[English] 日本語
Yorodumi
- PDB-5eya: TRIM25 RING domain in complex with Ubc13-Ub conjugate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eya
TitleTRIM25 RING domain in complex with Ubc13-Ub conjugate
Components
  • Polyubiquitin-B
  • Tripartite motif-containing 25 variant
  • Ubiquitin-conjugating enzyme E2 N
KeywordsSIGNALING PROTEIN/Transferase / Complex / E3 ligase / ubiquitination / SIGNALING PROTEIN-Transferase complex
Function / homology
Function and homology information


: / RIG-I binding / regulation of viral entry into host cell / : / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / suppression of viral release by host / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / negative regulation of viral entry into host cell ...: / RIG-I binding / regulation of viral entry into host cell / : / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / suppression of viral release by host / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / negative regulation of viral entry into host cell / DNA double-strand break processing / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / response to vitamin D / postreplication repair / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / positive regulation of intracellular signal transduction / positive regulation of double-strand break repair / mitochondrion transport along microtubule / fat pad development / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / E2 ubiquitin-conjugating enzyme / RSV-host interactions / female gonad development / seminiferous tubule development / male meiosis I / protein monoubiquitination / ligase activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / ubiquitin conjugating enzyme activity / TRAF6 mediated NF-kB activation / protein K63-linked ubiquitination / viral release from host cell / protein K48-linked ubiquitination / regulation of DNA repair / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / ERAD pathway / ubiquitin ligase complex / energy homeostasis / antiviral innate immune response / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / negative regulation of TORC1 signaling / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / positive regulation of DNA repair / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / neuron projection morphogenesis / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1
Similarity search - Function
TRIM25, PRY/SPRY domain / : / zinc finger of C3HC4-type, RING / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / Ubiquitin-conjugating enzyme, active site ...TRIM25, PRY/SPRY domain / : / zinc finger of C3HC4-type, RING / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / Ubiquitin-conjugating enzyme E2 N / E3 ubiquitin/ISG15 ligase TRIM25 / Tripartite motif-containing 25 variant
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsPornillos, O. / Sanchez, J.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM112508 United States
CitationJournal: Cell Rep / Year: 2016
Title: Mechanism of TRIM25 Catalytic Activation in the Antiviral RIG-I Pathway.
Authors: Sanchez, J.G. / Chiang, J.J. / Sparrer, K.M. / Alam, S.L. / Chi, M. / Roganowicz, M.D. / Sankaran, B. / Gack, M.U. / Pornillos, O.
History
DepositionNov 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 N
F: Tripartite motif-containing 25 variant
G: Tripartite motif-containing 25 variant
B: Ubiquitin-conjugating enzyme E2 N
C: Polyubiquitin-B
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,79310
Polymers70,5316
Non-polymers2624
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.047, 75.779, 169.101
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C
22chain D
13chain F
23chain G

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA3 - 151
211chain BB3 - 151
112chain CC1 - 76
212chain DD1 - 76
113chain FF101 - 102
213chain GG101 - 102

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / ...Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 17183.807 Da / Num. of mol.: 2 / Mutation: C87K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Production host: Escherichia coli (E. coli)
References: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#2: Protein Tripartite motif-containing 25 variant


Mass: 9504.903 Da / Num. of mol.: 2 / Fragment: UNP residues 12-97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q59GW5, UniProt: Q14258*PLUS
#3: Protein Polyubiquitin-B


Mass: 8576.831 Da / Num. of mol.: 2 / Fragment: UNP residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Li citrate, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 27181 / % possible obs: 98.2 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.066 / Rrim(I) all: 0.191 / Χ2: 0.736 / Net I/av σ(I): 9.625 / Net I/σ(I): 3.9 / Num. measured all: 220683
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.494.80.74323380.7240.3310.8210.45586.4
2.49-2.596.40.7426000.7550.3060.8050.47195.8
2.59-2.77.90.70527250.8580.2650.7550.48499.9
2.7-2.858.90.57527150.9140.2050.6110.525100
2.85-3.0290.41327340.9560.1460.4380.565100
3.02-3.2690.26627370.9850.0940.2820.648100
3.26-3.588.90.17827730.9930.0630.1890.777100
3.58-4.18.80.1327770.9950.0460.1381.148100
4.1-5.178.70.11928030.9920.0430.1270.97100
5.17-508.20.06629790.9990.0240.071.024100

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 2.4→28.966 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 24.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 1786 7.25 %
Rwork0.1891 22836 -
obs0.1919 24622 89.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.93 Å2 / Biso mean: 46.0471 Å2 / Biso min: 13.43 Å2
Refinement stepCycle: final / Resolution: 2.4→28.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4826 0 4 180 5010
Biso mean--26.67 37.82 -
Num. residues----612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064957
X-RAY DIFFRACTIONf_angle_d1.0986733
X-RAY DIFFRACTIONf_chiral_restr0.041757
X-RAY DIFFRACTIONf_plane_restr0.005878
X-RAY DIFFRACTIONf_dihedral_angle_d14.7661887
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1740X-RAY DIFFRACTION8.074TORSIONAL
12B1740X-RAY DIFFRACTION8.074TORSIONAL
21C902X-RAY DIFFRACTION8.074TORSIONAL
22D902X-RAY DIFFRACTION8.074TORSIONAL
31F856X-RAY DIFFRACTION8.074TORSIONAL
32G856X-RAY DIFFRACTION8.074TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.46490.3916980.28681261135966
2.4649-2.53740.27741160.25911473158976
2.5374-2.61920.26311230.23871585170883
2.6192-2.71270.26941320.23461686181887
2.7127-2.82130.27131340.2281713184789
2.8213-2.94960.27261390.2341784192392
2.9496-3.10490.28051420.21081799194193
3.1049-3.29920.25331420.21121823196594
3.2992-3.55350.23591470.20171870201796
3.5535-3.91030.23441470.17811899204697
3.9103-4.47440.18011530.14161950210398
4.4744-5.63040.17561520.14461935208797
5.6304-28.96850.18431610.16452058221997
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)
11.23940.27510.561.17020.43181.28260.0238-0.0522-0.6344-0.26680.0228-0.52280.5233-0.5701-0.02270.6622-0.5349-0.11540.1939-0.5398-0.2997-25.1007-11.242-15.6566
25.8962-0.7183-2.32581.70870.28661.3448-0.1455-0.37-0.71990.4969-0.0369-0.03520.80460.23560.03590.57990.0105-0.01370.36240.04230.3436-15.7739-11.9078-8.6204
33.21340.99790.28191.1776-0.05591.3672-0.38020.5116-0.32460.04130.2571-0.08740.4508-0.03120.07140.34940.0112-0.02340.3001-0.02520.1958-9.8921-4.1775-6.6646
43.24583.02230.9297.0249-1.76462.48570.391-0.36970.4776-0.0285-0.07560.3523-0.2447-1.2342-0.20010.3887-0.05050.02250.4389-0.05320.1905-26.3841.7104-13.973
53.1860.73291.25071.27650.1162.37170.0257-0.30520.3552-0.0216-0.08180.0643-0.08480.26820.10960.261-0.0135-0.01640.2654-0.05370.2596-12.36036.0226-9.6658
62.39660.12870.05351.82730.322.4171-0.21790.0350.2535-0.01370.1821-0.1790.15391.0626-0.0150.3107-0.0727-0.10830.29250.02220.1905-7.0174.3364-13.7274
73.8496-0.1298-1.13394.1144-1.74174.8180.0354-0.26960.86360.32890.3002-0.1415-0.4620.6576-0.09190.2486-0.0474-0.03640.5388-00.32563.51346.3811-2.9195
83.77121.8594-2.49513.86490.48744.96290.333-0.39870.03280.7563-0.1875-0.11750.43280.13810.04460.5251-0.00850.06850.2017-0.02730.397-21.3296-14.2552-32.3856
91.6394-0.85150.93171.969-0.32841.96270.00150.0557-0.18080.43650.0377-0.0182-0.0187-0.05610.06830.2588-0.0232-0.03560.1613-0.03410.2136-27.3211-4.0284-31.4164
104.4390.7831-0.12543.4186-1.07573.46820.13390.01520.69650.651-0.0638-0.0694-0.0063-0.1203-0.07620.24050.0072-0.02840.1215-0.02580.2446-29.94313.1791-27.7136
112.63771.02871.21022.78970.03661.6844-0.07410.21190.35160.18620.0208-0.0493-0.11640.20280.13980.2142-0.0306-0.02050.15080.00270.184-25.49068.4828-32.0363
123.4809-0.85610.80773.77170.0223.9718-0.4567-0.3808-0.3428-0.15750.66190.02440.5405-0.6014-0.25050.2482-0.0227-0.02520.24050.02560.2658-32.8511-14.8656-37.2126
130.69070.35830.42951.5107-0.41640.46310.01820.11280.00290.0523-0.1635-0.01590.19490.17910.0810.27280.0387-0.0510.13640.00820.2402-25.3718-10.6232-48.1396
142.26770.4545-0.65183.432-1.30261.06370.5211-0.1880.3112-0.0736-0.1477-0.3373-0.5178-0.02470.04670.29880.00260.03810.0614-0.00760.2362-22.83252.5093-53.6208
152.97740.8296-0.2816.3267-5.63875.10240.31690.6492-0.1404-1.5191-0.1259-0.4031.1444-0.00990.46780.81540.017-0.00430.2930.07740.3305-27.237413.1204-55.0199
162.50220.1168-0.78761.4087-0.09771.7264-0.13280.1931-0.2404-0.3070.16390.0656-0.0024-0.3396-0.25430.19820.0028-0.080.16020.05040.1941-32.92977.1898-50.8113
175.3018-4.68962.85244.6898-3.39142.9134-0.2199-0.24180.7470.3714-0.0617-0.96130.24970.0976-0.05560.25090.0374-0.03560.2134-0.04660.213-20.62575.879-44.416
180.3817-0.7603-0.67195.27823.05493.0838-0.0816-0.05970.03040.4107-0.1445-0.89720.39650.41330.0880.26960.0474-0.03840.15940.04660.2333-19.1185-12.6513-42.3179
191.3741-2.10161.32196.1451-0.37692.15640.35860.0374-0.1044-0.8311-0.153-1.10690.38790.472-0.05290.7610.0346-0.14120.4326-0.06970.9046-13.2966-27.595-42.7984
204.56861.1487-0.85345.29330.4273.02530.5593-0.1748-0.7329-0.23760.13110.06320.36350.1764-0.22820.47690.1759-0.10870.38570.05840.2666-27.7847-12.9514-64.8463
216.3221-0.39-2.99482.08370.54783.0050.14210.4556-0.2221-0.33280.0855-0.05320.8210.198-0.22670.47410.0396-0.13830.3565-0.06390.3853-37.329-13.8731-71.7737
224.5198-0.69391.43882.1855-0.20481.94490.1994-0.1617-0.11110.16240.02210.09090.10490.1739-0.19480.2911-0.0146-0.03320.22340.04730.1729-43.1126-6.3425-74.0606
230.756-1.36770.7016.22943.46258.1974-0.30540.1457-0.041-0.58420.6646-0.1951-0.5841.0568-0.3020.1891-0.03350.0260.2567-0.01170.2395-26.5327-0.1885-67.1161
242.3087-0.19141.49641.6469-0.36472.1276-0.20720.19770.30820.0413-0.09380.0468-0.0771-0.19390.22280.18860.0244-0.00770.26630.01990.2024-40.67294.0182-71.4059
252.2232-0.28981.54172.3185-0.14481.0221-0.1239-0.55420.46580.3907-0.07760.2563-0.156-1.06020.12360.31390.1422-0.00250.5201-0.08710.3339-49.41486.0275-69.786
262.2869-0.431-0.24913.70580.95993.42530.08150.4236-0.1571-0.3492-0.07680.73070.1586-0.8619-0.12110.26470.0142-0.07480.60330.06260.2526-56.9979-0.8707-79.758
272.5166-0.742-0.22421.73910.94980.78730.0197-0.828-0.85120.4268-0.23990.22020.6895-0.2254-0.30470.4168-0.1546-0.14440.32820.07520.1472-43.034-13.1945-50.2718
280.21290.0502-0.05560.0126-0.01330.0127-0.0432-0.05180.09420.1733-0.05960.37870.0037-0.2351-0.13610.1198-0.36190.06160.93430.14740.5839-56.503-9.9688-45.3713
295.0212.45632.47552.40390.88312.9340.066-0.1202-0.25290.5786-0.2030.1198-0.026-0.64940.04360.2992-0.12060.02470.4396-0.00810.2395-46.0448-4.4769-45.4953
306.48170.8531.85680.5302-0.3681.49830.2013-0.19361.27360.18480.32030.34050.0205-0.6780.46330.2331-0.0046-0.15290.2712-0.02460.3217-44.21270.4526-51.8195
312.362-1.343-3.244.3542.87424.76410.432-0.47690.6171-0.3442-0.290.3998-0.5558-0.4566-0.03560.2696-0.0255-0.07330.7644-0.0550.529-54.1014-3.726-57.315
323.15820.9536-0.93362.1221-0.48582.40230.1952-0.04150.00210.10810.04640.70390.2834-0.8052-0.21020.2768-0.0905-0.0490.4677-0.02530.2461-50.4668-7.1051-55.9751
331.9167-0.6712-0.35891.1535-0.21090.7386-0.11210.5-0.4662-0.2235-0.0964-0.07180.3870.20520.00740.37420.0627-0.05120.35-0.01570.282-5.6298-11.2108-31.1325
346.9357-0.39911.85443.0903-0.96494.731-0.01140.68130.2617-0.5209-0.4317-0.16130.13830.69710.42390.39150.1347-0.01810.36890.02060.2679-6.5176-3.5537-35.1472
352.21240.0325-0.39010.54980.29311.4680.26660.20670.3651-0.1239-0.28-0.14060.09211.24990.10190.27360.106-0.09070.56050.04150.345-0.858-4.1838-26.2518
361.9798-0.4267-0.39651.46951.74693.10520.07180.05920.0061-0.1283-0.0527-0.0351-0.07450.635-0.05550.29150.0121-0.0570.22920.05170.2401-8.54541.1606-22.1886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 17 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 30 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 57 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 67 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 68 through 100 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 101 through 122 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 123 through 151 )A0
8X-RAY DIFFRACTION8chain 'F' and (resid 6 through 10 )F0
9X-RAY DIFFRACTION9chain 'F' and (resid 11 through 30 )F0
10X-RAY DIFFRACTION10chain 'F' and (resid 31 through 43 )F0
11X-RAY DIFFRACTION11chain 'F' and (resid 44 through 66 )F0
12X-RAY DIFFRACTION12chain 'F' and (resid 67 through 81 )F0
13X-RAY DIFFRACTION13chain 'G' and (resid -2 through 30 )G0
14X-RAY DIFFRACTION14chain 'G' and (resid 31 through 43 )G0
15X-RAY DIFFRACTION15chain 'G' and (resid 44 through 48 )G0
16X-RAY DIFFRACTION16chain 'G' and (resid 49 through 58 )G0
17X-RAY DIFFRACTION17chain 'G' and (resid 59 through 66 )G0
18X-RAY DIFFRACTION18chain 'G' and (resid 67 through 78 )G0
19X-RAY DIFFRACTION19chain 'G' and (resid 79 through 83 )G0
20X-RAY DIFFRACTION20chain 'B' and (resid 3 through 17 )B0
21X-RAY DIFFRACTION21chain 'B' and (resid 18 through 30 )B0
22X-RAY DIFFRACTION22chain 'B' and (resid 31 through 57 )B0
23X-RAY DIFFRACTION23chain 'B' and (resid 58 through 67 )B0
24X-RAY DIFFRACTION24chain 'B' and (resid 68 through 100 )B0
25X-RAY DIFFRACTION25chain 'B' and (resid 101 through 132 )B0
26X-RAY DIFFRACTION26chain 'B' and (resid 133 through 151 )B0
27X-RAY DIFFRACTION27chain 'C' and (resid 1 through 16 )C0
28X-RAY DIFFRACTION28chain 'C' and (resid 17 through 22 )C0
29X-RAY DIFFRACTION29chain 'C' and (resid 23 through 34 )C0
30X-RAY DIFFRACTION30chain 'C' and (resid 35 through 44 )C0
31X-RAY DIFFRACTION31chain 'C' and (resid 45 through 54 )C0
32X-RAY DIFFRACTION32chain 'C' and (resid 55 through 76 )C0
33X-RAY DIFFRACTION33chain 'D' and (resid 1 through 22 )D0
34X-RAY DIFFRACTION34chain 'D' and (resid 23 through 34 )D0
35X-RAY DIFFRACTION35chain 'D' and (resid 35 through 65 )D0
36X-RAY DIFFRACTION36chain 'D' and (resid 66 through 76 )D0

+
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