[English] 日本語
Yorodumi
- PDB-6tmt: Crystal structure of the chaperonin gp146 from the bacteriophage ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tmt
TitleCrystal structure of the chaperonin gp146 from the bacteriophage EL 2 (Pseudomonas aeruginosa) in presence of ATP-BeFx, crystal form I
ComponentsPutative GroEL-like chaperonine protein
KeywordsCHAPERONE / molecular chaperone / ATPase / chaperonin
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / protein refolding / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
Chaperone tailless complex polypeptide 1 (TCP-1) / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Putative GroEL-like chaperonine protein
Similarity search - Component
Biological speciesPseudomonas phage EL (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.03 Å
AuthorsBracher, A. / Paul, S.S. / Wang, H. / Wischnewski, N. / Hartl, F.U. / Hayer-Hartl, M.
CitationJournal: PLoS One / Year: 2020
Title: Structure and conformational cycle of a bacteriophage-encoded chaperonin.
Authors: Andreas Bracher / Simanta S Paul / Huping Wang / Nadine Wischnewski / F Ulrich Hartl / Manajit Hayer-Hartl /
Abstract: Chaperonins are ubiquitous molecular chaperones found in all domains of life. They form ring-shaped complexes that assist in the folding of substrate proteins in an ATP-dependent reaction cycle. Key ...Chaperonins are ubiquitous molecular chaperones found in all domains of life. They form ring-shaped complexes that assist in the folding of substrate proteins in an ATP-dependent reaction cycle. Key to the folding cycle is the transient encapsulation of substrate proteins by the chaperonin. Here we present a structural and functional characterization of the chaperonin gp146 (ɸEL) from the phage EL of Pseudomonas aeruginosa. ɸEL, an evolutionarily distant homolog of bacterial GroEL, is active in ATP hydrolysis and prevents the aggregation of denatured protein in a nucleotide-dependent manner. However, ɸEL failed to refold the encapsulation-dependent model substrate rhodanese and did not interact with E. coli GroES, the lid-shaped co-chaperone of GroEL. ɸEL forms tetradecameric double-ring complexes, which dissociate into single rings in the presence of ATP. Crystal structures of ɸEL (at 3.54 and 4.03 Å) in presence of ATP•BeFx revealed two distinct single-ring conformational states, both with open access to the ring cavity. One state showed uniform ATP-bound subunit conformations (symmetric state), whereas the second combined distinct ATP- and ADP-bound subunit conformations (asymmetric state). Cryo-electron microscopy of apo-ɸEL revealed a double-ring structure composed of rings in the asymmetric state (3.45 Å resolution). We propose that the phage chaperonin undergoes nucleotide-dependent conformational switching between double- and single rings and functions in aggregation prevention without substrate protein encapsulation. Thus, ɸEL may represent an evolutionarily more ancient chaperonin prior to acquisition of the encapsulation mechanism.
History
DepositionDec 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative GroEL-like chaperonine protein
B: Putative GroEL-like chaperonine protein
C: Putative GroEL-like chaperonine protein
D: Putative GroEL-like chaperonine protein
E: Putative GroEL-like chaperonine protein
F: Putative GroEL-like chaperonine protein
G: Putative GroEL-like chaperonine protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)436,04721
Polymers432,3277
Non-polymers3,72014
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.920, 149.427, 268.830
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
11A
21B
31C
41D
51E
61F
71G
12A
22B
32C
42D
52E
62F
72G
13A
23B
33C
43D
53E
63F
73G

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERALAALAAA2 - 1292 - 129
211SERSERALAALABB2 - 1292 - 129
311SERSERALAALACC2 - 1292 - 129
411SERSERALAALADD2 - 1292 - 129
511SERSERALAALAEE2 - 1292 - 129
611SERSERALAALAFF2 - 1292 - 129
711SERSERALAALAGG2 - 1292 - 129
121ILEILEMGMGAA - H425 - 601425
221ILEILEMGMGBB - J425 - 601425
321ILEILEMGMGCC - L425 - 601425
421ILEILEMGMGDD - N425 - 601425
521ILEILEMGMGEE - P425 - 601425
621ILEILEMGMGFF - R425 - 601425
721ILEILEMGMGGG - U425 - 601425
112ILEILEARGARGAA130 - 189130 - 189
212ILEILEARGARGBB130 - 189130 - 189
312ILEILEARGARGCC130 - 189130 - 189
412ILEILEARGARGDD130 - 189130 - 189
512ILEILEARGARGEE130 - 189130 - 189
612ILEILEARGARGFF130 - 189130 - 189
712ILEILEARGARGGG130 - 189130 - 189
122LEULEUGLYGLYAA390 - 424390 - 424
222LEULEUGLYGLYBB390 - 424390 - 424
322LEULEUGLYGLYCC390 - 424390 - 424
422LEULEUGLYGLYDD390 - 424390 - 424
522LEULEUGLYGLYEE390 - 424390 - 424
622LEULEUGLYGLYFF390 - 424390 - 424
722LEULEUGLYGLYGG390 - 424390 - 424
113THRTHRLYSLYSAA190 - 389190 - 389
213THRTHRLYSLYSBB190 - 389190 - 389
313THRTHRLYSLYSCC190 - 389190 - 389
413THRTHRLYSLYSDD190 - 389190 - 389
513THRTHRLYSLYSEE190 - 389190 - 389
613THRTHRLYSLYSFF190 - 389190 - 389
713THRTHRLYSLYSGG190 - 389190 - 389

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.609771, 0.580494, 0.539636), (-0.617919, 0.774568, -0.134986), (-0.496343, -0.251141, 0.831007)28.73835, -7.60532, -10.28628
3given(-0.222562, 0.663892, 0.713942), (-0.768387, 0.331268, -0.547579), (-0.600039, -0.670454, 0.436399)35.22678, -29.833469, -29.91441
4given(-0.897471, 0.236552, 0.372276), (-0.391935, -0.040549, -0.919099), (-0.20232, -0.970772, 0.129105)16.39554, -48.31934, -45.346519
5given(-0.889662, -0.415953, -0.188372), (0.219296, -0.027372, -0.975274), (0.400512, -0.908974, 0.115569)-14.11369, -50.355919, -43.098469
6given(-0.207059, -0.760056, -0.615988), (0.680049, 0.340825, -0.649131), (0.70332, -0.553311, 0.446304)-32.352859, -32.375099, -27.11867
7given(0.619954, -0.60584, -0.498613), (0.58683, 0.779838, -0.217904), (0.520853, -0.157511, 0.838989)-26.600031, -11.74083, -8.45137
8given(1), (1), (1)
9given(0.599469, 0.589169, 0.541771), (-0.623621, 0.76811, -0.145274), (-0.501731, -0.250773, 0.827876)29.71105, -7.83244, -9.99128
10given(-0.221983, 0.656225, 0.721174), (-0.761177, 0.345612, -0.548782), (-0.609371, -0.670761, 0.422784)35.334099, -30.165751, -29.50313
11given(-0.8991, 0.225628, 0.375115), (-0.398027, -0.064722, -0.915088), (-0.182192, -0.972061, 0.147997)16.544439, -48.056961, -45.4016
12given(-0.887935, -0.417561, -0.192909), (0.219728, -0.016614, -0.97542), (0.404092, -0.908497, 0.106502)-14.17602, -50.291592, -42.87365
13given(-0.206852, -0.76898, -0.604882), (0.66784, 0.340834, -0.661681), (0.714984, -0.540834, 0.443054)-32.38472, -33.326038, -26.09971
14given(0.634412, -0.591714, -0.497389), (0.588375, 0.786965, -0.185742), (0.501335, -0.174814, 0.84741)-25.46269, -9.21303, -9.29786
15given(1), (1), (1)
16given(0.633946, 0.557778, 0.535721), (-0.597532, 0.793028, -0.118589), (-0.490988, -0.244931, 0.836026)27.349449, -8.03585, -10.27759
17given(-0.177019, 0.654187, 0.735326), (-0.75954, 0.384334, -0.524773), (-0.62591, -0.651404, 0.428847)34.008129, -30.88228, -29.44207
18given(-0.887078, 0.23847, 0.395253), (-0.42076, -0.065505, -0.904804), (-0.189878, -0.968938, 0.158446)16.472099, -48.750919, -45.57275
19given(-0.877992, -0.455076, -0.148446), (0.170943, -0.00842, -0.985245), (0.447111, -0.890413, 0.085185)-12.97519, -53.049889, -40.712921
20given(-0.226013, -0.777335, -0.587085), (0.656567, 0.323654, -0.681299), (0.719609, -0.539443, 0.437223)-32.763729, -35.60397, -26.10228
21given(0.629929, -0.580942, -0.515456), (0.609513, 0.781115, -0.135478), (0.481335, -0.228836, 0.846139)-26.148331, -5.73957, -12.62714

-
Components

#1: Protein
Putative GroEL-like chaperonine protein


Mass: 61760.941 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage EL (virus) / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2Z0T5
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 5 % PEG-4000, 0.2 M Na-acetate and 0.1 M Na3-citrate pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.85 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 4.03→48.98 Å / Num. obs: 46685 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.344 / Rpim(I) all: 0.099 / Rrim(I) all: 0.359 / Net I/σ(I): 6.9 / Num. measured all: 602390
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
4.03-4.1713.71.8916209945190.6610.5281.9641.6100
15.61-48.9810.10.06389788880.9970.0210.06722.297

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0
Highest resolutionLowest resolution
Rotation48.98 Å4.11 Å

-
Processing

Software
NameVersionClassification
XDSVERSION Jan 26, 2018data reduction
Aimless0.5.28data scaling
MOLREP11.4.06phasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TMU

6tmu


Resolution: 4.03→30 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.881 / SU B: 164.035 / SU ML: 0.941 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.999
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2991 2214 4.8 %RANDOM
Rwork0.2562 ---
obs0.2583 44298 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 415.04 Å2 / Biso mean: 170.382 Å2 / Biso min: 84.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å2-0 Å2-0 Å2
2---4.62 Å20 Å2
3---5.52 Å2
Refinement stepCycle: final / Resolution: 4.03→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29155 0 224 0 29379
Biso mean--112.43 --
Num. residues----3815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01929848
X-RAY DIFFRACTIONr_bond_other_d0.0010.0228259
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.96940558
X-RAY DIFFRACTIONr_angle_other_deg0.852364743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.42753801
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72124.451337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.193154984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.00415203
X-RAY DIFFRACTIONr_chiral_restr0.0550.24781
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0234006
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026664
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3841MEDIUM POSITIONAL0.160.5
12B3841MEDIUM POSITIONAL0.190.5
13C3841MEDIUM POSITIONAL0.180.5
14D3841MEDIUM POSITIONAL0.170.5
15E3841MEDIUM POSITIONAL0.190.5
16F3841MEDIUM POSITIONAL0.170.5
17G3841MEDIUM POSITIONAL0.190.5
11A3841MEDIUM THERMAL5.582
12B3841MEDIUM THERMAL5.192
13C3841MEDIUM THERMAL5.682
14D3841MEDIUM THERMAL5.132
15E3841MEDIUM THERMAL5.482
16F3841MEDIUM THERMAL5.12
17G3841MEDIUM THERMAL6.772
21A1425MEDIUM POSITIONAL0.170.5
22B1425MEDIUM POSITIONAL0.170.5
23C1425MEDIUM POSITIONAL0.170.5
24D1425MEDIUM POSITIONAL0.170.5
25E1425MEDIUM POSITIONAL0.170.5
26F1425MEDIUM POSITIONAL0.170.5
27G1425MEDIUM POSITIONAL0.220.5
21A1425MEDIUM THERMAL5.62
22B1425MEDIUM THERMAL6.672
23C1425MEDIUM THERMAL5.042
24D1425MEDIUM THERMAL6.992
25E1425MEDIUM THERMAL15.012
26F1425MEDIUM THERMAL82
27G1425MEDIUM THERMAL6.772
31A2968MEDIUM POSITIONAL0.20.5
32B2968MEDIUM POSITIONAL0.220.5
33C2968MEDIUM POSITIONAL0.170.5
34D2968MEDIUM POSITIONAL0.160.5
35E2968MEDIUM POSITIONAL0.20.5
36F2968MEDIUM POSITIONAL0.170.5
37G2968MEDIUM POSITIONAL0.230.5
31A2968MEDIUM THERMAL10.082
32B2968MEDIUM THERMAL7.412
33C2968MEDIUM THERMAL10.012
34D2968MEDIUM THERMAL142
35E2968MEDIUM THERMAL7.332
36F2968MEDIUM THERMAL8.532
37G2968MEDIUM THERMAL10.552
LS refinement shellResolution: 4.03→4.133 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 175 -
Rwork0.337 3172 -
all-3347 -
obs--100 %
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)
13.9507-0.12570.08082.26051.03684.21950.1670.2154-0.07570.0495-0.2327-0.37160.58450.16090.06580.09310.0340.03580.30450.02810.155635.222-55.563-40.318
26.4566-1.38980.78038.6285-2.24094.1813-0.26440.77660.1204-0.91370.21080.38910.1322-0.26030.05370.6034-0.0643-0.03130.7119-0.07050.283325.883-52.205-67.385
33.3883-3.25221.6137.605-2.82672.84280.04130.10560.5317-0.1579-0.2165-0.4729-0.0710.3030.17530.43680.15140.08120.63840.07710.56636.95-24.999-74.064
44.22040.9862-0.41462.74281.01084.5926-0.0948-0.00610.0930.24660.0968-0.19520.1840.6131-0.00190.03530.0071-0.05510.27360.02370.335148.499-25.813-15.004
54.3884-1.25.30665.64680.52867.20030.08460.59190.1967-0.8797-0.18240.0033-0.23070.66130.09780.2918-0.02370.08990.84250.05110.605254.149-21.875-43.091
60.6611-1.28690.56216.5811-0.43193.83410.11830.0590.6024-1.30860.0540.7108-1.2443-0.8514-0.17231.3796-0.0424-0.22421.35990.30281.826947.5577.517-46.161
73.27431.2879-0.38764.12421.1073.9585-0.2632-0.3266-0.08160.2214-0.0131-0.2691-0.33110.20980.27640.12760.0444-0.12340.2559-0.07480.365626.018-1.5459.521
82.662-0.02030.25973.2265-2.82179.35310.30790.56650.341-0.3706-0.4401-0.5316-0.87550.12950.13220.5526-0.13250.00480.76650.00480.80441.9411.651-10.713
91.8383-0.1045-0.3922.8464-1.79037.1187-0.26360.48450.6937-0.04080.19090.2631-0.9079-0.59520.07281.36340.0296-0.23211.0676-0.02181.145222.99133.267-20.055
103.57980.7352-1.48235.86371.13983.16090.2594-0.30340.04780.6246-0.01740.0746-0.2041-0.2412-0.24190.14970.1478-0.02960.4897-0.03540.2522-15.088-0.12514.305
113.87211.295-2.49132.2725-2.15916.4457-0.01430.53540.6809-0.2776-0.0833-0.9182-0.44930.09040.09750.6412-0.01780.07260.6777-0.10591.1246-2.84723.7643.889
122.0599-3.26611.61256.874-2.77541.4293-0.04540.60160.036-1.3510.29790.6483-0.2412-0.0538-0.25252.3238-0.09110.08312.36180.431.8037-22.73230.978-17.926
135.9211-0.5069-1.18344.77840.96771.9954-0.0329-0.30210.08250.12740.12210.3250.1544-0.1922-0.08930.08150.1168-0.07330.5702-0.00340.1597-43.921-22.894-3.918
143.49955.7292-0.583710.7363-1.82071.1277-0.55770.60270.6456-0.70180.19110.2565-0.87960.49170.36661.613-0.2409-0.21551.41930.0890.9371-45.8535.546-8.555
150.8714-0.32391.00685.6644-3.03422.74230.39550.8189-0.0257-3.0671-0.20330.21231.06060.892-0.19224.18610.109-0.65631.9850.01921.5251-53.9816.738-37.907
164.9043-0.43960.99775.41452.48622.1657-0.44530.0751-0.2726-0.11250.0740.63830.1769-0.21790.37130.2065-0.11250.06220.4262-0.03910.1749-39.041-51.979-32.481
172.4849-2.3291-1.68048.5538-0.46592.04750.78670.42990.4127-0.9438-0.53960.1969-0.943-0.2226-0.24711.13990.1056-0.29280.93720.02631.0449-54.179-28.933-41.13
182.03-0.92531.68331.42230.38952.79870.43210.69650.6393-1.9913-0.2272-0.9388-1.84690.3797-0.20494.26410.40660.361.68830.33691.8173-43.378-24.913-69.118
194.2263-0.79970.52942.83641.38533.6874-0.0422-0.0273-0.6579-0.2779-0.0315-0.04150.1402-0.04650.07360.1004-0.04880.07390.37480.01020.1827-3.979-66.63-48.008
201.254-0.073-0.26837.8081-1.22330.46270.15240.53580.24440.07390.07970.197-0.202-0.2797-0.23220.64120.0136-0.04950.8064-0.02480.6209-21.765-53.952-66.718
212.6189-1.3814-1.67468.8761-0.05122.31260.42910.08931.0868-1.01690.1076-0.52830.02980.212-0.53680.5869-0.11710.21020.9126-0.17541.0047-1.544-37.619-81.954
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 130
2X-RAY DIFFRACTION1A425 - 603
3X-RAY DIFFRACTION2A131 - 189
4X-RAY DIFFRACTION2A388 - 424
5X-RAY DIFFRACTION3A190 - 387
6X-RAY DIFFRACTION4B2 - 130
7X-RAY DIFFRACTION4B425 - 603
8X-RAY DIFFRACTION5B131 - 189
9X-RAY DIFFRACTION5B388 - 424
10X-RAY DIFFRACTION6B190 - 387
11X-RAY DIFFRACTION7C2 - 130
12X-RAY DIFFRACTION7C425 - 603
13X-RAY DIFFRACTION8C131 - 189
14X-RAY DIFFRACTION8C388 - 424
15X-RAY DIFFRACTION9C190 - 387
16X-RAY DIFFRACTION10D2 - 130
17X-RAY DIFFRACTION10D425 - 603
18X-RAY DIFFRACTION11D131 - 189
19X-RAY DIFFRACTION11D388 - 424
20X-RAY DIFFRACTION12D190 - 387
21X-RAY DIFFRACTION13E2 - 130
22X-RAY DIFFRACTION13E425 - 603
23X-RAY DIFFRACTION14E131 - 189
24X-RAY DIFFRACTION14E388 - 424
25X-RAY DIFFRACTION15E190 - 387
26X-RAY DIFFRACTION16F2 - 130
27X-RAY DIFFRACTION16F425 - 603
28X-RAY DIFFRACTION17F131 - 189
29X-RAY DIFFRACTION17F388 - 424
30X-RAY DIFFRACTION18F190 - 387
31X-RAY DIFFRACTION19G2 - 130
32X-RAY DIFFRACTION19G425 - 603
33X-RAY DIFFRACTION20G131 - 189
34X-RAY DIFFRACTION20G388 - 424
35X-RAY DIFFRACTION21G190 - 387

+
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