[English] 日本語
Yorodumi
- PDB-6weq: DENV1 NS1 in complex with neutralizing 2B7 Fab fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6weq
TitleDENV1 NS1 in complex with neutralizing 2B7 Fab fragment
Components
  • 2B7 Fab fragment heavy chain
  • 2B7 Fab fragment light chain
  • Non-structural protein 1
KeywordsVIRAL PROTEIN / Flavivirus NS1 / Antibody / Fab fragment
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
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 non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / 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. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / 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
Biological speciesDengue virus 1
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsAkey, D.L. / Smith, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Science / Year: 2021
Title: Structural basis for antibody inhibition of flavivirus NS1-triggered endothelial dysfunction.
Authors: Biering, S.B. / Akey, D.L. / Wong, M.P. / Brown, W.C. / Lo, N.T.N. / Puerta-Guardo, H. / Tramontini Gomes de Sousa, F. / Wang, C. / Konwerski, J.R. / Espinosa, D.A. / Bockhaus, N.J. / ...Authors: Biering, S.B. / Akey, D.L. / Wong, M.P. / Brown, W.C. / Lo, N.T.N. / Puerta-Guardo, H. / Tramontini Gomes de Sousa, F. / Wang, C. / Konwerski, J.R. / Espinosa, D.A. / Bockhaus, N.J. / Glasner, D.R. / Li, J. / Blanc, S.F. / Juan, E.Y. / Elledge, S.J. / Mina, M.J. / Beatty, P.R. / Smith, J.L. / Harris, E.
History
DepositionApr 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Experimental preparation / Category: citation / citation_author / exptl_crystal_grow
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _exptl_crystal_grow.temp
Revision 1.2Oct 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-structural protein 1
B: Non-structural protein 1
C: Non-structural protein 1
D: Non-structural protein 1
E: 2B7 Fab fragment heavy chain
F: 2B7 Fab fragment light chain
G: 2B7 Fab fragment heavy chain
H: 2B7 Fab fragment light chain
I: 2B7 Fab fragment heavy chain
J: 2B7 Fab fragment light chain
K: 2B7 Fab fragment heavy chain
L: 2B7 Fab fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,46921
Polymers390,60412
Non-polymers1,8669
Water00
1
A: Non-structural protein 1
B: Non-structural protein 1
E: 2B7 Fab fragment heavy chain
F: 2B7 Fab fragment light chain
G: 2B7 Fab fragment heavy chain
H: 2B7 Fab fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,18710
Polymers195,3026
Non-polymers8854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Non-structural protein 1
D: Non-structural protein 1
I: 2B7 Fab fragment heavy chain
J: 2B7 Fab fragment light chain
K: 2B7 Fab fragment heavy chain
L: 2B7 Fab fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,28311
Polymers195,3026
Non-polymers9815
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.446, 329.709, 86.717
Angle α, β, γ (deg.)90.000, 90.783, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
43

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A'A-10 - 108
121chain 'A'A129 - 349
131chain 'A'A401
141chain 'A'A421
251chain 'B'B-10 - 108
261chain 'B'B129 - 349
271chain 'B'B401
281chain 'B'B421
391chain 'C'C-10 - 108
3101chain 'C'C129 - 349
3111chain 'C'C401
3121chain 'C'C421
4131chain 'D'D-10 - 108
4141chain 'D'D129 - 349
4151chain 'D'D401
4161chain 'D'D421
1172(chain 'E' and (resid 2 through 132 or resid 136 through 219))E2 - 132
1182(chain 'E' and (resid 2 through 132 or resid 136 through 219))E136 - 162
1192(chain 'E' and (resid 2 through 132 or resid 136 through 219))E167 - 219
2202chain 'G'G2 - 132
2212chain 'G'G136 - 162
2222chain 'G'G167 - 219
3232chain 'I'I2 - 132
3242chain 'I'I136 - 162
3252chain 'I'I167 - 219
4262chain 'K'K2 - 132
4272chain 'K'K136 - 162
4282chain 'K'K167 - 219
1293chain 'F'F1 - 215
2303chain 'H'H1 - 215
3313chain 'J'J1 - 215
4323chain 'L'L1 - 215

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein
Non-structural protein 1


Mass: 42795.512 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 1 / Production host: unidentified baculovirus / References: UniProt: Q9J7C6
#2: Antibody
2B7 Fab fragment heavy chain


Mass: 28651.375 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody
2B7 Fab fragment light chain


Mass: 26204.037 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 22% PEG 3350, 0.2 M trisodium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.2→48.17 Å / Num. obs: 62008 / % possible obs: 99.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 95.38 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.3 / Rpim(I) all: 0.122 / Rrim(I) all: 0.3245 / Net I/av σ(I): 5.91 / Net I/σ(I): 5.91
Reflection shellResolution: 3.2→3.314 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.661 / Mean I/σ(I) obs: 0.87 / Num. unique obs: 6154 / CC1/2: 0.415 / CC star: 0.766 / Rpim(I) all: 0.6778 / Rrim(I) all: 1.795 / % possible all: 99.97

-
Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4o6b

4o6b


Resolution: 3.2→48.17 Å / SU ML: 0.5059 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 27.2833
RfactorNum. reflection% reflection
Rfree0.2612 3092 4.99 %
Rwork0.207 --
obs0.2097 61969 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 93.17 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24052 0 5 0 24057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010824660
X-RAY DIFFRACTIONf_angle_d1.245133523
X-RAY DIFFRACTIONf_chiral_restr0.0623708
X-RAY DIFFRACTIONf_plane_restr0.00774265
X-RAY DIFFRACTIONf_dihedral_angle_d21.90718897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.250.38321210.35712689X-RAY DIFFRACTION100
3.25-3.30.36441220.35262658X-RAY DIFFRACTION99.96
3.3-3.360.38381470.32112716X-RAY DIFFRACTION99.97
3.36-3.420.34081380.28332623X-RAY DIFFRACTION99.89
3.42-3.490.34011420.26422672X-RAY DIFFRACTION99.96
3.49-3.560.31831320.26242719X-RAY DIFFRACTION100
3.56-3.640.30931400.26492655X-RAY DIFFRACTION99.96
3.64-3.720.36031300.26522667X-RAY DIFFRACTION99.86
3.72-3.810.30431440.25352690X-RAY DIFFRACTION99.89
3.81-3.920.26161300.25242684X-RAY DIFFRACTION99.86
3.92-4.030.28341480.23782661X-RAY DIFFRACTION99.96
4.03-4.160.25211640.21332653X-RAY DIFFRACTION99.86
4.16-4.310.22511400.18332674X-RAY DIFFRACTION99.89
4.31-4.480.21141320.1682703X-RAY DIFFRACTION100
4.48-4.690.21781350.16272643X-RAY DIFFRACTION100
4.69-4.930.21811360.15922686X-RAY DIFFRACTION99.96
4.93-5.240.23141530.16622699X-RAY DIFFRACTION100
5.24-5.650.24941620.17362654X-RAY DIFFRACTION100
5.65-6.210.25931300.17772709X-RAY DIFFRACTION100
6.21-7.110.25021530.18172648X-RAY DIFFRACTION99.89
7.11-8.950.21591510.18652685X-RAY DIFFRACTION99.96
8.95-48.170.25991420.19232689X-RAY DIFFRACTION98.88
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)
12.141600490270.07630021480640.007109693342732.44710132316-0.2515191228961.938092204610.115869639936-0.149001141713-0.317457792569-0.0122837348033-0.01072508884840.1709887701120.271361388989-0.01514674510310.0001987336707150.596833795193-0.01875667112050.01029305792580.7223332884160.01113998832380.63243895309846.7872256446116.0390626633.80989119587
21.278843107180.2590484954940.2487363104871.7467687353-0.2131373742351.33503908704-0.170071594103-0.05240870773460.1484468192390.07859190474980.03994207845620.00030298813553-0.2379421034920.1517680191930.00120624240990.584689839661-0.0600823194197-0.009248971649090.751096636265-0.0292627198590.54506515738647.47464794151.105148964-5.83344810006
31.694059193690.1995113679790.1309906431132.34698993881-0.07504714399491.171922163090.006552641792720.02508744222880.2476268444420.07985551577220.01390566785080.241237787512-0.140252086871-0.01220177367610.0001219477399410.560969271076-0.04015581714030.05091632420550.7654196047090.05092880649890.59734444421847.0283132419163.44316799939.4262280294
41.688000051310.5992059116350.03912619720232.479508458340.1523246280771.099967696780.07490169468410.0446467881465-0.3490089245930.06870819903-0.137707441839-0.3600276046330.2899041080440.1339999235460.001089084589030.6923712096120.006157380997550.007612941163360.7124683072660.0004309845454590.61151134487248.4014935549128.30010201549.0238178059
51.97810166249-0.7100040877721.343961031021.023750170030.009985728194152.07378575221-0.0377623170036-0.0176429219161-0.3410611967790.4930610113920.0581844660365-0.2955327407550.0931522613040.0533087369195-0.002524937422220.9136300149280.0326046813573-0.115549814510.7744769192390.02678366182941.1150843516869.753019658590.066827059138.7464325659
61.798952215930.2976494277890.7136877169231.72611497321-0.7598958899110.9973871474050.465581476803-0.397532020812-0.6145594702930.28762642948-0.330938023585-0.1163754381550.741236295183-0.172041379838-0.0001727237279181.393795979360.0306106186691-0.1567500012710.8993991127780.09155735134631.1363622546164.445097672373.170715346333.6423198754
70.829924290795-0.6400517368670.1310525034482.028694729411.111628283641.85041226893-0.0750521188915-0.1330297672230.2851034370150.335028991479-0.1418835718730.595230678116-0.125809679793-0.388114343633-0.001056254004890.857053270316-0.00404698669629-0.01901836824940.910014335429-0.08660387001711.2092286810929.4547631225190.87997425413.1039843439
80.471903947243-0.0804919967964-0.4558873226252.3163344627-0.08203148378160.674653777572-0.0419236021803-0.04425589598990.463144938024-0.441516899040.02779416202220.245010825627-0.6328488280320.0929234986729-4.19175402718E-61.115447340190.00342988723457-0.1887722384050.796149005522-0.01263098602111.2068285249639.1817273307201.5421390591.85685182862
91.170406395910.168889716164-0.8798428319671.533231317490.5875072307711.915553978750.03704077300580.02359237190830.372338150823-0.5173915297220.109982431924-0.167304238786-0.1413566355530.0494279919145-0.002320695641480.854556111278-0.1146020601520.0608856518750.8871287950290.07871973470271.0025103935569.0482696735189.4681794264.33219970393
101.76507676918-0.469402906239-1.04904169452.275957803570.1894754832650.8110762206290.3283109187040.2393774238410.567164622948-0.736301171862-0.2418664428340.170681483992-0.710297792292-0.1784356626010.002411709545031.31204426077-0.1111545443880.009056055062730.9035089773540.03144499666881.0373948997963.3510363552206.2351269.132997554
111.173427131790.6493088340620.1139421863272.030557183230.9415020266211.61402504470.04366561125070.117202563023-0.3266986235690.017352259764-0.09733880802530.3161067137240.150528404014-0.275652198019-0.001353151481190.908828836475-0.0826086979127-0.02038173327070.911222919777-0.1182562585241.1132075933830.291266223988.322752098630.383955384
120.894819962149-0.348025328948-0.002115306387631.616282677880.09610266439450.934868537432-0.01456323875680.125106806667-0.4832226703270.232045976435-0.01246031658330.03244198744270.6125026738650.075657673059-0.000287574928291.36350344394-0.04183212218870.07495048582130.873466064606-0.05536353495751.1825098712940.371687757677.76849263141.5615867821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid -10 through 401)
2X-RAY DIFFRACTION2(chain 'B' and resid -10 through 401)
3X-RAY DIFFRACTION3(chain 'C' and resid -10 through 401)
4X-RAY DIFFRACTION4(chain 'D' and resid -10 through 401)
5X-RAY DIFFRACTION5(chain 'E' and resid 2 through 219)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 215)
7X-RAY DIFFRACTION7(chain 'G' and resid 2 through 219)
8X-RAY DIFFRACTION8(chain 'H' and resid 1 through 215)
9X-RAY DIFFRACTION9(chain 'I' and resid 2 through 219)
10X-RAY DIFFRACTION10(chain 'J' and resid 1 through 215)
11X-RAY DIFFRACTION11(chain 'K' and resid 2 through 219)
12X-RAY DIFFRACTION12(chain 'L' and resid 1 through 215)

+
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