[English] 日本語
Yorodumi
- PDB-5jem: Complex of IRF-3 with CBP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jem
TitleComplex of IRF-3 with CBP
Components
  • CREB-binding protein
  • Interferon regulatory factor 3
KeywordsIMMUNE SYSTEM / Innate Immunity / Signaling
Function / homology
Function and homology information


IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / programmed necrotic cell death / TRIF-dependent toll-like receptor signaling pathway / peptide lactyltransferase (CoA-dependent) activity / signal transduction involved in regulation of gene expression / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors ...IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / programmed necrotic cell death / TRIF-dependent toll-like receptor signaling pathway / peptide lactyltransferase (CoA-dependent) activity / signal transduction involved in regulation of gene expression / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / IRF3-mediated induction of type I IFN / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / positive regulation of cytokine production involved in inflammatory response / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / positive regulation of type I interferon-mediated signaling pathway / NFE2L2 regulating MDR associated enzymes / MRF binding / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / cGAS/STING signaling pathway / mRNA transcription / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of NFE2L2 gene expression / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / NFE2L2 regulating anti-oxidant/detoxification enzymes / toll-like receptor 4 signaling pathway / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / DNA-binding transcription activator activity / embryonic digit morphogenesis / cytoplasmic pattern recognition receptor signaling pathway / immune system process / type I interferon-mediated signaling pathway / homeostatic process / protein acetylation / cellular response to exogenous dsRNA / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / acetyltransferase activity / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / positive regulation of interferon-alpha production / histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of type I interferon production / Attenuation phase / cellular response to nutrient levels / canonical NF-kappaB signal transduction / regulation of cellular response to heat / histone acetyltransferase activity / antiviral innate immune response / histone acetyltransferase / lipopolysaccharide-mediated signaling pathway / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / TICAM1-dependent activation of IRF3/IRF7 / RORA activates gene expression / NPAS4 regulates expression of target genes / Regulation of lipid metabolism by PPARalpha / positive regulation of interferon-beta production / Regulation of innate immune responses to cytosolic DNA / CD209 (DC-SIGN) signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / Negative regulators of DDX58/IFIH1 signaling / promoter-specific chromatin binding / Formation of the beta-catenin:TCF transactivating complex / Heme signaling / protein destabilization / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Evasion by RSV of host interferon responses / chromatin DNA binding / NOTCH1 Intracellular Domain Regulates Transcription / cellular response to virus / ISG15 antiviral mechanism / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Transcriptional regulation of white adipocyte differentiation
Similarity search - Function
Creb-binding Protein; Chain: A / Nuclear receptor coactivator, CREB-bp-like, interlocking domain / Tumour Suppressor Smad4 - #10 / Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor ...Creb-binding Protein; Chain: A / Nuclear receptor coactivator, CREB-bp-like, interlocking domain / Tumour Suppressor Smad4 - #10 / Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / SMAD-like domain superfamily / Tumour Suppressor Smad4 / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / SMAD/FHA domain superfamily / Nuclear receptor coactivator, interlocking / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interferon regulatory factor 3 / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsZhao, B. / Li, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis for concerted recruitment and activation of IRF-3 by innate immune adaptor proteins.
Authors: Zhao, B. / Shu, C. / Gao, X. / Sankaran, B. / Du, F. / Shelton, C.L. / Herr, A.B. / Ji, J.Y. / Li, P.
History
DepositionApr 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interferon regulatory factor 3
C: CREB-binding protein
B: Interferon regulatory factor 3
D: CREB-binding protein
E: Interferon regulatory factor 3
F: CREB-binding protein
G: Interferon regulatory factor 3
H: CREB-binding protein


Theoretical massNumber of molelcules
Total (without water)116,1968
Polymers116,1968
Non-polymers00
Water4,071226
1
A: Interferon regulatory factor 3
C: CREB-binding protein
B: Interferon regulatory factor 3
D: CREB-binding protein


Theoretical massNumber of molelcules
Total (without water)58,0984
Polymers58,0984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-41 kcal/mol
Surface area21710 Å2
MethodPISA
2
E: Interferon regulatory factor 3
F: CREB-binding protein
G: Interferon regulatory factor 3
H: CREB-binding protein


Theoretical massNumber of molelcules
Total (without water)58,0984
Polymers58,0984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint-39 kcal/mol
Surface area21480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.230, 88.660, 92.810
Angle α, β, γ (deg.)90.00, 113.09, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Interferon regulatory factor 3 / IRF-3


Mass: 23774.992 Da / Num. of mol.: 4 / Fragment: UNP residues 189-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14653
#2: Protein/peptide
CREB-binding protein


Mass: 5274.103 Da / Num. of mol.: 4 / Fragment: UNP residues 2065-2111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q92793, histone acetyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.5→36.992 Å / Num. obs: 42426 / % possible obs: 96.3 % / Redundancy: 3.5 % / Net I/σ(I): 6.2

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.5→36.992 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.41
RfactorNum. reflection% reflection
Rfree0.242 1985 4.68 %
Rwork0.192 --
obs0.1943 42378 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→36.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7650 0 0 226 7876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037849
X-RAY DIFFRACTIONf_angle_d0.62410687
X-RAY DIFFRACTIONf_dihedral_angle_d14.5152871
X-RAY DIFFRACTIONf_chiral_restr0.0231159
X-RAY DIFFRACTIONf_plane_restr0.0031392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.37821180.33082579X-RAY DIFFRACTION86
2.5625-2.63180.38341310.30942568X-RAY DIFFRACTION87
2.6318-2.70920.36281260.28142677X-RAY DIFFRACTION89
2.7092-2.79660.29341390.26372775X-RAY DIFFRACTION92
2.7966-2.89660.2821460.2632842X-RAY DIFFRACTION96
2.8966-3.01250.30591380.26442878X-RAY DIFFRACTION97
3.0125-3.14950.31841630.24182938X-RAY DIFFRACTION98
3.1495-3.31550.24711320.20573015X-RAY DIFFRACTION100
3.3155-3.5230.23091440.19132985X-RAY DIFFRACTION100
3.523-3.79480.26931580.17612997X-RAY DIFFRACTION100
3.7948-4.17620.19191520.16293002X-RAY DIFFRACTION100
4.1762-4.77940.20451360.14983023X-RAY DIFFRACTION100
4.7794-6.01740.20961530.15993030X-RAY DIFFRACTION100
6.0174-36.99560.19821490.16523084X-RAY DIFFRACTION100
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)
17.0881-0.2782-2.47877.64080.40824.62570.1045-0.56840.82210.37340.0436-0.1338-0.68870.0983-0.1240.3902-0.0342-0.10860.32430.00590.3834-25.1657-7.19255.5507
25.9772-0.4130.50613.1861-0.47432.1739-0.08340.23550.0887-0.25420.0472-0.0335-0.1018-0.00110.03290.4060.00210.00170.25260.02510.3881-20.9538-7.8176-3.9329
35.60350.04110.48961.5258-0.12690.4081-0.06960.7524-0.6033-0.19270.05160.1149-0.0347-0.18190.03890.3386-0.0043-0.04270.3417-0.04690.4512-32.4327-16.9479-6.1792
46.6753-2.6943-1.38454.62851.74445.152-0.14220.72680.235-0.5050.2537-0.19070.11040.1249-0.04460.4559-0.1047-0.04730.6203-0.06010.5255-35.7107-40.5548-11.8113
57.5532-6.2263.75225.1671-3.25523.0615-0.8555-1.2729-1.91671.04841.81841.27570.178-0.7562-0.93890.6578-0.09190.0120.77420.09641.0803-51.0803-20.178710.8352
68.8883-1.81471.55132.1129-2.9444.47220.5295-0.3762-2.36270.07640.4548-0.95391.3146-0.7719-0.91650.66790.0609-0.07690.67960.11990.8434-39.6759-22.961710.6778
73.32071.66424.79842.62791.21037.9387-0.1759-0.61410.17530.1150.42130.2699-0.0705-0.5895-0.15830.42520.05890.02740.43130.04690.4826-44.3207-11.7398.131
87.0515-2.5519-5.45232.09811.83874.3382-0.491-0.4377-0.9031-0.2939-0.90360.43320.326-1.1471.13690.36930.0527-0.05810.8037-0.06290.6435-53.6279-21.0074-0.677
93.89331.28671.68292.8377-0.37294.3572-0.1008-0.33640.1170.25770.1086-0.24990.5198-0.0334-0.02390.40040.01170.10730.3198-0.05360.4569-15.5755-41.22863.8303
105.8319-4.8659-0.76114.7292.47086.4365-0.1073-1.9439-1.72262.83630.33342.28851.50340.4237-0.31721.6537-0.1451-0.13370.75820.09371.471-23.1877-54.71096.0826
112.4462-2.43420.22653.3234-0.72665.2474-0.2877-0.2884-0.04570.19620.29810.6199-0.0533-0.25330.06090.3172-0.05750.00390.4164-0.05770.6024-32.563-40.75131.1774
123.6511-3.18530.17994.5290.88664.2021-0.00060.2999-0.3559-0.08180.1171-0.130.47190.22-0.14380.4679-0.0240.03250.2931-0.03520.5364-15.1137-47.5554-6.7446
138.83765.38834.21026.11755.43767.3093-0.38120.64410.3429-1.65510.15450.4755-0.51090.21410.30650.53930.09130.12220.61080.02920.4943-16.3156-40.3286-11.6903
145.78153.36921.39575.73371.20582.2481-0.30151.14950.7034-0.63850.3389-0.0773-0.24280.2320.01140.3958-0.00630.12250.40480.08640.558-0.9624-33.6581-8.7134
153.2496-1.9101-0.32736.69461.74290.50850.53741.13940.4636-1.2591-0.5491-0.0897-0.05630.06320.02680.3743-0.05910.07710.47530.06860.4657-24.0417-35.5498-10.7489
160.19170.355-0.4622.03770.05652.62350.0327-0.15661.0973-0.253-0.2108-0.22370.15690.36250.19940.2722-0.00730.06560.2736-00.5798-6.5139-32.16940.3035
178.1922-2.32162.92654.9223-0.85923.06790.22610.5165-0.8711-0.7627-0.20820.4899-0.15850.421-0.07030.4169-0.04610.1850.51390.13810.6323-7.2786-10.0032-11.1376
185.616-0.7711-5.62011.69060.9615.6162-0.1512-2.02432.3886-0.36320.2580.0972-0.51350.4118-0.33750.57660.05510.01480.4824-0.11520.94853.2803-30.431410.0587
197.21772.7608-2.13385.6869-3.52827.5582-0.0120.09331.26110.3037-0.0547-0.4979-0.25440.70680.07230.32630.03090.03550.4402-0.01540.70536.3382-34.71952.5509
206.0599-0.74220.53478.39512.83936.98490.26630.324-0.1706-0.6081-0.0225-0.87260.0560.8815-0.21550.5466-0.0160.01580.61750.07210.3668-4.1645-35.780323.5481
212.9768-0.70010.37768.5825-0.57572.68960.0291-0.4807-0.01210.3155-0.0066-0.8733-0.01460.49570.07330.5860.0117-0.08160.6696-0.01220.4369-3.9553-31.963832.9006
223.49431.04660.8174.7076-0.88362.55640.0905-0.6554-0.07970.3758-0.1040.24930.2954-0.0440.03570.61220.0399-0.02280.52640.06640.2932-16.3659-40.037534.552
238.2781-0.4939-1.11795.94231.81615.5360.62-1.17290.91810.37160.33120.125-0.3831-0.844-0.77820.8343-0.02460.21190.80070.19690.6282-39.8823-35.860939.9489
244.31991.5683-2.18054.6037-5.15955.7751-0.02870.7041-0.8241-0.3292-0.031.13641.2513-1.4754-0.09791.0593-0.2057-0.04070.9362-0.06011.0008-24.8294-50.44117.0394
257.70114.2084-5.92399.7898-6.43428.18550.05950.1246-0.47540.07670.170.19341.4158-0.468-0.11291.0568-0.093-0.10370.4084-0.01940.4504-20.7171-55.684924.1999
266.1805-1.1307-1.25863.6222-3.65336.62750.45550.61120.1054-0.6232-0.04690.909-0.4271-1.0721-0.340.65170.1059-0.06620.6484-0.00550.4134-37.7043-18.335424.3328
272.6612-0.54720.87033.4097-0.61682.0042-0.0568-0.50880.03040.28220.14950.7776-0.1815-0.6427-0.12430.57440.0860.04850.6040.03120.4418-39.6869-23.475831.3127
284.1519-1.2626-2.84485.873-0.11214.2505-0.2515-1.94570.90621.16120.51290.0742-0.61930.3692-0.19930.9010.16970.10390.7244-0.04230.3919-33.6264-17.359640.2084
292.21010.90450.60193.76621.41441.4332-0.0893-0.50180.00760.51090.0505-0.1957-0.5164-0.120.04460.80290.1048-0.04010.563-0.03740.3039-25.7493-13.875635.4882
305.7577-0.63592.50414.4218-1.54263.01930.2705-0.9484-0.45340.42090.0297-0.121-0.2170.4731-0.40290.9609-0.0935-0.2610.7763-0.15870.6654-1.8804-18.2540.2316
313.73710.148-3.18452.29-1.40283.54431.15120.46790.0432-1.7444-0.6524-0.25242.0251-0.6241-0.59611.69870.006-0.31361.2573-0.01290.9271-17.38234.061119.3729
323.89672.36716.24084.94064.19532.01210.19980.86840.0709-1.25030.0303-1.389-1.87741.4924-0.49061.2531-0.1289-0.00260.9561-0.12090.7983-18.0808-6.98818.2576
337.45114.5514.47827.24835.30574.1913-0.5738-0.36620.78920.27530.49550.8255-2.32290.2850.12081.24880.10370.06560.4535-0.01950.443-27.8601-0.241222.0979
346.2158-1.58742.97845.9783-2.35765.6682-0.870.02181.35920.40910.1962-0.6005-1.22790.73540.43641.6348-0.1387-0.02980.5633-0.10170.8661-15.43565.059430.2984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 196 through 240 )
2X-RAY DIFFRACTION2chain 'A' and (resid 241 through 316 )
3X-RAY DIFFRACTION3chain 'A' and (resid 317 through 382 )
4X-RAY DIFFRACTION4chain 'A' and (resid 383 through 398 )
5X-RAY DIFFRACTION5chain 'C' and (resid 2065 through 2072 )
6X-RAY DIFFRACTION6chain 'C' and (resid 2073 through 2079 )
7X-RAY DIFFRACTION7chain 'C' and (resid 2080 through 2092 )
8X-RAY DIFFRACTION8chain 'C' and (resid 2093 through 2106 )
9X-RAY DIFFRACTION9chain 'B' and (resid 196 through 229 )
10X-RAY DIFFRACTION10chain 'B' and (resid 230 through 240 )
11X-RAY DIFFRACTION11chain 'B' and (resid 241 through 268 )
12X-RAY DIFFRACTION12chain 'B' and (resid 269 through 296 )
13X-RAY DIFFRACTION13chain 'B' and (resid 297 through 316 )
14X-RAY DIFFRACTION14chain 'B' and (resid 317 through 342 )
15X-RAY DIFFRACTION15chain 'B' and (resid 343 through 363 )
16X-RAY DIFFRACTION16chain 'B' and (resid 364 through 382 )
17X-RAY DIFFRACTION17chain 'B' and (resid 383 through 398 )
18X-RAY DIFFRACTION18chain 'D' and (resid 2065 through 2079 )
19X-RAY DIFFRACTION19chain 'D' and (resid 2080 through 2106 )
20X-RAY DIFFRACTION20chain 'E' and (resid 196 through 240 )
21X-RAY DIFFRACTION21chain 'E' and (resid 241 through 316 )
22X-RAY DIFFRACTION22chain 'E' and (resid 317 through 382 )
23X-RAY DIFFRACTION23chain 'E' and (resid 383 through 398 )
24X-RAY DIFFRACTION24chain 'F' and (resid 2065 through 2079 )
25X-RAY DIFFRACTION25chain 'F' and (resid 2080 through 2106 )
26X-RAY DIFFRACTION26chain 'G' and (resid 199 through 240 )
27X-RAY DIFFRACTION27chain 'G' and (resid 241 through 296 )
28X-RAY DIFFRACTION28chain 'G' and (resid 297 through 316 )
29X-RAY DIFFRACTION29chain 'G' and (resid 317 through 382 )
30X-RAY DIFFRACTION30chain 'G' and (resid 383 through 398 )
31X-RAY DIFFRACTION31chain 'H' and (resid 2065 through 2071 )
32X-RAY DIFFRACTION32chain 'H' and (resid 2072 through 2079 )
33X-RAY DIFFRACTION33chain 'H' and (resid 2080 through 2092 )
34X-RAY DIFFRACTION34chain 'H' and (resid 2093 through 2106 )

+
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://pdbjlc1.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