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- PDB-4r71: Structure of the Qbeta holoenzyme complex in the P1211 crystal form -

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Basic information

Entry
Database: PDB / ID: 4r71
TitleStructure of the Qbeta holoenzyme complex in the P1211 crystal form
Components
  • 30S ribosomal protein S1
  • Elongation factor Ts, Elongation factor Tu
  • RNA-directed RNA polymerase beta chain
KeywordsVIRAL PROTEIN/RIBOSOMAL PROTEIN / OB FOLD / TRANSLATION / VIRAL PROTEIN-RIBOSOMAL PROTEIN complex
Function / homology
Function and homology information


RNA secondary structure unwinding / guanyl-nucleotide exchange factor complex / positive regulation of cytoplasmic translation / translational elongation / guanosine tetraphosphate binding / negative regulation of cytoplasmic translation / translation elongation factor activity / guanyl-nucleotide exchange factor activity / ribosomal small subunit assembly / cytosolic small ribosomal subunit ...RNA secondary structure unwinding / guanyl-nucleotide exchange factor complex / positive regulation of cytoplasmic translation / translational elongation / guanosine tetraphosphate binding / negative regulation of cytoplasmic translation / translation elongation factor activity / guanyl-nucleotide exchange factor activity / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / single-stranded RNA binding / structural constituent of ribosome / translation / RNA-directed RNA polymerase / viral RNA genome replication / response to antibiotic / RNA-dependent RNA polymerase activity / nucleotide binding / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / membrane / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
RNA-directed RNA polymerase beta-chain / RNA replicase, beta-chain / Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / RNA-directed RNA polymerase, bacteriophage, catalytic domain ...RNA-directed RNA polymerase beta-chain / RNA replicase, beta-chain / Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / RNA-directed RNA polymerase, bacteriophage, catalytic domain / RdRp of RNA-containing bacteriophages catalytic domain profile. / Ribosomal protein S1 / Ribosomal protein S1-like / Ubiquitin-associated (UBA) domain / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / UBA-like superfamily / Translation factors / Tr-type G domain, conserved site / S1 domain profile. / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S1-like RNA-binding domain / Elongation factor Tu domain 2 / S1 RNA binding domain / S1 domain / Elongation Factor Tu (Ef-tu); domain 3 / Helicase, Ruva Protein; domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Nucleic acid-binding, OB-fold / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Elongation factor Ts / Small ribosomal subunit protein bS1 / Elongation factor Tu 2 / RNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Enterobacteria phage Qbeta (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.21 Å
AuthorsGytz, H. / Seweryn, P. / Kutlubaeva, Z. / Chetverin, A.B. / Brodersen, D.E. / Knudsen, C.R.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural basis for RNA-genome recognition during bacteriophage Q beta replication.
Authors: Gytz, H. / Mohr, D. / Seweryn, P. / Yoshimura, Y. / Kutlubaeva, Z. / Dolman, F. / Chelchessa, B. / Chetverin, A.B. / Mulder, F.A. / Brodersen, D.E. / Knudsen, C.R.
History
DepositionAug 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Elongation factor Ts, Elongation factor Tu
B: RNA-directed RNA polymerase beta chain
C: Elongation factor Ts, Elongation factor Tu
D: RNA-directed RNA polymerase beta chain
E: 30S ribosomal protein S1
F: 30S ribosomal protein S1


Theoretical massNumber of molelcules
Total (without water)320,3746
Polymers320,3746
Non-polymers00
Water00
1
A: Elongation factor Ts, Elongation factor Tu
B: RNA-directed RNA polymerase beta chain
E: 30S ribosomal protein S1


Theoretical massNumber of molelcules
Total (without water)160,1873
Polymers160,1873
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9110 Å2
ΔGint-49 kcal/mol
Surface area61570 Å2
MethodPISA
2
C: Elongation factor Ts, Elongation factor Tu
D: RNA-directed RNA polymerase beta chain
F: 30S ribosomal protein S1


Theoretical massNumber of molelcules
Total (without water)160,1873
Polymers160,1873
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9360 Å2
ΔGint-49 kcal/mol
Surface area61830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.730, 115.450, 178.520
Angle α, β, γ (deg.)90.00, 96.14, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D
13chain E
23chain F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILESERSERchain AAA4 - 13944 - 678
21ALAALASERSERchain CCC2 - 13932 - 678
12METMETVALVALchain BBB1 - 5717 - 577
22SERSERLEULEUchain DDD7 - 57213 - 578
13GLYGLYARGARGchain EEE1 - 1711 - 171
23GLYGLYARGARGchain FFF1 - 1711 - 171

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Elongation factor Ts, Elongation factor Tu / EF-Ts / EF-Tu


Mass: 75392.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tsf, b0170, JW0165, tufB, b3980, JW3943 / Plasmid: PBAD33 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6P1, UniProt: P0CE48
#2: Protein RNA-directed RNA polymerase beta chain / RNA replicase beta chain


Mass: 65997.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage Qbeta (virus) / Plasmid: PBAD33 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14647, RNA-directed RNA polymerase
#3: Protein 30S ribosomal protein S1


Mass: 18797.234 Da / Num. of mol.: 2 / Fragment: N-terminal domains OB1 and OB2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpsA, ssyF, b0911, JW0894 / Plasmid: pET11c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0AG67
Compound detailsCLEAVAGE BETWEEN THE EF-TS AND EF-TU SUBUNITS OCCUR DURING CRYSTALLIZATION. HENCE THERE ARE LARGE ...CLEAVAGE BETWEEN THE EF-TS AND EF-TU SUBUNITS OCCUR DURING CRYSTALLIZATION. HENCE THERE ARE LARGE GAPS BETWEEN RESIDUES GLN A282 AND SER A1002 AND LYS C281 AND LYS C1002
Sequence detailsTHE CHIMERIC CONSTRUCT EXPRESSED IN ESCHERICHIA COLI IS EF-TS-EF-TU_GASGAAGGGGENLYFQSGGGGS_BETA- ...THE CHIMERIC CONSTRUCT EXPRESSED IN ESCHERICHIA COLI IS EF-TS-EF-TU_GASGAAGGGGENLYFQSGGGGS_BETA-SUBUNIT. CLEAVAGE BETWEEN EF-TS-EF-TU_GASGAAGGGGENLYFQ AND SGGGGS_BETA-SUBUNIT OCCUR DURING PURIFICATION GASGAAGGGGENLYFQSGGGGS IS THE TEV CLEAVAGE LINKER

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 4000, 5% PEG 400, 0.4M ammonium sulfate, 0.1M sodium acetate, 0.01M betaine hydrochloride, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: PILATUS 2M / Detector: PIXEL / Date: Feb 6, 2014
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 3.21→67.32 Å / Num. all: 66067 / Num. obs: 65129 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.21→3.29 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PXIIIprogramdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1702)refinement
XDSdata reduction
XSCALEdata scaling
RefinementResolution: 3.21→59.827 Å / SU ML: 0.48 / σ(F): 1.34 / Phase error: 28.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2676 3260 5.01 %
Rwork0.2131 --
obs0.2158 65095 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.851 Å2
Refinement stepCycle: LAST / Resolution: 3.21→59.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21107 0 0 0 21107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321471
X-RAY DIFFRACTIONf_angle_d0.54629008
X-RAY DIFFRACTIONf_dihedral_angle_d12.37913020
X-RAY DIFFRACTIONf_chiral_restr0.0413300
X-RAY DIFFRACTIONf_plane_restr0.0033767
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B4328X-RAY DIFFRACTIONPOSITIONAL
12D4328X-RAY DIFFRACTIONPOSITIONAL0.027
21E1080X-RAY DIFFRACTIONPOSITIONAL
22F1080X-RAY DIFFRACTIONPOSITIONAL0.09
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2101-3.2580.37721400.3362666X-RAY DIFFRACTION99
3.258-3.30890.361510.31292739X-RAY DIFFRACTION99
3.3089-3.36310.36981480.29322641X-RAY DIFFRACTION99
3.3631-3.42110.32931310.28372721X-RAY DIFFRACTION100
3.4211-3.48330.30021450.26362718X-RAY DIFFRACTION100
3.4833-3.55030.28681450.25692685X-RAY DIFFRACTION100
3.5503-3.62280.36031530.27362661X-RAY DIFFRACTION99
3.6228-3.70150.56071400.47782101X-RAY DIFFRACTION78
3.7015-3.78760.31251400.27712665X-RAY DIFFRACTION98
3.7876-3.88230.30321480.24882696X-RAY DIFFRACTION100
3.8823-3.98730.32981220.24482754X-RAY DIFFRACTION100
3.9873-4.10460.26121250.21152705X-RAY DIFFRACTION100
4.1046-4.2370.25481390.19472716X-RAY DIFFRACTION100
4.237-4.38840.27521530.17742679X-RAY DIFFRACTION100
4.3884-4.56410.20681610.16132728X-RAY DIFFRACTION100
4.5641-4.77170.1981470.15752716X-RAY DIFFRACTION100
4.7717-5.02310.20951540.15382710X-RAY DIFFRACTION100
5.0231-5.33770.21411440.16892715X-RAY DIFFRACTION100
5.3377-5.74950.24891500.1842728X-RAY DIFFRACTION100
5.7495-6.32750.28681040.19862768X-RAY DIFFRACTION100
6.3275-7.24180.24821150.18562782X-RAY DIFFRACTION100
7.2418-9.11870.20841610.16472732X-RAY DIFFRACTION100
9.1187-59.83720.19171440.17162809X-RAY DIFFRACTION99
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)
13.0434-0.4636-1.26262.1972-1.3944.42620.11650.490.5571-0.1016-0.1329-0.1232-0.5556-0.0986-0.06020.5840.0821-0.14980.44550.08450.4757-15.269758.5518-35.9118
22.25992.44671.70235.18312.24522.75690.2585-0.1228-0.3675-0.3915-0.11740.39310.4744-0.2084-0.12580.61750.1203-0.21510.72390.07440.6532-32.841828.7478-18.2133
37.045-1.6493-2.38991.13890.48192.4258-0.15750.3122-0.1196-0.1563-0.0877-0.3246-0.07570.30830.26470.4838-0.0845-0.05350.54870.07180.40938.427846.0865-40.8751
43.9606-1.28850.27783.1346-0.68841.7543-0.1643-0.21160.1792-0.04210.2332-0.34-0.19930.0919-0.05820.3552-0.0268-0.0030.3098-0.06030.342912.658132.6608-10.6107
58.08130.4662-0.98784.11330.50226.26561.2492-1.69480.48252.9077-0.6484-1.04980.46550.5072-0.42540.8472-0.0044-0.09981.095-0.06650.441-15.327912.872711.7379
61.7234-0.2662-0.33090.78910.01320.1849-0.14610.3594-0.1224-0.40390.1240.20190.1203-0.10380.0260.6177-0.0849-0.08480.48230.02650.4368-4.2469-5.9538-21.7549
77.173-1.5421-0.9052.0083-0.31630.27050.2007-0.12580.1072-0.1837-0.05820.0531-0.0711-0.078-0.13780.47990.0049-0.0210.3503-0.09440.317-4.395918.6634-5.2295
85.4529-1.4021-2.79422.51122.55614.46380.09150.03350.6909-0.2633-0.02620.1443-0.60690.079-0.09330.4692-0.0014-0.12910.35330.11240.529-29.592454.981-63.7255
94.0028-1.1676-0.69430.82750.90470.9145-0.10880.1673-0.71350.3230.25250.00380.21660.2515-0.14920.68560.1287-0.11320.6987-0.03620.7071-22.719125.6044-68.7615
104.98431.5199-1.40163.39131.2595.741-0.1914-0.35560.50260.1446-0.33150.7064-0.2011-0.72970.48590.43880.1647-0.06390.6304-0.09590.6963-55.417646.548-55.0902
114.9291.66350.19532.54680.15811.1596-0.12890.32730.1426-0.32640.14990.3453-0.038-0.2507-0.01350.43720.0049-0.0580.41980.08990.4225-58.193923.5033-81.5344
121.68140.7891-1.59431.2405-0.23832.7818-0.155-0.0985-0.14740.0831-0.0107-0.25090.23040.13180.17910.64920.2531-0.06180.5048-0.04650.5721-32.0621-15.0859-66.1031
132.81150.11140.89310.6391-0.46231.3907-0.27150.01020.22540.07170.04430.04620.2377-0.0370.21070.72570.04610.09160.4953-0.03640.572-53.4069-10.8134-61.9467
141.6670.5348-1.721.755-1.36363.6999-0.0636-0.08070.08780.26610.0411-0.25240.0130.290.04090.49920.0701-0.0980.4801-0.08230.5185-27.6715-3.9932-66.7571
157.08891.5234-1.91343.1044-0.57470.52370.0823-0.19530.02130.2872-0.0204-0.03350.0220.1373-0.05710.72580.0598-0.00830.65220.14220.3731-45.24829.6143-82.2692
169.1483-3.75266.23243.5445-2.62678.5415-0.3781.15960.31210.0392-0.6049-0.45690.08661.07560.95060.7427-0.19750.15240.7277-0.04540.609334.3232-2.546-18.1344
174.4491-2.54810.7197.0546-1.20086.4802-0.39530.6526-0.6770.03390.2008-1.80180.00721.97990.23110.5518-0.09520.12791.0292-0.07591.081244.0747-9.0012-6.8788
181.17050.24740.19861.374-0.00720.0354-0.24130.4262-0.2424-1.14070.1406-0.63550.45440.7971-0.01611.34540.09060.33731.0916-0.14690.900221.0884-25.3277-33.8812
192.78761.1854-0.48366.1684-1.33262.8341-0.0460.7365-0.4172-0.6484-0.1151-0.06880.1415-0.31010.13711.12580.1560.16021.2208-0.32690.617510.6762-22.7667-49.9995
204.46585.854.87668.03275.27799.0518-0.1235-0.21930.58560.217-0.1951.28160.503-0.74480.350.64760.02390.15230.98960.02950.8624-81.3278-13.0663-69.5548
217.1097-7.5611.37458.457-3.04169.3-0.6251-0.194-2.726-0.2059-0.4188-0.1382.1106-2.1490.98981.1502-0.3070.41231.3724-0.18351.6814-98.671-17.5056-75.51
223.4701-3.60122.19583.8109-2.95038.5037-0.32870.32110.25530.9967-0.57590.19960.56590.52340.7620.9443-0.1843-0.01810.72340.21351.5078-71.9993-24.5312-63.2141
237.59456.8436-2.55416.2507-2.60875.67380.8623-0.58990.0652-0.2715-0.2590.54160.5298-1.8299-0.47881.4022-0.15090.14871.10970.14350.7588-66.0497-26.2585-39.1762
245.9122-0.048-1.21842.0378-2.46073.24080.4161-1.3450.44681.4914-0.94190.44130.753-0.1970.47091.216-0.05370.16560.9398-0.19570.5275-55.891-21.071-31.2727
258.72422.17854.32137.1087-3.21199.2854-1.53440.3066-0.18321.2927-0.8749-1.514-0.09321.38852.05161.24-0.37670.14281.44630.12860.7227-49.1257-21.4466-23.6664
267.2238-5.2682.81354.0698-3.12687.29610.1985-0.74030.0268-1.2520.5388-0.19880.1699-1.5544-0.75561.3114-0.1010.28561.30430.01390.7496-62.0197-19.1004-30.801
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 176 )
2X-RAY DIFFRACTION2chain 'A' and (resid 177 through 251 )
3X-RAY DIFFRACTION3chain 'A' and (resid 252 through 1198 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1199 through 1394 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 28 )
6X-RAY DIFFRACTION6chain 'B' and (resid 29 through 451 )
7X-RAY DIFFRACTION7chain 'B' and (resid 452 through 571 )
8X-RAY DIFFRACTION8chain 'C' and (resid 2 through 176 )
9X-RAY DIFFRACTION9chain 'C' and (resid 177 through 1010 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1011 through 1197 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1198 through 1393 )
12X-RAY DIFFRACTION12chain 'D' and (resid 7 through 139 )
13X-RAY DIFFRACTION13chain 'D' and (resid 140 through 346 )
14X-RAY DIFFRACTION14chain 'D' and (resid 347 through 475 )
15X-RAY DIFFRACTION15chain 'D' and (resid 476 through 572 )
16X-RAY DIFFRACTION16chain 'E' and (resid 1 through 34 )
17X-RAY DIFFRACTION17chain 'E' and (resid 35 through 71 )
18X-RAY DIFFRACTION18chain 'E' and (resid 72 through 106 )
19X-RAY DIFFRACTION19chain 'E' and (resid 107 through 171 )
20X-RAY DIFFRACTION20chain 'F' and (resid 1 through 53 )
21X-RAY DIFFRACTION21chain 'F' and (resid 54 through 66 )
22X-RAY DIFFRACTION22chain 'F' and (resid 67 through 86 )
23X-RAY DIFFRACTION23chain 'F' and (resid 87 through 103 )
24X-RAY DIFFRACTION24chain 'F' and (resid 104 through 131 )
25X-RAY DIFFRACTION25chain 'F' and (resid 132 through 150 )
26X-RAY DIFFRACTION26chain 'F' and (resid 151 through 171 )

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