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- PDB-4d18: Crystal structure of the COP9 signalosome -

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Basic information

Entry
Database: PDB / ID: 4d18
TitleCrystal structure of the COP9 signalosome
Components(COP9 SIGNALOSOME COMPLEX SUBUNIT ...) x 8
KeywordsSIGNALING PROTEIN / PCI COMPLEX / CSN / SGN / MPN DOMAIN
Function / homology
Function and homology information


COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / GTPase inhibitor activity / deNEDDylase activity / protein deneddylation / regulation of protein neddylation / eukaryotic translation initiation factor 3 complex ...COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / GTPase inhibitor activity / deNEDDylase activity / protein deneddylation / regulation of protein neddylation / eukaryotic translation initiation factor 3 complex / activation of NF-kappaB-inducing kinase activity / COP9 signalosome / protein neddylation / regulation of JNK cascade / Hydrolases; Acting on peptide bonds (peptidases) / metal-dependent deubiquitinase activity / RHOBTB1 GTPase cycle / regulation of DNA damage response, signal transduction by p53 class mediator / inner cell mass cell proliferation / skeletal muscle cell differentiation / response to light stimulus / JNK cascade / translation initiation factor activity / post-translational protein modification / positive regulation of DNA-binding transcription factor activity / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / neuron differentiation / metallopeptidase activity / transcription corepressor activity / cell junction / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / Neddylation / ubiquitin-dependent protein catabolic process / in utero embryonic development / transcription by RNA polymerase II / transcription coactivator activity / regulation of cell cycle / nuclear speck / protein phosphorylation / translation / negative regulation of cell population proliferation / negative regulation of apoptotic process / chromatin / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / 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 3-like, C-terminal helix / CSN7 helical bundle subdomain / COP9 signalosome complex subunit 3, N-terminal helical repeats / COP9 signalosome subunit 6 / : ...COP9 signalosome, subunit CSN8 / COP9 signalosome complex subunit 7, helix I / : / : / COP9 signalosome complex subunit 7a helix I domain / COP9 signalosome complex subunit 3-like, C-terminal helix / CSN7 helical bundle subdomain / COP9 signalosome complex subunit 3, N-terminal helical repeats / COP9 signalosome subunit 6 / : / COP9 signalosome complex subunit 1, C-terminal helix / 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 / : / : / : / PSMD12/CSN4, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory subunit Rpn7, N-terminal / 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. / Tetratricopeptide-like helical domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
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: 4.08 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
DepositionMay 1, 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 1.4Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)645,73718
Polymers645,60616
Non-polymers1312
Water00
1
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)322,8689
Polymers322,8038
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38300 Å2
ΔGint-245.9 kcal/mol
Surface area120310 Å2
MethodPISA
2
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)322,8689
Polymers322,8038
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38280 Å2
ΔGint-250 kcal/mol
Surface area120400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.680, 147.680, 317.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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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: 48252.355 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: 36928.902 Da / Num. of mol.: 2 / Fragment: RESIDUES 12-334
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-CONTAINING SIGNALOSOME SUBUNIT 8


Mass: 23573.895 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

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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

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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: 3.15 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growMethod: vapor diffusion / pH: 5.4
Details: CRYSTAL 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. CRYSTAL ...Details: CRYSTAL 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. CRYSTAL DEHYDRATED OVERNIGHT WITH 20% PEG 6000 IN WELL

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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
ReflectionResolution: 4.08→53 Å / Num. obs: 61692 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 151.99 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.7
Reflection shellResolution: 4.08→4.09 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XDSAIMLESSdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 4.08→52.98 Å / Cor.coef. Fo:Fc: 0.9308 / Cor.coef. Fo:Fc free: 0.917 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.802
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 3085 5 %RANDOM
Rwork0.2362 ---
obs0.237 61643 99.99 %-
Displacement parametersBiso mean: 213.65 Å2
Baniso -1Baniso -2Baniso -3
1-7.9146 Å20 Å20 Å2
2--7.9146 Å20 Å2
3----15.8292 Å2
Refine analyzeLuzzati coordinate error obs: 1.538 Å
Refinement stepCycle: LAST / Resolution: 4.08→52.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41420 0 2 0 41422
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00842168HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8956968HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d15162SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes1196HARMONIC2
X-RAY DIFFRACTIONt_gen_planes5962HARMONIC5
X-RAY DIFFRACTIONt_it42168HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion19.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion5530SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance3515HARMONIC1
X-RAY DIFFRACTIONt_utility_angle12HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact48660SEMIHARMONIC4
LS refinement shellResolution: 4.08→4.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2138 236 5.22 %
Rwork0.218 4286 -
all0.2177 4522 -
obs--99.99 %
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)
12.7586-0.62821.82391.0785-0.06362.6255-0.09170.09550.854-0.0714-0.31430.6978-1.1147-0.24630.4060.12820.2375-0.0201-0.3653-0.16270.60730.040695.738725.5261
20.9407-0.34780.3399-0.2497-0.72522.05940.14440.29940.2760.15580.51090.2079-0.1081-1.134-0.6553-0.05410.1690.1230.45070.38570.4381-32.111869.380917.5784
32.04710.615-1.10731.099-0.12972.75410.5324-0.74730.38180.3637-0.47710.0322-0.85770.7617-0.05530.1494-0.47770.0684-0.0009-0.3115-0.150953.839580.789748.533
42.82691.1839-0.92772.6702-1.30521.7959-0.26440.6788-0.206-0.41760.83250.42160.4697-0.9857-0.56810.0716-0.1701-0.40230.26020.0888-0.3139-19.138815.973531.2494
54.18871.2572-1.03962.28370.13912.11550.4942-0.64340.32750.5654-0.17640.18320.01510.1476-0.31780.0578-0.21-0.0636-0.0314-0.0379-0.38766.116849.107766.8048
62.02670.3177-0.66951.9169-0.21291.59170.0936-0.4223-0.10660.1784-0.02420.03450.49770.3608-0.06950.12610.0215-0.2678-0.160.0079-0.436712.63229.481955.5491
70.59021.15520.62232.78650.68988.18210.04340.0862-0.3217-0.1002-0.5032-0.3570.90750.60510.4598-0.2130.4685-0.14-0.1985-0.35310.016431.736320.270136.7642
81.5744-0.2541-0.84271.087-0.67522.45640.4168-0.3337-0.3721-0.252-0.4505-0.35480.20351.10070.0337-0.2074-0.0145-0.00390.3102-0.3229-0.200759.158163.135727.9093
91.92640.4891-0.93591.32410.04672.7193-0.1867-0.1068-0.05020.2611-0.01520.42781.1072-0.45250.2020.3615-0.08260.1973-0.2452-0.0594-0.33312.3214-3.6549-13.5495
101.8693-0.1523-0.1343-0.1564-0.11660.53480.0337-0.26960.0447-0.23970.1047-0.0396-0.1019-0.4756-0.1384-0.16090.2117-0.06130.27730.0837-0.1618-19.119522.6696-5.3596
112.8644-0.5267-0.54711.55370.55062.43130.10930.409-0.0015-0.1692-0.1417-0.29020.04620.14080.0325-0.14360.23870.0225-0.2197-0.1547-0.219866.759311.8682-35.0468
126.1535-6.65760.383412.43590.50862.87110.4586-0.2520.3984-0.9264-0.59441.4869-0.3984-1.48690.13590.35820.32950.25840.2043-0.17380.1093-5.652476.5157-16.2522
132.4143-0.84790.85562.29950.90754.00660.30780.7157-0.2097-0.9136-0.21040.3611-0.7873-0.8133-0.09740.09060.6257-0.1024-0.00790.2479-0.607919.214244.33-52.8296
142.7054-1.8539-1.01752.78060.73881.88430.55250.73780.3605-0.6923-0.3361-0.0722-1.0982-0.2749-0.21640.410.45890.1918-0.3880.2757-0.489225.976463.483-40.6865
151.2346-0.6434-0.55971.74390.96053.26760.2333-0.07931.0389-0.0575-0.1931-0.1318-0.78190.4565-0.04020.2412-0.02810.3946-0.4284-0.12310.244745.297871.7024-21.2656
161.9685-0.32650.09711.3761-0.76032.13190.2056-0.11860.87170.1937-0.2577-0.5508-0.67740.69720.0521-0.148-0.08640.14930.0986-0.2543-0.05771.50829.7705-14.3028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J
11X-RAY DIFFRACTION11CHAIN K
12X-RAY DIFFRACTION12CHAIN L
13X-RAY DIFFRACTION13CHAIN M
14X-RAY DIFFRACTION14CHAIN N
15X-RAY DIFFRACTION15CHAIN O
16X-RAY DIFFRACTION16CHAIN P

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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

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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

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