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- PDB-3mop: The ternary Death Domain complex of MyD88, IRAK4, and IRAK2 -

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Basic information

Entry
Database: PDB / ID: 3mop
TitleThe ternary Death Domain complex of MyD88, IRAK4, and IRAK2
Components
  • Interleukin-1 receptor-associated kinase 4
  • Interleukin-1 receptor-associated kinase-like 2
  • Myeloid differentiation primary response protein MyD88
KeywordsSIGNALING PROTEIN / IMMUNE SYSTEM / Death domain complex / helical symmetry / single-stranded helical assembly / left-handed helical assembly
Function / homology
Function and homology information


regulation of cytokine-mediated signaling pathway / : / regulation of chemokine (C-X-C motif) ligand 1 production / Toll binding / MyD88 deficiency (TLR5) / regulation of chemokine (C-X-C motif) ligand 2 production / ATP-dependent histone chaperone activity / neutrophil-mediated killing of bacterium / induced systemic resistance / leukocyte activation involved in inflammatory response ...regulation of cytokine-mediated signaling pathway / : / regulation of chemokine (C-X-C motif) ligand 1 production / Toll binding / MyD88 deficiency (TLR5) / regulation of chemokine (C-X-C motif) ligand 2 production / ATP-dependent histone chaperone activity / neutrophil-mediated killing of bacterium / induced systemic resistance / leukocyte activation involved in inflammatory response / TIR domain binding / : / response to molecule of fungal origin / toll-like receptor 8 signaling pathway / positive regulation of lymphocyte proliferation / response to peptidoglycan / positive regulation of interleukin-23 production / establishment of endothelial intestinal barrier / IRAK4 deficiency (TLR5) / regulation of neutrophil migration / cellular response to oxidised low-density lipoprotein particle stimulus / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / Toll signaling pathway / Toll-like receptor binding / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / neutrophil activation involved in immune response / neutrophil migration / interleukin-33-mediated signaling pathway / microglia differentiation / toll-like receptor 9 signaling pathway / RIP-mediated NFkB activation via ZBP1 / neutrophil mediated immunity / positive regulation of cytokine production involved in inflammatory response / death receptor binding / interleukin-1 receptor binding / MyD88 deficiency (TLR2/4) / positive regulation of macrophage cytokine production / MyD88-dependent toll-like receptor signaling pathway / interleukin-1-mediated signaling pathway / IRAK4 deficiency (TLR2/4) / 3'-UTR-mediated mRNA stabilization / skin development / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / toll-like receptor signaling pathway / extrinsic component of plasma membrane / type I interferon-mediated signaling pathway / negative regulation of NF-kappaB transcription factor activity / defense response to protozoan / positive regulation of interleukin-17 production / response to amine / immunoglobulin mediated immune response / positive regulation of type I interferon production / canonical NF-kappaB signal transduction / response to amino acid / phagocytosis / signaling adaptor activity / positive regulation of chemokine production / JNK cascade / lipopolysaccharide-mediated signaling pathway / extrinsic component of cytoplasmic side of plasma membrane / IRAK2 mediated activation of TAK1 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / p75NTR recruits signalling complexes / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / response to interleukin-1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / activated TAK1 mediates p38 MAPK activation / positive regulation of JNK cascade / positive regulation of smooth muscle cell proliferation / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / response to organic cyclic compound / cytokine-mediated signaling pathway / Interleukin-1 signaling / cellular response to mechanical stimulus / : / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / PIP3 activates AKT signaling / kinase activity / positive regulation of NF-kappaB transcription factor activity / gene expression / ER-Phagosome pathway / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cellular response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / defense response to virus / molecular adaptor activity / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / endosome membrane
Similarity search - Function
Interleukin-1 receptor-associated kinase-like 2 / IRAK2, death domain / Myeloid differentiation primary response protein MyD88 / MyD88, death domain / Interleukin-1 receptor-associated kinase 4 / IRAK4, Death domain / Death Domain, Fas / Death Domain, Fas / TIR domain / Death domain profile. ...Interleukin-1 receptor-associated kinase-like 2 / IRAK2, death domain / Myeloid differentiation primary response protein MyD88 / MyD88, death domain / Interleukin-1 receptor-associated kinase 4 / IRAK4, Death domain / Death Domain, Fas / Death Domain, Fas / TIR domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Death-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Interleukin-1 receptor-associated kinase-like 2 / Myeloid differentiation primary response protein MyD88 / Interleukin-1 receptor-associated kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.4 Å
AuthorsLin, S.-C. / Lo, Y.-C. / Wu, H.
CitationJournal: Nature / Year: 2010
Title: Helical assembly in the MyD88-IRAK4-IRAK2 complex in TLR/IL-1R signalling.
Authors: Lin, S.C. / Lo, Y.C. / Wu, H.
History
DepositionApr 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myeloid differentiation primary response protein MyD88
B: Myeloid differentiation primary response protein MyD88
C: Myeloid differentiation primary response protein MyD88
D: Myeloid differentiation primary response protein MyD88
E: Myeloid differentiation primary response protein MyD88
F: Myeloid differentiation primary response protein MyD88
G: Interleukin-1 receptor-associated kinase 4
H: Interleukin-1 receptor-associated kinase 4
I: Interleukin-1 receptor-associated kinase 4
J: Interleukin-1 receptor-associated kinase 4
K: Interleukin-1 receptor-associated kinase-like 2
L: Interleukin-1 receptor-associated kinase-like 2
M: Interleukin-1 receptor-associated kinase-like 2
N: Interleukin-1 receptor-associated kinase-like 2


Theoretical massNumber of molelcules
Total (without water)179,45614
Polymers179,45614
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.709, 307.116, 187.619
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11F
21C
12E
22D
13H
23G
33I
43J
14L
24K
34M
44N
15B
25A

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain F and (resseq 19:123 ) and backboneF0
211chain C and (resseq 19:123 ) and backboneC0
112chain E and (resseq 19:123 ) and backboneE0
212chain D and (resseq 19:123 ) and backboneD0
113chain H and (resseq 2:108 ) and backboneH0
213chain G and (resseq 2:108 ) and backboneG0
313chain I and (resseq 2:108 ) and backboneI0
413chain J and (resseq 2:108 ) and backboneJ0
114chain L and (resseq 2:94 ) and backboneL0
214chain K and (resseq 2:94 ) and backboneK0
314chain M and (resseq 2:94 ) and backboneM0
414chain N and (resseq 2:94 ) and backboneN0
115chain B and (resseq 19:123 ) and backboneB0
215chain A and (resseq 19:123 ) and backboneA0

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein
Myeloid differentiation primary response protein MyD88


Mass: 12581.377 Da / Num. of mol.: 6 / Fragment: death domain residues 20-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYD88 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q99836
#2: Protein
Interleukin-1 receptor-associated kinase 4 / IRAK-4 / Renal carcinoma antigen NY-REN-64


Mass: 12804.617 Da / Num. of mol.: 4 / Fragment: death domain residues 4-106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRAK4 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL
References: UniProt: Q9NWZ3, non-specific serine/threonine protein kinase
#3: Protein
Interleukin-1 receptor-associated kinase-like 2 / IRAK-2


Mass: 13187.364 Da / Num. of mol.: 4 / Fragment: death domain residues 2-112 / Mutation: R50W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRAK2 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: O43187

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.08 Å3/Da / Density % sol: 69.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100-250 mM MgCl2, 8-15 % ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 39643 / % possible obs: 94.3 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.079 / Χ2: 1.233 / Net I/σ(I): 17
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.3-3.414.40.54623211.18161.8
3.41-3.535.20.531181.1782.5
3.53-3.676.70.4535931.20295.4
3.67-3.848.30.44837371.16399.3
3.84-4.049.40.33737871.21199.7
4.04-4.299.80.21238231.29599.9
4.29-4.62100.14437991.32199.8
4.62-5.0810.60.11238201.2799.9
5.08-5.8111.40.09238431.242100
5.81-7.3111.60.06938761.159100
7.31-3010.10.04239261.25297.6

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Phasing

PhasingMethod: MIR
Phasing dmFOM : 0.57 / FOM acentric: 0.56 / FOM centric: 0.65 / Reflection: 19786 / Reflection acentric: 17822 / Reflection centric: 1964
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
11.9-29.6820.960.970.94976735241
7.4-11.90.920.930.8930502602448
5.9-7.40.740.750.6836313246385
5.2-5.90.520.520.5135163208308
4.4-5.20.380.380.4356405244396
4.2-4.40.260.260.2729732787186
Phasing MIRResolution: 5.8→35 Å / FOM: 0.64 / Reflection: 8164
Phasing MIR der
IDDer set-ID
11
21
31
41
51
61
71
81
91
Phasing MIR der site
IDDer-IDBiso (Å)Atom type symbolFract xFract yFract zOccupancy
1160Tas0.03010.49790.01020.7326
1260Tas0.25860.4620.10920.1757
1360Tas0.77790.05470.06560.1092
1460Tas0.67440.06990.04810.204
1560Tas0.26110.4150.11180.1283
1660Tas0.62970.00480.00520.0437
1760Tas0.44280.00670.00570.2058
1860Tas0.8270.01090.01370.1138
191Tas0.73760.49780.00970.0213
2160Ptp0.11180.4960.00880.2056
2260Ptp0.28650.46730.09130.3708
2360Ptp0.03740.23160.23260.2478
2460Ptp0.29360.30050.09080.1316
2551.364Ptp0.46910.15810.10170.0643
2660Ptp0.01140.26920.00760.0849
2760Ptp0.01030.24510.0020.124
286.454Ptp0.28640.41690.01540.0761
2960Ptp0.48550.15120.10330.0953
3160Aus0.44370.2540.02630.2376
3260Aus0.48680.24910.23550.3692
3360Aus0.50390.15110.08720.2795
3460Aus0.0110.2220.22040.391
3560Aus0.70980.16390.24630.1196
3660Aus0.48640.22140.02920.3527
3760Aus0.83140.10710.20940.2967
3832.2723Aus0.49890.48080.10120.0852
3922.3418Aus0.98350.49940.01850.131
4160Ses0.63640.19970.02380.4914
4248.7728Ses0.94730.2470.15230.526
4343.3461Ses0.58080.23550.13730.4118
4460Ses0.83510.03050.15090.4648
4546.4381Ses0.95680.20640.0540.5473
4660Ses0.82790.24150.02830.9271
4760Ses0.24540.33180.10320.648
5160Hgs0.46710.25050.22750.2009
5260Hgs0.45430.22130.03080.3843
5360Hgs0.68410.16520.24840.4027
5460Hgs0.45710.25020.03980.3068
5560Hgs0.48930.47690.12530.1855
5660Hgs0.38350.47270.08780.3553
5752.3611Hgs0.27490.32190.10150.1213
5860Hgs0.04150.49010.13540.1032
6160Hgp0.53480.25630.23840.4986
6260Hgp0.96220.15830.22660.4959
6360Hgp0.47420.24580.02870.2755
6413.3036Hgp0.14170.48590.01220.1517
6560Hgp0.30520.31510.05740.376
663.6776Hgp0.97810.27180.00060.0605
6758.0533Hgp0.61520.28220.01820.2216
6860Hgp0.36830.32610.11540.5316
6960Hgp0.34730.22240.12810.3008
Phasing MIR shell
Resolution (Å)FOMReflection
18.75-350.78459
12.57-18.750.77722
10.05-12.570.75887
8.61-10.050.711030
7.64-8.610.681143
6.95-7.640.581229
6.41-6.950.521309
5.98-6.410.521385

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 3.4→19.958 Å / Occupancy max: 1 / Occupancy min: 0.86 / SU ML: 0.54 / σ(F): 0.02 / Phase error: 29.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 1696 5.07 %
Rwork0.216 --
obs0.218 33422 82.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 127.601 Å2 / ksol: 0.241 e/Å3
Displacement parametersBiso max: 444.62 Å2 / Biso mean: 179.952 Å2 / Biso min: 62.12 Å2
Baniso -1Baniso -2Baniso -3
1-8.693 Å2-0 Å20 Å2
2---26.436 Å20 Å2
3---17.742 Å2
Refinement stepCycle: LAST / Resolution: 3.4→19.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11534 0 0 0 11534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211784
X-RAY DIFFRACTIONf_angle_d1.58816012
X-RAY DIFFRACTIONf_chiral_restr0.1011812
X-RAY DIFFRACTIONf_plane_restr0.0062040
X-RAY DIFFRACTIONf_dihedral_angle_d22.5494346
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11F420X-RAY DIFFRACTIONPOSITIONAL0.071
12C420X-RAY DIFFRACTIONPOSITIONAL0.071
21E420X-RAY DIFFRACTIONPOSITIONAL0.068
22D420X-RAY DIFFRACTIONPOSITIONAL0.068
31H428X-RAY DIFFRACTIONPOSITIONAL0.062
32G428X-RAY DIFFRACTIONPOSITIONAL0.062
33I428X-RAY DIFFRACTIONPOSITIONAL0.062
34J428X-RAY DIFFRACTIONPOSITIONAL0.062
41L372X-RAY DIFFRACTIONPOSITIONAL0.062
42K372X-RAY DIFFRACTIONPOSITIONAL0.062
43M372X-RAY DIFFRACTIONPOSITIONAL0.052
44N372X-RAY DIFFRACTIONPOSITIONAL0.055
51B420X-RAY DIFFRACTIONPOSITIONAL0.054
52A420X-RAY DIFFRACTIONPOSITIONAL0.054
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.50.507820.4471667174952
3.5-3.6120.4071130.3861990210363
3.612-3.740.4171310.3422463259477
3.74-3.8890.3061260.3062410253676
3.889-4.0640.2931330.2662533266679
4.064-4.2770.3071380.2522513265179
4.277-4.5420.2871470.2262723287085
4.542-4.8880.2491550.2062866302190
4.888-5.3710.2351610.182999316093
5.371-6.1280.2331650.173087325296
6.128-7.6480.2431700.163201337198
7.648-19.9580.1971750.1553274344997
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)
11.04660.57261.40340.24960.91470.40660.51640.33270.23420.6992-0.1651-0.94290.0684-0.5771-0.00011.4052-0.2941-0.17751.0819-0.03831.728682.256368.286598.2742
20.79070.84410.17640.4498-1.27922.65720.2039-0.10890.3878-0.09830.01170.25260.3337000.9339-0.068-0.04020.9001-0.1630.619891.253281.8803126.2912
32.1723-1.04681.24091.94891.50050.22690.4656-0.1165-0.29630.066-0.3315-0.1203-0.3146-0.06010.00020.9829-0.28210.03041.14320.18920.85660.421586.665896.746
41.413-1.6830.73221.4551-1.16391.3230.051-0.0168-0.0483-0.0990.08760.43630.09440.47580.00010.7579-0.08470.13090.844-0.08840.945891.956592.725499.4712
50.77750.28090.06230.3292-0.5850.9641-0.3976-0.27160.1579-0.1342-0.0304-0.34650.2299-0.1160.00021.10370.18680.17960.8842-0.31140.550683.2967107.0175127.1829
61.27672.15070.61461.2823-0.05290.69520.3423-0.4791-0.1532-0.2105-0.41590.01440.14780.1534-01.18740.12430.21561.3150.0731.108460.343889.5275128.5006
71.1927-0.1795-0.50420.81110.9281.1013-0.48470.1466-0.11830.4657-0.12170.5721-0.27160.3802-0.00020.9947-0.16410.05071.07190.13230.988470.043109.970384.4133
81.0363-1.12310.9451.06980.98490.01610.0059-0.2730.3855-0.33870.0466-0.08710.1796-0.0602-0.00011.0172-0.26280.09620.89380.04481.425896.7466120.352101.6456
90.515-0.5347-0.26270.5574-0.97390.6021-0.62540.01670.04640.36860.1185-0.51110.1871-0.37670.00011.79720.14480.20561.2169-0.40491.575973.6349132.8293122.5331
10-0.0155-0.5561-0.41090.06060.12320.843-0.07350.42210.09650.3188-0.25480.9918-0.19940.8019-0.00241.32610.3294-0.18551.25880.16481.706655.4573131.031295.0004
110.9827-0.7122-0.2902-0.5942-0.28730.50610.11540.16650.05370.0322-0.010.3149-0.67040.45030.00011.4368-0.26590.24971.15250.22821.316483.528132.038980.4064
120.19790.0320.5328-0.3142-0.60620.61720.35730.13610.7257-0.2755-0.1368-0.26790.3801-0.1297-0.00111.2978-0.11560.09020.9914-0.23751.98592.8722145.539107.7144
13-0.2337-0.0265-0.31960.04290.6932-0.65250.189-0.20670.1935-0.3489-0.61540.30280.33210.4423-0.00081.95910.1406-0.05421.4012-0.08442.087761.9708152.8165109.9176
141.14911.6028-0.55670.64610.31040.06110.8649-0.30940.52560.0986-0.0910.03150.2691-0.14890.00030.62320.10980.191.25570.00221.117754.8269112.7494113.8702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA19 - 123
2X-RAY DIFFRACTION2chain BB19 - 123
3X-RAY DIFFRACTION3chain DD19 - 123
4X-RAY DIFFRACTION4chain EE19 - 123
5X-RAY DIFFRACTION5chain FF19 - 123
6X-RAY DIFFRACTION6chain CC19 - 123
7X-RAY DIFFRACTION7chain HH2 - 108
8X-RAY DIFFRACTION8chain II2 - 108
9X-RAY DIFFRACTION9chain JJ2 - 108
10X-RAY DIFFRACTION10chain KK2 - 94
11X-RAY DIFFRACTION11chain LL2 - 94
12X-RAY DIFFRACTION12chain MM2 - 94
13X-RAY DIFFRACTION13chain NN2 - 94
14X-RAY DIFFRACTION14chain GG2 - 108

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