[English] 日本語
Yorodumi
- PDB-4p4h: Caught-in-action signaling complex of RIG-I 2CARD domain and MAVS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p4h
TitleCaught-in-action signaling complex of RIG-I 2CARD domain and MAVS CARD domain
Components
  • Mitochondrial antiviral-signaling protein
  • Probable ATP-dependent RNA helicase DDX58
  • Ubiquitin-60S ribosomal protein L40
KeywordsSIGNALING PROTEIN / signaling complex
Function / homology
Function and homology information


positive regulation of IP-10 production / regulation of peroxisome organization / regulation of type III interferon production / RIG-I signaling pathway / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / CARD domain binding / detection of virus / positive regulation of response to cytokine stimulus ...positive regulation of IP-10 production / regulation of peroxisome organization / regulation of type III interferon production / RIG-I signaling pathway / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / CARD domain binding / detection of virus / positive regulation of response to cytokine stimulus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / protein localization to mitochondrion / positive regulation of type I interferon-mediated signaling pathway / response to insecticide / positive regulation of granulocyte macrophage colony-stimulating factor production / Modulation of host responses by IFN-stimulated genes / peroxisomal membrane / TRAF6 mediated IRF7 activation / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / pattern recognition receptor activity / RSV-host interactions / response to exogenous dsRNA / positive regulation of NLRP3 inflammasome complex assembly / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / positive regulation of type I interferon production / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / bicellular tight junction / Viral mRNA Translation / ubiquitin ligase complex / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / positive regulation of defense response to virus by host / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / signaling adaptor activity / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / antiviral innate immune response / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / activation of innate immune response / APC/C:Cdc20 mediated degradation of Cyclin B / protein serine/threonine kinase binding / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / cytosolic ribosome / regulation of cell migration / APC-Cdc20 mediated degradation of Nek2A / positive regulation of interferon-beta production / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of pyruvate metabolism / TRAF6-mediated induction of TAK1 complex within TLR4 complex / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Josephin domain DUBs
Similarity search - Function
IPS1, CARD domain / : / RIG-I, CARD domain repeat 2 / Death Domain, Fas / Death Domain, Fas / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : ...IPS1, CARD domain / : / RIG-I, CARD domain repeat 2 / Death Domain, Fas / Death Domain, Fas / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / Caspase recruitment domain / Caspase recruitment domain / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Death-like domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / helicase superfamily c-terminal domain / Ubiquitin domain profile. / Ubiquitin-like domain / 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 / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Antiviral innate immune response receptor RIG-I / Ubiquitin-ribosomal protein eL40 fusion protein / Mitochondrial antiviral-signaling protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.4 Å
AuthorsWu, B. / Hur, S.
CitationJournal: Mol Cell / Year: 2014
Title: Molecular imprinting as a signal-activation mechanism of the viral RNA sensor RIG-I.
Authors: Bin Wu / Alys Peisley / David Tetrault / Zongli Li / Edward H Egelman / Katharine E Magor / Thomas Walz / Pawel A Penczek / Sun Hur /
Abstract: RIG-I activates interferon signaling pathways by promoting filament formation of the adaptor molecule, MAVS. Assembly of the MAVS filament is mediated by its CARD domain (CARD(MAVS)), and requires ...RIG-I activates interferon signaling pathways by promoting filament formation of the adaptor molecule, MAVS. Assembly of the MAVS filament is mediated by its CARD domain (CARD(MAVS)), and requires its interaction with the tandem CARDs of RIG-I (2CARD(RIG-I)). However, the precise nature of the interaction between 2CARD(RIG-I) and CARD(MAVS), and how this interaction leads to CARD(MAVS) filament assembly, has been unclear. Here we report a 3.6 Å electron microscopy structure of the CARD(MAVS) filament and a 3.4 Å crystal structure of the 2CARD(RIG-I):CARD(MAVS) complex, representing 2CARD(RIG-I) "caught in the act" of nucleating the CARD(MAVS) filament. These structures, together with functional analyses, show that 2CARD(RIG-I) acts as a template for the CARD(MAVS) filament assembly, by forming a helical tetrameric structure and recruiting CARD(MAVS) along its helical trajectory. Our work thus reveals that signal activation by RIG-I occurs by imprinting its helical assembly architecture on MAVS, a previously uncharacterized mechanism of signal transmission.
History
DepositionMar 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Jan 7, 2015Group: Database references
Revision 1.3Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX58
B: Probable ATP-dependent RNA helicase DDX58
C: Probable ATP-dependent RNA helicase DDX58
D: Probable ATP-dependent RNA helicase DDX58
E: Probable ATP-dependent RNA helicase DDX58
F: Probable ATP-dependent RNA helicase DDX58
G: Probable ATP-dependent RNA helicase DDX58
H: Probable ATP-dependent RNA helicase DDX58
I: Mitochondrial antiviral-signaling protein
J: Mitochondrial antiviral-signaling protein
K: Mitochondrial antiviral-signaling protein
L: Mitochondrial antiviral-signaling protein
N: Mitochondrial antiviral-signaling protein
O: Mitochondrial antiviral-signaling protein
P: Mitochondrial antiviral-signaling protein
S: Ubiquitin-60S ribosomal protein L40
T: Ubiquitin-60S ribosomal protein L40
U: Ubiquitin-60S ribosomal protein L40
W: Ubiquitin-60S ribosomal protein L40
X: Ubiquitin-60S ribosomal protein L40
M: Mitochondrial antiviral-signaling protein


Theoretical massNumber of molelcules
Total (without water)334,39321
Polymers334,39321
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50470 Å2
ΔGint-52 kcal/mol
Surface area99430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.810, 117.330, 257.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 1:188 ) and (not element H)
21chain E and (resseq 1:188 ) and (not element H)
12chain B and (resseq 1:189 ) and (not element H)
22chain F and (resseq 1:189 ) and (not element H)
13chain C and (resseq 1:189 ) and (not element H)
23chain G and (resseq 1:189 ) and (not element H)
14chain D and (resseq 1:188 ) and (not element H)
24chain H and (resseq 1:188 ) and (not element H)
15chain I and (resseq 1:97 ) and (not element H)
25chain M and (resseq 1:97 ) and (not element H)
16chain J and (resseq 1:97 ) and (not element H)
26chain N and (resseq 1:97 ) and (not element H)
17chain K and (resseq 1:78 ) and (not element H)
27chain O and (resseq 1:78 ) and (not element H)
18chain L and (resseq 1:78 ) and (not element H)
28chain P and (resseq 1:78 ) and (not element H)
19chain S and (resseq 1:71 ) and (not element H)
29chain U and (resseq 1:72 ) and (not element H)
39chain W and (resseq 1:71 ) and (not element H)
110chain T and (resseq 1:73 ) and (not element H)
210chain X and (resseq 1:73 ) and (not element H)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 1:188 ) and (not element H)A0
211chain E and (resseq 1:188 ) and (not element H)E0
112chain B and (resseq 1:189 ) and (not element H)B0
212chain F and (resseq 1:189 ) and (not element H)F0
113chain C and (resseq 1:189 ) and (not element H)C0
213chain G and (resseq 1:189 ) and (not element H)G0
114chain D and (resseq 1:188 ) and (not element H)D0
214chain H and (resseq 1:188 ) and (not element H)H0
115chain I and (resseq 1:97 ) and (not element H)I0
215chain M and (resseq 1:97 ) and (not element H)M0
116chain J and (resseq 1:97 ) and (not element H)J0
216chain N and (resseq 1:97 ) and (not element H)N0
117chain K and (resseq 1:78 ) and (not element H)K0
217chain O and (resseq 1:78 ) and (not element H)O0
118chain L and (resseq 1:78 ) and (not element H)L0
218chain P and (resseq 1:78 ) and (not element H)P0
119chain S and (resseq 1:71 ) and (not element H)S0
219chain U and (resseq 1:72 ) and (not element H)U0
319chain W and (resseq 1:71 ) and (not element H)W0
1110chain T and (resseq 1:73 ) and (not element H)T0
2110chain X and (resseq 1:73 ) and (not element H)X0

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

-
Components

#1: Protein
Probable ATP-dependent RNA helicase DDX58 / DEAD box protein 58 / RIG-I-like receptor 1 / RLR-1 / Retinoic acid-inducible gene 1 protein / RIG- ...DEAD box protein 58 / RIG-I-like receptor 1 / RLR-1 / Retinoic acid-inducible gene 1 protein / RIG-1 / Retinoic acid-inducible gene I protein / RIG-I


Mass: 24014.543 Da / Num. of mol.: 8 / Mutation: E52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX58 / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: O95786, RNA helicase
#2: Protein
Mitochondrial antiviral-signaling protein / MAVS / CARD adapter inducing interferon beta / Cardif / Interferon beta promoter stimulator protein ...MAVS / CARD adapter inducing interferon beta / Cardif / Interferon beta promoter stimulator protein 1 / IPS-1 / Putative NF-kappa-B-activating protein 031N / Virus-induced-signaling adapter / VISA


Mass: 12292.028 Da / Num. of mol.: 8 / Mutation: D23K, E26K, E80K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IPS1, KIAA1271, MAVS, pstS, VISA / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q7Z434
#3: Protein
Ubiquitin-60S ribosomal protein L40 / CEP52 / Ubiquitin A-52 residue ribosomal protein fusion product 1


Mass: 8788.049 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA52, UBCEP2 / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62987

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.3 % / Description: hexagonal rods
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Tri-Li Citrate, PEG 3350, Cr(III) Cl3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→46.8 Å / Num. obs: 89450 / % possible obs: 99.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.28
Reflection shellResolution: 3.4→3.438 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.315 / Mean I/σ(I) obs: 1.26 / % possible all: 97.8

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 3.4→46.8 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 4448 4.97 %
Rwork0.1911 --
obs0.1936 89450 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21711 0 0 0 21711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01122154
X-RAY DIFFRACTIONf_angle_d1.26829912
X-RAY DIFFRACTIONf_dihedral_angle_d16.988420
X-RAY DIFFRACTIONf_chiral_restr0.0513300
X-RAY DIFFRACTIONf_plane_restr0.0073792
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1549X-RAY DIFFRACTIONPOSITIONAL0.079
12E1549X-RAY DIFFRACTIONPOSITIONAL0.079
21B1555X-RAY DIFFRACTIONPOSITIONAL0.054
22F1555X-RAY DIFFRACTIONPOSITIONAL0.054
31C1563X-RAY DIFFRACTIONPOSITIONAL0.068
32G1563X-RAY DIFFRACTIONPOSITIONAL0.068
41D1562X-RAY DIFFRACTIONPOSITIONAL0.058
42H1562X-RAY DIFFRACTIONPOSITIONAL0.058
51I789X-RAY DIFFRACTIONPOSITIONAL0.108
52M789X-RAY DIFFRACTIONPOSITIONAL0.108
61J796X-RAY DIFFRACTIONPOSITIONAL0.058
62N796X-RAY DIFFRACTIONPOSITIONAL0.058
71K648X-RAY DIFFRACTIONPOSITIONAL0.057
72O648X-RAY DIFFRACTIONPOSITIONAL0.057
81L648X-RAY DIFFRACTIONPOSITIONAL0.07
82P648X-RAY DIFFRACTIONPOSITIONAL0.07
91S555X-RAY DIFFRACTIONPOSITIONAL0.065
92U555X-RAY DIFFRACTIONPOSITIONAL0.065
93W555X-RAY DIFFRACTIONPOSITIONAL0.039
101T582X-RAY DIFFRACTIONPOSITIONAL0.042
102X582X-RAY DIFFRACTIONPOSITIONAL0.042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.43870.32921800.32012825X-RAY DIFFRACTION100
3.4387-3.47910.38451320.32522875X-RAY DIFFRACTION100
3.4791-3.52160.36221370.30832867X-RAY DIFFRACTION100
3.5216-3.56610.37011350.30942835X-RAY DIFFRACTION100
3.5661-3.6130.3331290.29752884X-RAY DIFFRACTION100
3.613-3.66250.31281540.28782860X-RAY DIFFRACTION100
3.6625-3.71480.26571640.26152797X-RAY DIFFRACTION100
3.7148-3.77020.29461510.26032888X-RAY DIFFRACTION100
3.7702-3.82910.31941710.2582817X-RAY DIFFRACTION100
3.8291-3.89190.32421480.24692810X-RAY DIFFRACTION100
3.8919-3.95890.31441590.25122836X-RAY DIFFRACTION100
3.9589-4.03090.2431300.24272847X-RAY DIFFRACTION100
4.0309-4.10840.29441550.21972844X-RAY DIFFRACTION100
4.1084-4.19220.26481500.20482846X-RAY DIFFRACTION100
4.1922-4.28330.23881510.19912827X-RAY DIFFRACTION100
4.2833-4.38280.23071530.20032842X-RAY DIFFRACTION100
4.3828-4.49240.25391330.1912888X-RAY DIFFRACTION100
4.4924-4.61370.21881500.18172811X-RAY DIFFRACTION100
4.6137-4.74940.23511350.17722874X-RAY DIFFRACTION100
4.7494-4.90250.26551360.17832846X-RAY DIFFRACTION100
4.9025-5.07750.26551710.18342841X-RAY DIFFRACTION100
5.0775-5.28060.20891640.17412799X-RAY DIFFRACTION100
5.2806-5.52050.2411640.18522837X-RAY DIFFRACTION100
5.5205-5.81110.30361130.19022882X-RAY DIFFRACTION100
5.8111-6.17440.26181400.19312842X-RAY DIFFRACTION100
6.1744-6.64990.28111390.18792841X-RAY DIFFRACTION100
6.6499-7.31690.25221610.15832818X-RAY DIFFRACTION99
7.3169-8.37040.17591380.11812809X-RAY DIFFRACTION99
8.3704-10.52610.12551470.11382804X-RAY DIFFRACTION98
10.5261-46.84990.17141580.14092610X-RAY DIFFRACTION92
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)
18.7594-0.0185-4.17334.0451-1.20375.17960.05440.64250.4905-0.48190.2980.63120.4384-0.7592-0.31360.5468-0.1147-0.18840.55950.07290.7858-26.9914-12.62688.7553
23.8182.5338-1.68625.4702-1.48043.0891-0.3105-0.4548-0.702-0.2195-0.2447-0.77560.60210.54860.47380.60350.26630.01730.78910.00190.73743.387-17.393915.7396
34.47760.30060.03814.6551-1.81283.45020.2425-1.0091-0.10670.7717-0.4771-0.6845-0.44240.78190.20030.5207-0.2233-0.0741.0257-0.11550.79851.067912.597725.3593
43.8861-0.5051-1.88482.5716-0.77215.80090.14380.32160.4049-0.09770.18080.7857-0.0302-0.5297-0.29480.3664-0.0896-0.07160.5713-0.051.0278-23.282111.9995.4324
52.880.6627-0.19136.9025-1.2176.27910.1847-0.32860.29260.61910.3277-0.414-0.53010.9511-0.40290.6126-0.0042-0.13040.8406-0.26360.8042-15.0981-2.934854.543
62.97680.2341-0.39433.8124-2.04784.02180.1436-0.1402-0.70620.1148-0.0601-0.62821.07251.1918-0.02431.07760.4491-0.30.9898-0.1680.9495-11.5272-33.042846.2456
74.7423-0.0724-1.17393.49652.20156.574-0.11950.0551-0.42790.18920.05420.07370.8229-0.24350.1140.7643-0.0734-0.11950.42440.01730.5913-42.1362-29.613638.5634
83.9022-0.21210.32055.3136-1.1287.8103-0.0788-0.41650.55480.7931-0.00410.0709-0.609-0.41840.13510.6640.1081-0.08250.5862-0.20670.6334-39.4966-6.060659.3613
95.3183-1.5404-0.67955.1566-0.56297.9176-0.07330.0374-0.2081-0.13890.1748-0.10620.90870.1417-0.05430.58620.01570.09810.4866-0.05940.51635.1511-10.9467-11.708
104.92563.87180.33188.06613.46865.72470.3817-0.64770.00890.6597-0.3411-0.56920.38820.13590.06350.3658-0.0096-0.09830.77310.11061.004920.185415.34215.1638
116.6633-4.7677-2.83036.28862.02253.78610.1518-0.2081.1268-0.17960.2273-0.6004-0.23840.0607-0.42410.3752-0.04630.02430.62210.03541.1369-8.335431.5617-5.9395
124.7525-0.02732.63747.0032.42387.54140.21790.8383-0.1698-1.26730.00780.25530.6377-0.3673-0.25721.0266-0.1082-0.04891.10230.06380.4896-6.87364.4672-28.8559
130.9239-0.7724-0.75982.3175-1.18833.2831-0.0554-0.8429-0.56531.1470.6151-0.80371.26190.8253-0.42372.480.5408-0.72421.38750.03211.2007-16.1367-35.654873.8269
143.11840.18990.79020.4107-0.3520.88751.3524-0.3825-1.8841.4437-0.2701-0.13651.5968-0.7923-0.57962.6553-0.6161-0.40530.90110.39281.4663-43.6345-49.542758.1713
152.58890.3637-0.48320.25620.20545.04890.3446-2.30710.97520.438-0.78910.60120.7262-2.46540.21511.3876-0.65730.46142.4043-0.69931.2378-58.8845-20.52371.4354
161.75650.047-1.91930.9538-0.69912.83590.2343-0.6422-0.15610.94370.233-0.17191.2168-0.1976-0.44922.56580.0582-0.30681.62770.12190.7812-30.5347-24.031992.5215
176.7168-2.50250.04417.0155-3.05412.327-0.4411-0.75590.68821.11710.01230.7898-1.0964-0.48040.60240.9318-0.09340.15540.8881-0.36381.2416-21.29136.355223.3076
186.56591.0972-0.57922.7162-0.53360.99560.21860.18172.2732-1.04750.62612.6809-0.1612-0.3725-0.42470.6543-0.0676-0.07861.15470.49912.9505-49.89616.463413.0592
198.42760.36160.30155.31461.55763.29210.544-0.87210.19531.2025-0.0365-2.06120.64971.6125-0.33451.39110.434-0.56552.3485-0.16741.66410.9984-20.956162.1166
209.45911.4029-0.57345.8120.99277.6124-0.5632-0.3151.3121-0.8746-0.37511.0884-0.7981-1.88920.82151.05260.4391-0.25251.4298-0.29461.3172-64.7904-6.368342.7107
219.5019-3.0171.69895.7922-4.02376.07430.0387-0.69560.84090.140.5460.2114-1.44480.0067-0.27461.5510.04930.13340.6113-0.11780.891-33.538520.408452.9529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A')
2X-RAY DIFFRACTION2(chain 'B')
3X-RAY DIFFRACTION3(chain 'C')
4X-RAY DIFFRACTION4(chain 'D')
5X-RAY DIFFRACTION5(chain 'E')
6X-RAY DIFFRACTION6(chain 'F')
7X-RAY DIFFRACTION7(chain 'G')
8X-RAY DIFFRACTION8(chain 'H')
9X-RAY DIFFRACTION9(chain 'I')
10X-RAY DIFFRACTION10(chain 'J')
11X-RAY DIFFRACTION11(chain 'K')
12X-RAY DIFFRACTION12(chain 'L')
13X-RAY DIFFRACTION13(chain 'M')
14X-RAY DIFFRACTION14(chain 'N')
15X-RAY DIFFRACTION15(chain 'O')
16X-RAY DIFFRACTION16(chain 'P')
17X-RAY DIFFRACTION17(chain 'S')
18X-RAY DIFFRACTION18(chain 'T')
19X-RAY DIFFRACTION19(chain 'U')
20X-RAY DIFFRACTION20(chain 'W')
21X-RAY DIFFRACTION21(chain 'X')

+
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