B3
#2: Protein Protease 3C / Picornain 3C / P3C


Mass: 21468.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 / Production host: Escherichia coli (E. coli) / References: UniProt: P03313, picornain 3C
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.11 Å3/Da / Density % sol: 70.05 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 7 / Details: Glycerol, Bis-Tris, Ammonium Sulfate

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid Nitrogen Jet / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.69→37.45 Å / Num. obs: 59666 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 61.25 Å2 / CC1/2: 0.997 / Net I/σ(I): 19.2
Reflection shellResolution: 2.69→2.74 Å / Num. unique obs: 5248 / CC1/2: 0.93

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487phasing
DIALSdata reduction
xia2data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→37.45 Å / SU ML: 0.3489 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.297
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2316 3800 6.39 %
Rwork0.1982 55699 -
obs0.2003 59499 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103.38 Å2
Refinement stepCycle: LAST / Resolution: 2.69→37.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2844 1904 25 98 4871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00795045
X-RAY DIFFRACTIONf_angle_d1.14887248
X-RAY DIFFRACTIONf_chiral_restr0.0528878
X-RAY DIFFRACTIONf_plane_restr0.0095600
X-RAY DIFFRACTIONf_dihedral_angle_d20.11871469
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.677567932351 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.720.37261390.38532028X-RAY DIFFRACTION94.01
2.72-2.760.40021430.36772057X-RAY DIFFRACTION95.94
2.76-2.80.31171280.33511959X-RAY DIFFRACTION94.65
2.8-2.840.29591400.31692054X-RAY DIFFRACTION95.47
2.84-2.880.37711380.29582084X-RAY DIFFRACTION96.61
2.88-2.930.31411350.29521976X-RAY DIFFRACTION95.65
2.93-2.970.32561410.2762075X-RAY DIFFRACTION94.54
2.97-3.020.2911330.26571967X-RAY DIFFRACTION94.89
3.02-3.080.25421460.24822110X-RAY DIFFRACTION98.26
3.08-3.140.26491390.25462079X-RAY DIFFRACTION98.4
3.14-3.20.30291440.26422077X-RAY DIFFRACTION98.14
3.2-3.270.26771450.26892096X-RAY DIFFRACTION98.51
3.27-3.350.30811380.22222070X-RAY DIFFRACTION98.31
3.35-3.430.24321470.19622113X-RAY DIFFRACTION98.39
3.43-3.520.24631370.1922062X-RAY DIFFRACTION98.04
3.53-3.630.25741410.18782101X-RAY DIFFRACTION98.51
3.63-3.750.18561390.19012078X-RAY DIFFRACTION97.62
3.75-3.880.22481390.17492018X-RAY DIFFRACTION97.43
3.88-4.030.22631400.1892054X-RAY DIFFRACTION95.31
4.03-4.220.19221450.16312079X-RAY DIFFRACTION96.61
4.22-4.440.19351420.14792020X-RAY DIFFRACTION96.52
4.44-4.720.19181420.14712075X-RAY DIFFRACTION97.97
4.72-5.080.16171430.15632113X-RAY DIFFRACTION98.9
5.08-5.590.1921420.17392091X-RAY DIFFRACTION98.94
5.59-6.40.23031460.20772106X-RAY DIFFRACTION98.86
6.4-8.040.21691430.19092051X-RAY DIFFRACTION97.38
8.05-37.450.21951450.16372106X-RAY DIFFRACTION98.95
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)
12.872636195752.21054052848-3.256878017385.442241186680.7276068611396.53653123325-0.5221920263220.506138824896-0.5855519454510.2851873259430.0558880672218-1.684172064480.3810886037121.500478551380.4571965220630.600800872014-0.0634687961914-0.2466679168381.06913557915-0.04156178232251.411440860536.7826324294-12.66554910818.14198401178
22.674983335762.33175535946-2.900004653434.052505319660.1182516183556.648368674290.253692981014-0.3685567774540.08990102611060.255371647136-0.210765647798-0.08105410903530.1410370396580.283418403032-0.05366378520830.463877043063-0.175023108208-0.2137022160110.6663335896930.0192283350140.82729326191431.4558631012-4.4864199617816.1548996916
32.006272864442.96720649086-0.6200836128266.148399386142.41975013216.1570148009-0.0354274515005-0.332595515810.641173597246-0.3928376314660.12595505673-0.368455109901-0.5458777557620.686057997428-0.1156893458310.473189332141-0.249946574943-0.1665380226450.610971428056-0.0155818353570.7350236766331.90552015452.3920039956311.7745910341
44.754831385021.106035494060.6286762278683.4199723297-0.3858803247621.797689127470.509223213325-0.497902636761-0.4298198174020.467391124106-0.501374066823-0.4449573441620.2156329959540.322887336117-0.01898430781070.420285538125-0.169513315983-0.161692250140.8134736286140.04648918180110.71545445819512.7047731179-27.386262737521.4863462278
51.57493962906-0.0752115354640.5213383700863.97089518165-0.5444624822653.365797538380.40006345475-0.209816033672-0.3555505071710.165985396939-0.3673518792610.1085590897090.1180488980180.0878664334077-0.07156031885620.294573410533-0.103799739677-0.1151245613040.766775299020.02232800919030.829251660973.40357187805-30.670054172117.3088477728
63.90570978347-0.141955395003-0.867943917363.445412564140.7163142220992.318013968330.343339849762-0.238709773088-0.5379839595960.050759523515-0.3098294778080.2360705175920.3462622572970.0720536058767-0.1242185243860.3553265943-0.0644334239542-0.1967993153170.6468540268790.04130364779630.8886687666772.05293788596-32.402453127913.9131150766
75.13285789581-1.624843230485.699502955278.8580152589-3.491986929376.657159127340.815947012709-0.646786818345-0.4379580430651.24262698872-0.952049863013-0.7140040999040.5158321221941.740968545880.1867695713631.41444256567-0.0428437543906-0.2628218304582.52882683090.2404760497681.4086134215330.3653562498-11.138177719450.1702540837
84.0457788079-2.863509696454.476644359122.05266014128-3.219112758025.0749533978-1.74614976424-1.685649192762.042553288472.133567796840.334252850266-1.30973855735-1.269429127230.7417660240021.370663616552.46138769523-0.0840138542029-0.7082647489783.01429687231-0.5700462212232.1278709231130.765709174110.209431952358.1797286724
94.68356618729-0.4951653634351.477455956852.37022503534-0.07532406425323.85090678764-0.0516857241759-0.9489300484730.4940353973970.7027875704790.07169466857250.130419299003-0.676573477202-0.3185762277730.0495785060290.64630808119-0.128608922492-0.002616641279680.831277326029-0.1851269268180.808417676748.40794768301-0.55834963515931.8001950272
102.10962723731-0.9233777475632.894254894320.432120114165-1.335054430344.18977806479-0.92523362065-0.9469309879790.1415853934871.48423620190.0110384410297-1.14650010771-0.7129458747770.3180090888980.9134839313121.44158615138-0.156047466803-0.3563957462691.776940841010.08351065387591.1321192322832.3642145958-10.862734413852.7679867048
113.053209230180.906122863816-3.553605084192.275180135890.949502629346.50789732075-0.0951419826617-0.119909960532-0.121716813880.50024281646-0.380243222419-0.04990913808680.763512466966-0.01389696392540.3660053501090.511769895594-0.121522451696-0.1620207732340.5213841863670.06943759936360.73325863027722.9069965357-11.068924034216.5384021461
126.781596347530.497382269054-2.462937389552.912545216731.597017903013.42256409236-0.1816182867410.9768560308880.271408594642-0.487303077537-0.4009971011360.221215327129-0.136839337332-0.420992469040.4767769711050.388268610623-0.0721706307211-0.1105376730260.6202909636180.0388392615860.71685497557124.0802517844-5.326933320394.05026323698
136.907724702041.24630444387-1.229634124163.855053972050.9408092054064.093186004570.003173786683650.354114414931-0.135433476012-0.218511713419-0.08628177416580.0968154466052-0.1445308461010.4880163883830.188791475650.377953820154-0.106096510747-0.1977726988890.7143095872130.013179442950.8617056105321.2797625297-3.130795464531.82890911161
144.423316068290.876085457158-1.992313658567.55776829174-0.457955774156.662885846520.03456852526740.7420883590411.14698074049-0.565086988482-0.3157493665770.298915200151-0.600290995304-0.3591675659640.3048181038730.428949839412-0.0859286068599-0.164684037920.703335462860.006961725761240.79202158465617.76818360160.0956815805867-0.393120508456
152.532651729193.66853460633-0.7117888419365.68096974359-0.4468033985893.10248551292-0.156355380825-0.2483438245250.797406656525-0.1714579321540.1773609977390.0294856954006-0.3932758706030.254561649461-0.04333830801740.400083813704-0.0632189466313-0.1177163810670.6693749614030.1208580928970.74719911878829.44976261827.171598091294.52706083181
161.25270661878-0.123881053624-1.38866566092.03085440276-1.485964408542.93194854157-0.078417197394-0.05389660143580.7224152161030.0825645562676-0.1292665212450.832154658781-0.242281402119-0.09655063180150.1172708619280.358802739208-0.166927189806-0.03712302952840.727354637367-0.08938278551630.98213920367414.8547100648-0.92818518754513.5826700421
176.08839409747-5.063375944461.048757208396.67350596237-2.295148101712.81260369064-0.266129241676-0.6098066922720.752029845611.646805228050.10261298077-0.689913226206-0.6766004295190.5620989032470.05879221939230.7297545476-0.350608181553-0.2030632148670.879799145621-0.03248845861881.0210922802134.87434278522.0870454567921.8826382212
182.469223090782.4038428128-1.650954686164.189230509591.821874501857.58462857628-0.1341288795450.179920103891-0.05979765347910.314094658722-0.3992385149220.6196125355190.739440198419-0.3677567954150.4901152459490.463908883043-0.0900034211589-0.1798382478230.606626666282-0.1090068387810.9463474033829.1304207639-15.399367349510.5422471987
193.644277315451.93692014012-1.030173370924.96975912387-0.9803921679291.895054518680.136544643719-0.343245558806-0.5150620748640.3401874566680.290966336299-0.7747648728010.1860476591140.5614674052-0.5062257800410.536285717399-0.0135579732947-0.3002802078260.739083032864-0.04226826665361.0873155283138.7010240178-5.696819199716.1186067325
204.14496880952.1073455037-2.401720634631.94140141391-1.181539535251.667407044260.199831689969-0.137748195536-0.114473737507-0.0347400674498-0.123038859689-0.4194500784060.2623503671850.1880424094830.03204697029310.415000731516-0.11018948705-0.2202149130630.67759588059-0.02270069512651.0050829822540.88690669581.266440435727.89389701384
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 141 through 150 )AB141 - 150141 - 150
22chain 'A' and (resid 151 through 165 )AB151 - 165151 - 165
33chain 'A' and (resid 166 through 183 )AB166 - 183166 - 183
44chain 'B' and (resid 1 through 62 )BC1 - 621 - 62
55chain 'B' and (resid 63 through 133 )BC63 - 13363 - 133
66chain 'B' and (resid 134 through 183 )BC134 - 183134 - 183
77chain 'R' and (resid 1 through 10 )RA1 - 10
88chain 'R' and (resid 11 through 30 )RA11 - 30
99chain 'R' and (resid 31 through 80 )RA31 - 80
1010chain 'R' and (resid 81 through 90 )RA81 - 90
1111chain 'A' and (resid 1 through 21 )AB1 - 211 - 21
1212chain 'A' and (resid 22 through 32 )AB22 - 3222 - 32
1313chain 'A' and (resid 33 through 52 )AB33 - 5233 - 52
1414chain 'A' and (resid 53 through 62 )AB53 - 6253 - 62
1515chain 'A' and (resid 63 through 78 )AB63 - 7863 - 78
1616chain 'A' and (resid 79 through 90 )AB79 - 9079 - 90
1717chain 'A' and (resid 91 through 100 )AB91 - 10091 - 100
1818chain 'A' and (resid 101 through 112 )AB101 - 112101 - 112
1919chain 'A' and (resid 113 through 125 )AB113 - 125113 - 125
2020chain 'A' and (resid 126 through 140 )AB126 - 140126 - 140

+
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