[English] 日本語
Yorodumi
- PDB-3fbv: Crystal structure of the oligomer formed by the kinase-ribonuclea... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fbv
TitleCrystal structure of the oligomer formed by the kinase-ribonuclease domain of Ire1
ComponentsSerine/threonine-protein kinase/endoribonuclease IRE1
KeywordsTRANSFERASE / HYDROLASE / IRE1 / RNase / ribonuclease / complex / kinase / inhibitor / oligomer / cytoplasmic / APY29 / aminopyrazole / ATP-binding / Endoplasmic reticulum / Glycoprotein / Magnesium / Membrane / Metal-binding / Multifunctional enzyme / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Transcription / Transcription regulation / Transmembrane / Unfolded protein response
Function / homology
Function and homology information


IRE1alpha activates chaperones / Ire1 complex / IRE1-TRAF2-ASK1 complex / fungal-type cell wall organization / protein localization to Golgi apparatus / inositol metabolic process / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / IRE1-mediated unfolded protein response / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / endoplasmic reticulum unfolded protein response ...IRE1alpha activates chaperones / Ire1 complex / IRE1-TRAF2-ASK1 complex / fungal-type cell wall organization / protein localization to Golgi apparatus / inositol metabolic process / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / IRE1-mediated unfolded protein response / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / endoplasmic reticulum unfolded protein response / RNA endonuclease activity / response to endoplasmic reticulum stress / mRNA processing / unfolded protein binding / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / endoplasmic reticulum / ATP binding / metal ion binding / identical protein binding / nucleus
Similarity search - Function
KEN domain / Serine/threonine-protein kinase/endoribonuclease IRE1/2-like / KEN domain / KEN domain superfamily / Ribonuclease 2-5A / KEN domain profile. / domain in protein kinases, N-glycanases and other nuclear proteins / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / de novo design (two linked rop proteins) ...KEN domain / Serine/threonine-protein kinase/endoribonuclease IRE1/2-like / KEN domain / KEN domain superfamily / Ribonuclease 2-5A / KEN domain profile. / domain in protein kinases, N-glycanases and other nuclear proteins / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / de novo design (two linked rop proteins) / Quinoprotein alcohol dehydrogenase-like superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-APJ / Serine/threonine-protein kinase/endoribonuclease IRE1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKorennykh, A.V. / Egea, P.F. / Korostelev, A.A. / Finer-Moore, J. / Zhang, C. / Shokat, K.M. / Stroud, R.M. / Walter, P.
CitationJournal: Nature / Year: 2009
Title: The unfolded protein response signals through high-order assembly of Ire1.
Authors: Korennykh, A.V. / Egea, P.F. / Korostelev, A.A. / Finer-Moore, J. / Zhang, C. / Shokat, K.M. / Stroud, R.M. / Walter, P.
History
DepositionNov 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase/endoribonuclease IRE1
B: Serine/threonine-protein kinase/endoribonuclease IRE1
C: Serine/threonine-protein kinase/endoribonuclease IRE1
D: Serine/threonine-protein kinase/endoribonuclease IRE1
E: Serine/threonine-protein kinase/endoribonuclease IRE1
F: Serine/threonine-protein kinase/endoribonuclease IRE1
G: Serine/threonine-protein kinase/endoribonuclease IRE1
H: Serine/threonine-protein kinase/endoribonuclease IRE1
I: Serine/threonine-protein kinase/endoribonuclease IRE1
J: Serine/threonine-protein kinase/endoribonuclease IRE1
K: Serine/threonine-protein kinase/endoribonuclease IRE1
L: Serine/threonine-protein kinase/endoribonuclease IRE1
M: Serine/threonine-protein kinase/endoribonuclease IRE1
N: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)731,02128
Polymers726,36714
Non-polymers4,65314
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Serine/threonine-protein kinase/endoribonuclease IRE1
B: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4324
Polymers103,7672
Non-polymers6652
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-7 kcal/mol
Surface area36840 Å2
MethodPISA
3
C: Serine/threonine-protein kinase/endoribonuclease IRE1
D: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4324
Polymers103,7672
Non-polymers6652
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-7 kcal/mol
Surface area37220 Å2
MethodPISA
4
E: Serine/threonine-protein kinase/endoribonuclease IRE1
F: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4324
Polymers103,7672
Non-polymers6652
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-7 kcal/mol
Surface area36990 Å2
MethodPISA
5
G: Serine/threonine-protein kinase/endoribonuclease IRE1
H: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4324
Polymers103,7672
Non-polymers6652
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-7 kcal/mol
Surface area36880 Å2
MethodPISA
6
I: Serine/threonine-protein kinase/endoribonuclease IRE1
J: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4324
Polymers103,7672
Non-polymers6652
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-7 kcal/mol
Surface area36780 Å2
MethodPISA
7
K: Serine/threonine-protein kinase/endoribonuclease IRE1
L: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4324
Polymers103,7672
Non-polymers6652
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-6 kcal/mol
Surface area37390 Å2
MethodPISA
8
M: Serine/threonine-protein kinase/endoribonuclease IRE1
N: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4324
Polymers103,7672
Non-polymers6652
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-7 kcal/mol
Surface area37000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.820, 163.470, 292.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
12
22
32
42
52
62
72
82
92
102
112
122
132

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and not resi 1037:1045 and not resi 660:680
211chain B and not resi 1037:1045 and not resi 660:680
311chain C and not resi 1037:1045 and not resi 660:680
411chain D and not resi 1037:1045 and not resi 660:680
511chain E and not resi 1037:1045 and not resi 660:680
611chain F and not resi 1037:1045 and not resi 660:680
711chain G and not resi 1037:1045 and not resi 660:680
811chain H and not resi 1037:1045 and not resi 660:680
911chain I and not resi 1037:1045 and not resi 660:680
1011chain J and not resi 1037:1045 and not resi 660:680
1111chain K and not resi 1037:1045 and not resi 660:680
1211chain L and not resi 1037:1045 and not resi 660:680
1311chain M and not resi 1037:1045 and not resi 660:680
1411chain N and not resi 1037:1045 and not resi 660:680
112chain B and resi 1037:1045
212resid 1037:1045 and chain C
312resid 1037:1045 and chain E
412resid 1037:1045 and chain M
512resid 1037:1045 and chain I
612resid 1037:1045 and chain N
712resid 1037:1045 and chain D
812resid 1037:1045 and chain F
912resid 1037:1045 and chain H
1012resid 1037:1045 and chain J
1112resid 1037:1045 and chain L
1212resid 1037:1045 and chain K
1312resid 1037:1045 and chain G

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Serine/threonine-protein kinase/endoribonuclease IRE1


Mass: 51883.391 Da / Num. of mol.: 14 / Fragment: Ire1 Kinase-RNase domain: UNP residues 641-1115 / Mutation: Amino acids 865-892 deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: IRE1, ERN1 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: P32361, non-specific serine/threonine protein kinase, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: Chemical
ChemComp-APJ / N~2~-1H-benzimidazol-5-yl-N~4~-(3-cyclopropyl-1H-pyrazol-5-yl)pyrimidine-2,4-diamine


Mass: 332.363 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C17H16N8
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: Sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2008 / Details: Mirrors
RadiationMonochromator: KOHZU: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. obs: 123887 / % possible obs: 100 % / Redundancy: 23.2 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 16
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 23 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 2.2 / % possible all: 100

-
Processing

Software
NameClassification
ELVESrefinement
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2RIO

2rio


Resolution: 3.2→19.983 Å / SU ML: 0.6 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.2835 6727 5.43 %
Rwork0.2352 --
obs0.2374 123887 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.707 Å2 / ksol: 0.24 e/Å3
Refinement stepCycle: LAST / Resolution: 3.2→19.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47668 0 350 0 48018
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3249X-RAY DIFFRACTIONPOSITIONAL
12B3249X-RAY DIFFRACTIONPOSITIONAL0.026
13C3249X-RAY DIFFRACTIONPOSITIONAL0.027
14D3249X-RAY DIFFRACTIONPOSITIONAL0.026
15E3249X-RAY DIFFRACTIONPOSITIONAL0.024
16F3249X-RAY DIFFRACTIONPOSITIONAL0.026
17G3249X-RAY DIFFRACTIONPOSITIONAL0.023
18H3249X-RAY DIFFRACTIONPOSITIONAL0.022
19I3249X-RAY DIFFRACTIONPOSITIONAL0.023
110J3249X-RAY DIFFRACTIONPOSITIONAL0.021
111K3249X-RAY DIFFRACTIONPOSITIONAL0.022
112L3249X-RAY DIFFRACTIONPOSITIONAL0.022
113M3249X-RAY DIFFRACTIONPOSITIONAL0.025
114N3249X-RAY DIFFRACTIONPOSITIONAL0.026
21B88X-RAY DIFFRACTIONPOSITIONAL
22C88X-RAY DIFFRACTIONPOSITIONAL0.033
23E88X-RAY DIFFRACTIONPOSITIONAL0.016
24M88X-RAY DIFFRACTIONPOSITIONAL0.035
25I88X-RAY DIFFRACTIONPOSITIONAL0.017
26N88X-RAY DIFFRACTIONPOSITIONAL0.027
27D88X-RAY DIFFRACTIONPOSITIONAL0.019
28F88X-RAY DIFFRACTIONPOSITIONAL0.018
29H88X-RAY DIFFRACTIONPOSITIONAL0.018
210J88X-RAY DIFFRACTIONPOSITIONAL0.04
211L88X-RAY DIFFRACTIONPOSITIONAL0.016
212K88X-RAY DIFFRACTIONPOSITIONAL0.013
213G88X-RAY DIFFRACTIONPOSITIONAL0.031
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.2-3.236200.40024045
3.2362-3.27410.392510630.40573065
3.2741-3.31390.40021390.3983873
3.3139-3.355600.38444124
3.3556-3.399600.37014105
3.3996-3.44590.35287890.36093273
3.4459-3.49490.38562790.35073843
3.4949-3.546800.34154089
3.5468-3.601900.31864075
3.6019-3.66060.31779060.32223222
3.6606-3.72330.3606970.30443992
3.7233-3.790600.29284078
3.7906-3.86300.28634103
3.863-3.94120.31038660.27213230
3.9412-4.026200.26794150
4.0262-4.119100.2564114
4.1191-4.22120.25896060.24053477
4.2212-4.33420.26611130.22824003
4.3342-4.460400.21744117
4.4604-4.60260.2262560.21253878
4.6026-4.7650.23423770.19623750
4.765-4.95300.18494140
4.953-5.17470.22664640.18713668
5.1747-5.44230.2434260.19974138
5.4423-5.775500.20414163
5.7755-6.2090.24453650.19613807
6.209-6.811300.18364197
6.8113-7.74620.22072560.17253941
7.7462-9.577100.1424248
9.5771-19.9830.17371250.16794252
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)
13.7793-0.658-0.3308-0.68910.6072.3037-0.3203-0.1198-1.2026-0.00750.3210.53420.63760.10580.05740.89890.19450.15970.30150.09751.150619.940930.5055121.1772
22.145-1.2527-0.37516.1796-0.28542.4165-0.1617-0.1369-0.0434-0.59610.0557-0.43510.14240.72870.11530.61360.34930.21110.87560.10670.733849.977747.3744114.0723
36.23391.2029-1.24032.8196-0.59653.76090.2727-0.3432-1.0150.157-0.0911-0.48580.47990.3918-0.16410.4590.0849-0.1560.20110.1990.724140.785127.7862161.7662
43.74982.0737-0.49035.4596-0.86272.3182-0.1686-0.2608-0.28490.39950.0517-0.4051-0.2648-0.00730.10360.99880.0175-0.01760.5677-0.1210.68753.013640.5813206.081
56.33860.33190.05950.55240.00281.90710.00220.12720.56020.30390.0947-0.0926-0.6301-0.1522-0.15091.22330.17950.14360.5824-0.14390.745830.319366.6357199.0838
64.851-1.68920.7534.27-0.55112.54150.18080.30880.4623-0.0414-0.0823-0.6454-0.47420.441-0.06480.5699-0.12360.10.42670.10930.661147.242762.1432157.0477
71.50961.2478-0.50363.16070.1783-1.4654-0.09810.01590.17910.0150.14680.16160.0162-0.04980.00721.5960.50340.06771.57-0.28040.946314.131358.6196239.7544
81.8662-0.9134-0.87862.5595-0.7645-1.8836-0.267-0.65440.1970.56380.2241-0.21330.1465-0.03390.02291.70370.019-0.12611.6782-0.41230.902548.552159.8916247.1684
91.3402-0.98210.92192.7352-1.6793-2.0160.3825-0.46460.0474-0.2876-0.36330.07550.09240.1777-0.01291.7681-0.02260.17892.451-0.42750.968210.844643.6479282.0171
102.1015-0.0833-0.01990.3744-0.8428-1.6721-0.1204-1.23110.3259-0.0198-0.13120.03670.09990.46490.00582.2119-0.21630.11242.25-0.79621.302931.370972.3381286.8238
114.5328-0.40310.41181.19450.2204-2.8026-0.01181.0054-0.1659-0.0768-0.09880.0443-0.0554-0.05760.11861.5543-0.40980.12261.9493-0.33030.75620.805233.000531.1
123.36032.4405-0.30553.74720.1130.0565-0.04070.2430.66430.2517-0.140.90220.04910.29880.15371.3441-0.430.09331.8779-0.16441.388813.058566.994537.0922
134.93261.8205-0.30452.1016-0.11761.3857-0.27260.2647-0.5414-0.27860.2531-0.1730.53290.1120.06121.28560.22340.27280.7923-0.13620.846938.639133.756172.6915
141.91250.02920.31845.07961.06322.0098-0.2180.1315-0.1017-0.00760.19150.12650.19430.01530.05151.19190.12780.21330.58070.00640.75757.314648.138979.9111
153.24540.25560.36952.34320.32392.6872-0.0805-0.05190.3158-0.13390.25060.3454-0.201-0.2603-0.12490.58140.0849-0.00190.38360.11190.93167.571764.9776124.1199
164.0935-1.7042-0.51911.82820.87153.1463-0.0692-0.32870.6477-0.41530.137-0.24-0.50460.1095-0.04970.6539-0.02130.03490.3808-0.00150.766828.449677.0842116.5238
171.9470.36481.0712.93381.03693.49470.1341-0.18980.31430.0335-0.01360.72950.1542-1.0355-0.07740.466-0.085-0.05550.62090.23451.07155.865738.8605164.2838
182.551-0.3449-1.63171.93670.52481.3777-0.2826-0.0983-0.40750.16280.05710.20350.0346-0.02930.20050.93410.03820.24980.7586-0.01471.067622.236720.4561206.8227
191.3760.1883-0.35762.63180.98952.6518-0.0097-0.3184-0.05730.08280.42940.45990.0443-0.5245-0.24281.04140.07960.23771.13060.14221.09046.348738.7371199.4405
202.0989-1.02240.36682.44290.5222.54710.0411-0.3841-0.19890.26420.02750.6249-0.1888-0.6793-0.0720.55660.16240.19450.39550.11470.88869.866963.5065159.1052
211.9083-0.1952-0.57912.2554-0.50750.41680.3765-0.3509-0.35910.3246-0.0703-0.1025-0.5393-0.2997-0.29271.24380.25080.06791.4258-0.11820.973720.427522.4672242.0038
221.97081.21060.46533.32890.5958-1.06330.1597-0.2831-0.2240.3460.2511-0.1368-0.2627-0.0862-0.30351.48890.32440.0371.8774-0.18271.120744.41823.4196249.6015
232.694-0.14311.74991.01470.1378-1.17060.5912-0.3768-0.04980.5659-0.2357-0.3334-0.4053-0.959-0.15391.6057-0.1199-0.12952.0487-0.05411.011942.582325.6276284.5428
241.7026-0.5766-0.39242.53671.2762-1.87050.0704-0.4212-0.2548-0.27040.1757-0.1325-0.7363-0.3608-0.23041.7779-0.34050.38252.6231-0.37951.24356.690446.1791290.1072
251.15921.60810.62383.03261.45211.2038-0.54240.6801-0.04120.16460.7593-0.48260.2523-0.5568-0.23211.271-0.2599-0.01261.8082-0.32880.983255.651946.706432.5066
262.5942-0.52950.28131.32211.0386-1.6743-0.4251.06670.09370.09760.2757-0.12630.2917-0.26010.12791.6087-0.30320.15391.99990.23121.257349.589670.722338.9556
272.09380.08820.13962.17040.63321.0596-0.1226-0.01170.5642-0.09990.1526-0.07710.21970.2785-0.02691.03570.04910.23460.8051-0.0640.888349.26468.936574.1421
282.35781.02680.55451.5825-0.4671.9067-0.15960.20140.2938-0.31120.2060.145-0.63220.22010.01971.09610.13790.18430.51720.09480.914927.228179.023781.531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1resid 1:965 and chain A
2X-RAY DIFFRACTION2resid 1:965 and chain B
3X-RAY DIFFRACTION3resid 1:965 and chain C
4X-RAY DIFFRACTION4resid 1:965 and chain F
5X-RAY DIFFRACTION5resid 1:965 and chain E
6X-RAY DIFFRACTION6resid 1:965 and chain D
7X-RAY DIFFRACTION7resid 1:965 and chain G
8X-RAY DIFFRACTION8resid 1:965 and chain H
9X-RAY DIFFRACTION9resid 1:965 and chain I
10X-RAY DIFFRACTION10resid 1:965 and chain J
11X-RAY DIFFRACTION11resid 1:965 and chain K
12X-RAY DIFFRACTION12resid 1:965 and chain L
13X-RAY DIFFRACTION13resid 1:965 and chain M
14X-RAY DIFFRACTION14resid 1:965 and chain N
15X-RAY DIFFRACTION15resid 966:2000 and chain A
16X-RAY DIFFRACTION16resid 966:2000 and chain B
17X-RAY DIFFRACTION17resid 966:2000 and chain C
18X-RAY DIFFRACTION18resid 966:2000 and chain F
19X-RAY DIFFRACTION19resid 966:2000 and chain E
20X-RAY DIFFRACTION20resid 966:2000 and chain D
21X-RAY DIFFRACTION21resid 966:2000 and chain G
22X-RAY DIFFRACTION22resid 966:2000 and chain H
23X-RAY DIFFRACTION23resid 966:2000 and chain I
24X-RAY DIFFRACTION24resid 966:2000 and chain J
25X-RAY DIFFRACTION25resid 966:2000 and chain K
26X-RAY DIFFRACTION26resid 966:2000 and chain L
27X-RAY DIFFRACTION27resid 966:2000 and chain M
28X-RAY DIFFRACTION28resid 966:2000 and chain N

+
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