[English] 日本語
Yorodumi
- PDB-5nt2: Complex of influenza A NS1 with TRIM25 coiled coil domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nt2
TitleComplex of influenza A NS1 with TRIM25 coiled coil domain
Components
  • E3 ubiquitin/ISG15 ligase TRIM25
  • Non-structural protein 1
KeywordsLIGASE / Viral protein/host protein/E3 ligase/TRIM protein
Function / homology
Function and homology information


: / Inhibition of IFN-beta / Inhibition of PKR / Inhibition of Host mRNA Processing and RNA Silencing / regulation of viral entry into host cell / RIG-I binding / symbiont-mediated suppression of host mRNA processing / suppression of viral release by host / Microbial modulation of RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host PKR/eIFalpha signaling ...: / Inhibition of IFN-beta / Inhibition of PKR / Inhibition of Host mRNA Processing and RNA Silencing / regulation of viral entry into host cell / RIG-I binding / symbiont-mediated suppression of host mRNA processing / suppression of viral release by host / Microbial modulation of RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host PKR/eIFalpha signaling / host-mediated suppression of symbiont invasion / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / NS1 Mediated Effects on Host Pathways / response to vitamin D / protein serine/threonine kinase inhibitor activity / Modulation of host responses by IFN-stimulated genes / RIPK1-mediated regulated necrosis / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / ligase activity / RSV-host interactions / TRAF6 mediated NF-kB activation / viral release from host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / Viral mRNA Translation / protein monoubiquitination / protein K48-linked ubiquitination / ERAD pathway / antiviral innate immune response / cellular response to leukemia inhibitory factor / positive regulation of DNA-binding transcription factor activity / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / RING-type E3 ubiquitin transferase / PKR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / response to estrogen / cytoplasmic stress granule / Interferon gamma signaling / positive regulation of NF-kappaB transcription factor activity / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Ovarian tumor domain proteases / regulation of protein localization / TRAF3-dependent IRF activation pathway / ubiquitin-dependent protein catabolic process / response to oxidative stress / positive regulation of canonical NF-kappaB signal transduction / host cell cytoplasm / transcription coactivator activity / nuclear body / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / cadherin binding / symbiont-mediated suppression of host gene expression / innate immune response / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
TRIM25, PRY/SPRY domain / : / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / SPRY-associated domain / SPRY-associated ...TRIM25, PRY/SPRY domain / : / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / S15/NS1, RNA-binding / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Non-structural protein 1 / E3 ubiquitin/ISG15 ligase TRIM25
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.259 Å
AuthorsKoliopoulos, M.G. / Rittinger, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick InstituteFC001142 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Molecular mechanism of influenza A NS1-mediated TRIM25 recognition and inhibition.
Authors: Koliopoulos, M.G. / Lethier, M. / van der Veen, A.G. / Haubrich, K. / Hennig, J. / Kowalinski, E. / Stevens, R.V. / Martin, S.R. / Reis E Sousa, C. / Cusack, S. / Rittinger, K.
History
DepositionApr 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
F: Non-structural protein 1
C: Non-structural protein 1
D: Non-structural protein 1
E: Non-structural protein 1
I: E3 ubiquitin/ISG15 ligase TRIM25
A: E3 ubiquitin/ISG15 ligase TRIM25
V: E3 ubiquitin/ISG15 ligase TRIM25
N: E3 ubiquitin/ISG15 ligase TRIM25


Theoretical massNumber of molelcules
Total (without water)191,5188
Polymers191,5188
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALLS analysis shows that full-length NS1 is a dimer., gel filtration, SEC-MALLS analysis shows that TRIM25 coiled-coil is dimeric. Additional structural data show that ...Evidence: gel filtration, SEC-MALLS analysis shows that full-length NS1 is a dimer., gel filtration, SEC-MALLS analysis shows that TRIM25 coiled-coil is dimeric. Additional structural data show that it is an antiparallel dimer (see 4LTB in PDB).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32560 Å2
ΔGint-203 kcal/mol
Surface area69220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.257, 76.296, 92.072
Angle α, β, γ (deg.)100.04, 93.71, 111.14
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Non-structural protein 1 / NS1 / NS1A


Mass: 25867.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
Strain: A/Puerto Rico/8/1934 H1N1 / Gene: NS / Production host: Escherichia coli (E. coli) / References: UniProt: P03496
#2: Protein
E3 ubiquitin/ISG15 ligase TRIM25 / Estrogen-responsive finger protein / RING finger protein 147 / RING-type E3 ubiquitin transferase / ...Estrogen-responsive finger protein / RING finger protein 147 / RING-type E3 ubiquitin transferase / RING-type E3 ubiquitin transferase TRIM25 / Tripartite motif-containing protein 25 / Ubiquitin/ISG15-conjugating enzyme TRIM25 / Zinc finger protein 147


Mass: 22011.930 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM25, EFP, RNF147, ZNF147 / Production host: Escherichia coli (E. coli)
References: UniProt: Q14258, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases), RING-type E3 ubiquitin transferase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM sodium citrate pH 6.5, 24% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 4.259→61.51 Å / Num. obs: 12516 / % possible obs: 98.6 % / Redundancy: 2.6 % / CC1/2: 0.985 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.14 / Net I/σ(I): 5.7
Reflection shellResolution: 4.26→4.33 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 630 / CC1/2: 0.8 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LTB

4ltb


Resolution: 4.259→61.684 Å / SU ML: 0.78 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 38.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3088 635 5.1 %
Rwork0.2702 --
obs0.2721 12451 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.259→61.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10516 0 0 0 10516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410633
X-RAY DIFFRACTIONf_angle_d0.814298
X-RAY DIFFRACTIONf_dihedral_angle_d12.9076705
X-RAY DIFFRACTIONf_chiral_restr0.0451678
X-RAY DIFFRACTIONf_plane_restr0.0051834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2585-4.58730.39431280.30972341X-RAY DIFFRACTION97
4.5873-5.04870.30691340.29752355X-RAY DIFFRACTION98
5.0487-5.77880.37191240.32452377X-RAY DIFFRACTION99
5.7788-7.27880.40851260.34262396X-RAY DIFFRACTION99
7.2788-61.69070.22131230.20042347X-RAY DIFFRACTION98
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)
16.32522.838-4.06467.80844.09318.43251.50640.46181.9186-0.054-1.1066-0.641-0.7840.5151-0.11531.70290.3645-0.26021.3278-0.35681.6546-136.6101-75.8288-197.6639
21.96071.5648-0.39514.96725.23755.81781.5373-4.30631.53831.2681.94120.5509-0.23560.70950.87142.20730.54870.33042.39370.57840.3712-150.0506-76.7036-210.8737
37.3227-0.0759-0.23152.81312.0976.99220.14141.4032-2.1823-0.5447-0.68550.99111.1438-1.4199-0.13641.80240.1083-0.37521.19710.35930.894-145.0457-85.0576-214.1167
47.57180.6272-0.10385.39411.51278.60890.1153-1.9804-0.71440.81230.5651-2.4040.7367-0.3229-0.23421.20920.4275-0.28461.3608-0.14471.2888-131.0545-83.2523-201.3731
54.36680.4689-2.64694.07580.54427.3246-1.69580.53680.27520.37460.80750.76270.46352.6412-0.00291.21180.03570.18850.88110.08490.9333-139.448-80.1826-204.363
66.0275-0.73190.86023.73163.46777.8374-0.148-0.63541.92040.52950.4318-1.65-0.0987-0.26060.17361.3770.5066-0.181.8835-0.22331.4581-142.0312-77.4693-209.7861
75.6473-2.0888-1.44221.08730.96490.9033-2.4663-1.0161-0.48970.41540.0239-0.43951.0996-0.38770.25741.84810.46690.05430.9099-0.34961.3646-142.9369-93.1775-198.3719
85.8151.2753-2.57875.60293.09077.03550.3593-0.7366-0.86030.94050.1952-3.24491.86372.68850.47651.80910.09280.33870.57630.50961.7136-136.1873-88.3846-213.0649
95.5197-1.1633-1.3973.891-1.37633.2249-0.30211.19481.36880.57581.0449-0.1846-0.80850.5488-0.21351.00510.08830.11711.2671-0.10191.2336-133.261-78.3855-217.0923
104.63612.8047-2.07935.43171.29672.7752-1.5696-0.28-0.3414-0.01070.9133-0.5-0.27813.1539-0.27661.15210.0074-0.33951.2505-0.12021.533-126.3161-81.8527-204.492
118.9438-3.454-2.03576.4919-0.66065.1326-0.9015-1.0249-2.88771.27823.05960.64141.89051.1658-0.01861.61050.06950.47832.0554-0.59950.9021-102.5399-36.5781-78.8204
125.20983.13262.30794.78861.28995.2568-1.70980.28930.3827-1.19151.1342.0237-2.57090.1562-0.44991.20760.37640.26511.42170.02521.7581-107.0707-23.0074-67.016
132.011-2.3319-3.28692.2789-1.29853.2154-0.93340.00531.78270.7683-0.30880.1582-0.88110.3845-1.4729-1.18460.05393.19742.07490.3666-0.455-93.5674-20.2828-64.3732
142.89681.45992.64413.3560.93085.0659-3.39670.6668-0.472-0.65281.4451-0.2927-0.94381.8833-1.8771-0.05471.02771.75751.8345-1.0799-0.975-98.6333-25.6719-62.0294
151.64652.7040.76777.0761-2.59926.3062-1.02561.8195-1.206-2.0951-0.3659-0.97820.7154-1.1171-0.691.31880.5091-0.02891.7844-0.59591.5231-93.6625-37.9821-75.2851
162.11910.59592.03795.52250.35126.5964-0.307-0.8221-1.1857-0.506-0.1916-0.41121.51812.236-0.46771.22190.33960.20341.4174-0.01390.7401-101.5647-30.6278-69.5343
173.7377-4.5949-1.3626.23631.86110.5301-0.9943-0.0201-0.6794-0.7444-1.5849-0.517-0.23573.5081-0.441.57230.0865-0.09312.88510.02571.4569-88.7898-23.8872-78.7356
182.49980.49721.14565.28360.81616.01050.33270.2934-0.01040.62191.048-1.13891.6799-0.0328-0.38430.92130.07790.14322.113-0.21491.2808-93.2867-33.2441-62.4961
195.0459-0.69040.70882.9541-1.87542.69920.25431.4801-1.4123-0.33512.1862-1.29363.46620.12550.40042.14960.69630.64091.1526-0.33431.3278-92.938-43.0208-71.9975
202.5302-2.9977-1.82984.58340.62221.94870.34440.5045-2.6994-1.0272-0.17170.2680.2008-0.222-0.33141.5434-0.0314-0.14141.8303-0.38392.5404-131.9299-53.7667-138.9206
214.79690.37450.65082.7587-2.0071.07130.35720.915-1.4106-1.6139-3.6836-0.17582.6134-0.4019-0.36452.5052-0.30020.02441.817-1.33012.3965-123.0518-59.6382-147.2425
226.3666-1.79543.03240.6106-1.13627.7218-0.0447-0.21593.062-0.7591-0.2820.74150.26861.15040.04722.1081-0.00770.78462.6498-1.30432.9986-107.0087-54.3323-138.2643
235.3895-1.1242-2.77098.30670.42021.35570.1435-0.2086-0.1213-2.463-0.09131.499-0.2261-0.50630.06341.7322-0.2159-0.34260.98480.18951.3433-102.8189-91.5188-150.0916
245.0159-2.06722.93136.2297-1.54651.28040.63630.5202-1.1102-0.8175-1.25430.49410.16960.7529-0.44781.43110.2759-0.06211.5325-0.02381.7565-119.9987-48.248-140.6156
255.1114-2.1826-1.08646.0743-0.32364.06150.5649-0.90380.81450.9497-0.2286-0.5398-0.03360.5454-0.08061.2402-0.04120.07191.0551-0.19021.2691-81.8887-53.5412-128.58
262.4352-3.9089-3.51543.92374.35535.65360.5560.13060.6621-0.15170.4029-1.4341-0.3229-0.00770.2841.1781-0.24910.37751.4545-0.04791.4102-92.6875-57.7482-109.8755
27-0.03970.17570.03920.51010.32790.12051.73510.36570.7573-1.93730.471-0.21260.962-3.50730.29012.43910.68290.02943.3013-0.15671.9515-69.8115-111.334-159.6486
282.0634-2.3824-1.79386.42991.48662.118-0.6623-0.3609-1.10060.8763-0.25661.42550.14160.21271.19461.0839-0.27650.19941.9731-0.30721.5389-101.9007-78.4512-118.5277
292.9726-0.91082.4657-0.1015-1.18913.37751.0730.5806-1.52820.18390.15840.14881.00870.31320.00251.18950.0841-0.26531.14680.00721.2954-115.7147-77.0707-170.1752
303.06391.0859-0.91151.88421.29471.5738-1.9193-0.0363-0.2172.018-1.7865-0.3392-0.25761.8318-0.46032.67580.8582-0.51443.4860.32992.1306-54.2418-78.7691-115.8427
314.20830.92872.05780.2598-0.31482.0243-1.3147-0.4882.12980.12240.0871-0.135-1.6616-0.06960.43231.3462-0.114-0.24121.5153-0.09131.5146-96.1621-61.4091-158.7691
324.06560.3662.2740.96070.1142.0356-0.7709-0.42010.65840.16750.0961-0.18-0.9004-0.34030.74021.055-0.02980.11141.45-0.25621.0037-109.1192-70.1499-156.9016
332.8109-0.2463.04280.0357-0.07893.4791-1.1837-3.48491.9769-1.2504-3.21541.329-2.6829-0.31190.77522.7226-0.0558-0.31312.7861-0.70683.3481-176.2499-80.2189-202.1172
344.9703-0.38423.80752.14191.45013.2359-1.61752.629-0.03850.22280.7083-0.6468-0.94742.0760.88751.0239-0.20440.06541.97420.51940.978-118.516-66.5406-182.3212
350.7603-0.3770.02375.62852.77161.66630.16750.23670.0295-0.6417-0.14420.0757-0.3008-0.18810.30821.31670.0611-0.17821.26220.00390.7927-97.8843-62.7646-120.1335
363.9278-4.3112-2.29084.74942.4981.3296-2.8602-1.05582.00240.0559-1.16380.0646-1.67460.5275-0.19562.03640.38330.32732.35350.07813.6568-108.10465.9517-74.4916
373.8017-0.6429-0.21743.45533.01313.6384-0.0596-0.71550.36590.8418-1.07050.0663-0.73380.31780.13773.8476-0.7967-2.61672.33061.87148.0441-116.17714.2732-73.0675
386.2223-1.9414-0.08033.9115-0.11280.57470.86870.37172.2258-0.63550.04220.5187-1.011-0.1716-0.0820.7171-0.21262.1373.95233.03816.5511-116.6642-5.1908-73.3309
392.9296-0.7564-0.26939.75973.96943.5292-0.09970.28571.35330.89-1.14790.1935-0.0153-1.04860.24641.52950.08760.36191.8713-0.12372.0875-114.1942-30.773-81.1462
403.2477-2.0538-3.32334.94511.06665.1174-0.8737-0.0898-0.31472.6368-0.61110.07142.1255-0.69890.4491.90630.11180.38421.4429-0.13891.1582-100.7412-67.6295-100.0697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'F' and (resid 87 through 99 )
2X-RAY DIFFRACTION2chain 'F' and (resid 100 through 106 )
3X-RAY DIFFRACTION3chain 'F' and (resid 107 through 126 )
4X-RAY DIFFRACTION4chain 'F' and (resid 127 through 142 )
5X-RAY DIFFRACTION5chain 'F' and (resid 143 through 151 )
6X-RAY DIFFRACTION6chain 'F' and (resid 152 through 162 )
7X-RAY DIFFRACTION7chain 'F' and (resid 163 through 170 )
8X-RAY DIFFRACTION8chain 'F' and (resid 171 through 188 )
9X-RAY DIFFRACTION9chain 'F' and (resid 189 through 195 )
10X-RAY DIFFRACTION10chain 'F' and (resid 196 through 201 )
11X-RAY DIFFRACTION11chain 'C' and (resid 87 through 98 )
12X-RAY DIFFRACTION12chain 'C' and (resid 99 through 106 )
13X-RAY DIFFRACTION13chain 'C' and (resid 107 through 112 )
14X-RAY DIFFRACTION14chain 'C' and (resid 113 through 126 )
15X-RAY DIFFRACTION15chain 'C' and (resid 127 through 142 )
16X-RAY DIFFRACTION16chain 'C' and (resid 143 through 162 )
17X-RAY DIFFRACTION17chain 'C' and (resid 163 through 170 )
18X-RAY DIFFRACTION18chain 'C' and (resid 171 through 195 )
19X-RAY DIFFRACTION19chain 'C' and (resid 196 through 201 )
20X-RAY DIFFRACTION20chain 'D' and (resid 4 through 50 )
21X-RAY DIFFRACTION21chain 'D' and (resid 51 through 74 )
22X-RAY DIFFRACTION22chain 'D' and (resid 75 through 84 )
23X-RAY DIFFRACTION23chain 'D' and (resid 85 through 203 )
24X-RAY DIFFRACTION24chain 'E' and (resid 3 through 85 )
25X-RAY DIFFRACTION25chain 'E' and (resid 86 through 203 )
26X-RAY DIFFRACTION26chain 'I' and (resid 190 through 304 )
27X-RAY DIFFRACTION27chain 'I' and (resid 305 through 316 )
28X-RAY DIFFRACTION28chain 'I' and (resid 317 through 362 )
29X-RAY DIFFRACTION29chain 'A' and (resid 190 through 298 )
30X-RAY DIFFRACTION30chain 'A' and (resid 299 through 316 )
31X-RAY DIFFRACTION31chain 'A' and (resid 317 through 362 )
32X-RAY DIFFRACTION32chain 'V' and (resid 190 through 298 )
33X-RAY DIFFRACTION33chain 'V' and (resid 299 through 316 )
34X-RAY DIFFRACTION34chain 'V' and (resid 317 through 362 )
35X-RAY DIFFRACTION35chain 'N' and (resid 190 through 298 )
36X-RAY DIFFRACTION36chain 'N' and (resid 299 through 304 )
37X-RAY DIFFRACTION37chain 'N' and (resid 305 through 311 )
38X-RAY DIFFRACTION38chain 'N' and (resid 312 through 316 )
39X-RAY DIFFRACTION39chain 'N' and (resid 317 through 330 )
40X-RAY DIFFRACTION40chain 'N' and (resid 331 through 362 )

+
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