[English] 日本語
Yorodumi
- PDB-4d10: Crystal structure of the COP9 signalosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4d10
TitleCrystal structure of the COP9 signalosome
Components(COP9 SIGNALOSOME COMPLEX SUBUNIT ...) x 8
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / deNEDDylase activity / GTPase inhibitor activity / eukaryotic translation initiation factor 3 complex / regulation of protein neddylation ...regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / deNEDDylase activity / GTPase inhibitor activity / eukaryotic translation initiation factor 3 complex / regulation of protein neddylation / protein deneddylation / COP9 signalosome / metal-dependent deubiquitinase activity / activation of NF-kappaB-inducing kinase activity / protein neddylation / Hydrolases; Acting on peptide bonds (peptidases) / RHOBTB1 GTPase cycle / inner cell mass cell proliferation / protein deubiquitination / skeletal muscle cell differentiation / regulation of JNK cascade / response to light stimulus / JNK cascade / translation initiation factor activity / post-translational protein modification / DNA Damage Recognition in GG-NER / neuron differentiation / Formation of TC-NER Pre-Incision Complex / transcription corepressor activity / metallopeptidase activity / positive regulation of DNA-binding transcription factor activity / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / cell junction / Neddylation / ubiquitin-dependent protein catabolic process / in utero embryonic development / transcription by RNA polymerase II / transcription coactivator activity / regulation of cell cycle / nuclear speck / translation / negative regulation of cell population proliferation / protein phosphorylation / chromatin / negative regulation of apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular exosome / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
COP9 signalosome, subunit CSN8 / COP9 signalosome complex subunit 7, helix I / : / : / COP9 signalosome complex subunit 7a helix I domain / COP9 signalosome complex subunit 1, C-terminal helix / COP9 signalosome complex subunit 3-like, C-terminal helix / COP9 signalosome subunit 6 / Cop9 signalosome subunit 5 C-terminal domain / COP9 signalosome complex subunit 4, helix turn helix domain ...COP9 signalosome, subunit CSN8 / COP9 signalosome complex subunit 7, helix I / : / : / COP9 signalosome complex subunit 7a helix I domain / COP9 signalosome complex subunit 1, C-terminal helix / COP9 signalosome complex subunit 3-like, C-terminal helix / COP9 signalosome subunit 6 / Cop9 signalosome subunit 5 C-terminal domain / COP9 signalosome complex subunit 4, helix turn helix domain / Cop9 signalosome subunit 5 C-terminal domain / CSN4/RPN5/eIF3a helix turn helix domain / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome subunit RPN7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / PCI/PINT associated module / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Tetratricopeptide-like helical domain superfamily / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COP9 signalosome complex subunit 2 / COP9 signalosome complex subunit 1 / COP9 signalosome complex subunit 6 / COP9 signalosome complex subunit 5 / COP9 signalosome complex subunit 8 / COP9 signalosome complex subunit 4 / COP9 signalosome complex subunit 7a / COP9 signalosome complex subunit 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.8 Å
AuthorsBunker, R.D. / Lingaraju, G.M. / Thoma, N.H.
CitationJournal: Nature / Year: 2014
Title: Crystal Structure of the Human Cop9 Signalosome
Authors: Lingaraju, G.M. / Bunker, R.D. / Cavadini, S. / Hess, D. / Hassiepen, U. / Renatus, M. / Fischer, E.S. / Thoma, N.H.
History
DepositionApr 30, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Aug 20, 2014Group: Database references
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Mar 27, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: COP9 SIGNALOSOME COMPLEX SUBUNIT 1
B: COP9 SIGNALOSOME COMPLEX SUBUNIT 2
C: COP9 SIGNALOSOME COMPLEX SUBUNIT 3
D: COP9 SIGNALOSOME COMPLEX SUBUNIT 4
E: COP9 SIGNALOSOME COMPLEX SUBUNIT 5
F: COP9 SIGNALOSOME COMPLEX SUBUNIT 6
G: COP9 SIGNALOSOME COMPLEX SUBUNIT 7A
H: COP9 SIGNALOSOME COMPLEX SUBUNIT 8
I: COP9 SIGNALOSOME COMPLEX SUBUNIT 1
J: COP9 SIGNALOSOME COMPLEX SUBUNIT 2
K: COP9 SIGNALOSOME COMPLEX SUBUNIT 3
L: COP9 SIGNALOSOME COMPLEX SUBUNIT 4
M: COP9 SIGNALOSOME COMPLEX SUBUNIT 5
N: COP9 SIGNALOSOME COMPLEX SUBUNIT 6
O: COP9 SIGNALOSOME COMPLEX SUBUNIT 7A
P: COP9 SIGNALOSOME COMPLEX SUBUNIT 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)646,20318
Polymers646,07216
Non-polymers1312
Water0
1
I: COP9 SIGNALOSOME COMPLEX SUBUNIT 1
J: COP9 SIGNALOSOME COMPLEX SUBUNIT 2
K: COP9 SIGNALOSOME COMPLEX SUBUNIT 3
L: COP9 SIGNALOSOME COMPLEX SUBUNIT 4
M: COP9 SIGNALOSOME COMPLEX SUBUNIT 5
N: COP9 SIGNALOSOME COMPLEX SUBUNIT 6
O: COP9 SIGNALOSOME COMPLEX SUBUNIT 7A
P: COP9 SIGNALOSOME COMPLEX SUBUNIT 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,1029
Polymers323,0368
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37150 Å2
ΔGint-248.8 kcal/mol
Surface area114490 Å2
MethodPISA
2
A: COP9 SIGNALOSOME COMPLEX SUBUNIT 1
B: COP9 SIGNALOSOME COMPLEX SUBUNIT 2
C: COP9 SIGNALOSOME COMPLEX SUBUNIT 3
D: COP9 SIGNALOSOME COMPLEX SUBUNIT 4
E: COP9 SIGNALOSOME COMPLEX SUBUNIT 5
F: COP9 SIGNALOSOME COMPLEX SUBUNIT 6
G: COP9 SIGNALOSOME COMPLEX SUBUNIT 7A
H: COP9 SIGNALOSOME COMPLEX SUBUNIT 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,1029
Polymers323,0368
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37050 Å2
ΔGint-252 kcal/mol
Surface area122820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.615, 151.615, 343.069
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11I
21A
12J
22B
13K
23C
14L
24D
15M
25E
16N
26F
17O
27G
18P
28H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010I77 - 505
2010A77 - 505
1020J30 - 443
2020B30 - 443
1030K3 - 403
2030C3 - 403
1040L182 - 405
2040D182 - 405
1050M24 - 333
2050E24 - 333
1060N29 - 316
2060F29 - 316
1070O8 - 215
2070G8 - 215
1080P11 - 209
2080H11 - 209

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

-
Components

-
COP9 SIGNALOSOME COMPLEX SUBUNIT ... , 8 types, 16 molecules AIBJCKDLEMFNGOHP

#1: Protein COP9 SIGNALOSOME COMPLEX SUBUNIT 1 / / SGN1 / SIGNALOSOME SUBUNIT 1 / G PROTEIN PATHWAY SUPPRESSOR 1 / GPS-1 / JAB1-CONTAINING SIGNALOSOME ...SGN1 / SIGNALOSOME SUBUNIT 1 / G PROTEIN PATHWAY SUPPRESSOR 1 / GPS-1 / JAB1-CONTAINING SIGNALOSOME SUBUNIT 1 / PROTEIN MFH


Mass: 54222.805 Da / Num. of mol.: 2 / Fragment: RESIDUES 52-527
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q13098
#2: Protein COP9 SIGNALOSOME COMPLEX SUBUNIT 2 / / SGN2 / SIGNALOSOME SUBUNIT 2 / ALIEN HOMOLOG / JAB1-CONTAINING SIGNALOSOME SUBUNIT 2 / THYROID ...SGN2 / SIGNALOSOME SUBUNIT 2 / ALIEN HOMOLOG / JAB1-CONTAINING SIGNALOSOME SUBUNIT 2 / THYROID RECEPTOR-INTERACTING PROTEIN 15 / TR- INTERACTING PROTEIN 15 / TRIP-15


Mass: 51992.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P61201
#3: Protein COP9 SIGNALOSOME COMPLEX SUBUNIT 3 / / SGN3 / SIGNALOSOME SUBUNIT 3 / JAB1-CONTAINING SIGNALOSOME SUBUNIT 3


Mass: 47924.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q9UNS2
#4: Protein COP9 SIGNALOSOME COMPLEX SUBUNIT 4 / / SGN4 / SIGNALOSOME SUBUNIT 4 / JAB1-CONTAINING SIGNALOSOME SUBUNIT 4


Mass: 46651.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q9BT78
#5: Protein COP9 SIGNALOSOME COMPLEX SUBUNIT 5 / / SGN5 / SIGNALOSOME SUBUNIT 5 / JUN ACTIVATION DOMAIN-BINDING PROTEIN 1


Mass: 37621.742 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper)
References: UniProt: Q92905, Hydrolases; Acting on peptide bonds (peptidases)
#6: Protein COP9 SIGNALOSOME COMPLEX SUBUNIT 6 / / SGN6 / SIGNALOSOME SUBUNIT 6 / JAB1-CONTAINING SIGNALOSOME SUBUNIT 6 / MOV34 HOMOLOG / VPR- ...SGN6 / SIGNALOSOME SUBUNIT 6 / JAB1-CONTAINING SIGNALOSOME SUBUNIT 6 / MOV34 HOMOLOG / VPR-INTERACTING PROTEIN / HVIP


Mass: 36531.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q7L5N1
#7: Protein COP9 SIGNALOSOME COMPLEX SUBUNIT 7A / / SGN7A / SIGNALOSOME SUBUNIT 7A / DERMAL PAPILLA-DERIVED PROTEIN 10 / JAB1-CONTAINING SIGNALOSOME SUBUNIT 7A


Mass: 24649.197 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q9UBW8
#8: Protein COP9 SIGNALOSOME COMPLEX SUBUNIT 8 / / SGN8 / SIGNALOSOME SUBUNIT 8 / COP9 HOMOLOG / HCOP9 / JAB1-CONT AINING SIGNALOSOME SUBUNIT 8 / SGN8 ...SGN8 / SIGNALOSOME SUBUNIT 8 / COP9 HOMOLOG / HCOP9 / JAB1-CONT AINING SIGNALOSOME SUBUNIT 8 / SGN8 / SIGNALOSOME SUBUNIT 8 / COP9 HO MOLOG / JAB1-CONTAINING SIGNALOSOME SUBUNIT 8


Mass: 23442.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q99627

-
Non-polymers , 1 types, 2 molecules

#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Details

Sequence detailsCHAINS A AND I MAPS TO UNIPROT Q13098 ISOFORM 4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growMethod: vapor diffusion / pH: 5.4
Details: CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4, 10 MM UREA.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2011 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.636
11K, H, -L20.364
ReflectionResolution: 3.8→52 Å / Num. obs: 86875 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.3
Reflection shellResolution: 3.8→3.81 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
XDSAIMLESSdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 3.8→50.87 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 45.893 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 1656 1.9 %RANDOM
Rwork0.1994 ---
obs0.19993 85161 99.94 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 189.557 Å2
Refinement stepCycle: LAST / Resolution: 3.8→50.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39974 0 2 0 39976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01940705
X-RAY DIFFRACTIONr_bond_other_d0.0020.0239458
X-RAY DIFFRACTIONr_angle_refined_deg1.0951.96454972
X-RAY DIFFRACTIONr_angle_other_deg0.826390737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.71654967
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.7624.7331927
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.297157505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9715228
X-RAY DIFFRACTIONr_chiral_restr0.0590.26207
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0245822
X-RAY DIFFRACTIONr_gen_planes_other0.0020.029282
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.54415.25219958
X-RAY DIFFRACTIONr_mcbond_other1.54315.25219957
X-RAY DIFFRACTIONr_mcangle_it2.75422.87224895
X-RAY DIFFRACTIONr_mcangle_other2.75422.87224896
X-RAY DIFFRACTIONr_scbond_it1.13515.31820747
X-RAY DIFFRACTIONr_scbond_other1.13515.31820747
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.08922.94230077
X-RAY DIFFRACTIONr_long_range_B_refined7.593161331
X-RAY DIFFRACTIONr_long_range_B_other7.593161331
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11I251670.04
12A251670.04
21J251510.04
22B251510.04
31K238740.04
32C238740.04
41L129310.09
42D129310.09
51M173230.05
52E173230.05
61N155190.05
62F155190.05
71O123220.05
72G123220.05
81P100900.04
82H100900.04
LS refinement shellResolution: 3.8→3.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 121 -
Rwork0.29 6253 -
obs--99.72 %
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)
10.25410.302-0.03460.4516-0.04960.060.1486-0.0965-0.06510.2225-0.0849-0.03670.01430.1589-0.06360.6667-0.105-0.11720.5066-0.12590.119930.846853.520854.306
20.3732-0.4603-0.00650.7450.02940.0632-0.108-0.0137-0.0273-0.066-0.01210.2186-0.08210.03210.12010.41410.0745-0.31480.3957-0.28340.6183-7.358698.802925.6237
32.6849-0.85660.39380.2861-0.1370.1106-0.06640.16540.16170.03010.0268-0.09140.0141-0.0490.03960.1144-0.01970.0160.5972-0.1320.5508-40.082170.600815.327
40.35270.24320.1750.8240.48270.49380.24210.0374-0.01220.2321-0.031-0.10050.02440.1996-0.2110.5642-0.29370.04080.564-0.21450.16453.399287.633149.7854
51.62040.52120.04870.5362-0.17240.1665-0.07830.1564-0.25280.00120.1805-0.04340.1092-0.0393-0.10220.7073-0.2286-0.0130.5583-0.04530.1381-17.81424.941922.389
60.9452-0.0266-0.37510.85740.33210.31450.1842-0.2018-0.07090.2513-0.1808-0.00560.07270.101-0.00340.8976-0.32210.01680.4092-0.06090.02452.597933.84967.2814
71.0745-0.6378-0.28762.2061-0.39090.27450.06740.1457-0.21270.0935-0.1483-0.05790.05780.00910.08080.58240.1082-0.12360.341-0.28160.332730.124214.595927.6211
82.78851.51872.02371.42161.13722.49260.08880.0088-0.1281-0.0398-0.0528-0.21780.29270.3198-0.0360.2340.0703-0.09920.5925-0.15730.266759.563568.290825.3496
90.0229-0.05390.00050.7042-0.12850.24750.08430.00280.0044-0.10950.00410.1549-0.02830.3294-0.08840.50940.02640.02490.595-0.16790.14944.245242.1244-39.6411
100.34630.39650.1011.15790.05880.0592-0.09490.0922-0.13330.10140.22350.22630.02730.0707-0.12860.5558-0.06380.08470.3535-0.18780.43585.6307-5.1091-12.2322
112.52230.6948-0.32220.2103-0.06560.18510.035-0.0136-0.097-0.0453-0.0098-0.022-0.072-0.1297-0.02520.25420.0235-0.16440.6772-0.13190.3096-27.424823.0842-1.8652
120.5957-0.008-0.47160.67510.0960.60380.171-0.03970.043-0.0764-0.0248-0.19580.14220.2183-0.14610.47860.395-0.13790.6936-0.2680.168167.33358.2848-35.8154
130.3295-0.0636-0.04560.126-0.1831.0273-0.077-0.183-0.18570.0230.24650.0253-0.5148-0.1395-0.16950.71740.03520.0430.5503-0.02960.263210.297272.0627-12.643
140.3440.27810.3530.86680.27410.480.04240.06530.0055-0.1885-0.07950.0456-0.23420.07050.03710.81110.0417-0.08590.402-0.01710.011416.005161.7447-52.7057
151.39820.4759-0.11290.4997-0.27910.1910.2292-0.31510.11720.1798-0.3119-0.0372-0.11730.12150.08270.631-0.22720.02190.5175-0.22950.224441.92479.8666-11.4149
160.62740.1981-0.65281.3165-0.37041.00070.2172-0.0134-0.00580.2106-0.2679-0.095-0.31530.46730.05070.14-0.0432-0.1020.9597-0.21710.253272.506926.7756-10.5396
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A464 - 505
2X-RAY DIFFRACTION1B412 - 443
3X-RAY DIFFRACTION1C346 - 403
4X-RAY DIFFRACTION1D367 - 406
5X-RAY DIFFRACTION1E250 - 333
6X-RAY DIFFRACTION1F208 - 316
7X-RAY DIFFRACTION1G166 - 216
8X-RAY DIFFRACTION1H194 - 208
9X-RAY DIFFRACTION2A77 - 463
10X-RAY DIFFRACTION3B30 - 411
11X-RAY DIFFRACTION4C3 - 345
12X-RAY DIFFRACTION5D1 - 366
13X-RAY DIFFRACTION6E24 - 249
14X-RAY DIFFRACTION6F29 - 207
15X-RAY DIFFRACTION7G8 - 165
16X-RAY DIFFRACTION8H12 - 167
17X-RAY DIFFRACTION9I464 - 505
18X-RAY DIFFRACTION9J412 - 443
19X-RAY DIFFRACTION9K346 - 403
20X-RAY DIFFRACTION9L367 - 406
21X-RAY DIFFRACTION9M250 - 333
22X-RAY DIFFRACTION9N208 - 316
23X-RAY DIFFRACTION9O166 - 216
24X-RAY DIFFRACTION9P194 - 208
25X-RAY DIFFRACTION10I77 - 463
26X-RAY DIFFRACTION11J30 - 411
27X-RAY DIFFRACTION12K3 - 345
28X-RAY DIFFRACTION13L78 - 366
29X-RAY DIFFRACTION14M24 - 249
30X-RAY DIFFRACTION14N29 - 207
31X-RAY DIFFRACTION15O8 - 165
32X-RAY DIFFRACTION16P12 - 167

+
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