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- PDB-3d8a: Co-crystal structure of TraM-TraD complex. -

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Basic information

Entry
Database: PDB / ID: 3d8a
TitleCo-crystal structure of TraM-TraD complex.
Components
  • Protein traD
  • Relaxosome protein TraM
KeywordsDNA BINDING PROTEIN / TraM tetramerization domain / TraD C-terminal peptide / protein complex / Conjugation / DNA-binding / ATP-binding / Inner membrane / Membrane / Nucleotide-binding / Transmembrane
Function / homology
Function and homology information


unidirectional conjugation / membrane => GO:0016020 / DNA binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Type IV conjugative transfer system, coupling protein TraD / TraD coupling protein, N-terminal / F sex factor protein N terminal / Helix Hairpins - #2320 / Type IV secretion system coupling protein TraD, DNA-binding domain / Type IV secretion-system coupling protein DNA-binding domain / Relaxosome protein TraM / TraM, DNA-binding domain / TraM protein, DNA-binding / Integration host factor (IHF)-like DNA-binding domain superfamily ...Type IV conjugative transfer system, coupling protein TraD / TraD coupling protein, N-terminal / F sex factor protein N terminal / Helix Hairpins - #2320 / Type IV secretion system coupling protein TraD, DNA-binding domain / Type IV secretion-system coupling protein DNA-binding domain / Relaxosome protein TraM / TraM, DNA-binding domain / TraM protein, DNA-binding / Integration host factor (IHF)-like DNA-binding domain superfamily / Helix Hairpins / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Coupling protein TraD / Relaxosome protein TraM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsGlover, J.N.M. / Lu, J. / Wong, J.J. / Edwards, R.A.
CitationJournal: Mol.Microbiol. / Year: 2008
Title: Structural basis of specific TraD-TraM recognition during F plasmid-mediated bacterial conjugation.
Authors: Lu, J. / Wong, J.J. / Edwards, R.A. / Manchak, J. / Frost, L.S. / Glover, J.N.
History
DepositionMay 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_gen.gene_src_strain ..._entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_seq_type
Revision 1.3Aug 30, 2023Group: 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.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Relaxosome protein TraM
B: Relaxosome protein TraM
C: Relaxosome protein TraM
D: Relaxosome protein TraM
E: Relaxosome protein TraM
F: Relaxosome protein TraM
G: Relaxosome protein TraM
H: Relaxosome protein TraM
S: Protein traD
T: Protein traD
U: Protein traD
V: Protein traD
W: Protein traD
X: Protein traD
Y: Protein traD
Z: Protein traD


Theoretical massNumber of molelcules
Total (without water)72,47916
Polymers72,47916
Non-polymers00
Water21612
1
E: Relaxosome protein TraM
F: Relaxosome protein TraM
G: Relaxosome protein TraM
H: Relaxosome protein TraM
W: Protein traD
X: Protein traD
Y: Protein traD
Z: Protein traD


Theoretical massNumber of molelcules
Total (without water)36,2408
Polymers36,2408
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15640 Å2
ΔGint-150 kcal/mol
Surface area11790 Å2
MethodPISA
2
A: Relaxosome protein TraM
B: Relaxosome protein TraM
C: Relaxosome protein TraM
D: Relaxosome protein TraM
S: Protein traD
T: Protein traD
U: Protein traD
V: Protein traD


Theoretical massNumber of molelcules
Total (without water)36,2408
Polymers36,2408
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15690 Å2
ΔGint-149 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.246, 142.246, 70.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
12A
22B
32C
42D
52E
62F
72G
82H
13A
23B
33C
43D
53E
63F
73G
83H
14S
24T
34U
44V
54W
64X
74Y
84Z

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNSERSER2AA62 - 915 - 34
21ASNASNSERSER2BB62 - 915 - 34
31ASNASNSERSER2CC62 - 915 - 34
41ASNASNSERSER2DD62 - 915 - 34
51ASNASNSERSER2EE62 - 915 - 34
61ASNASNSERSER2FF62 - 915 - 34
71ASNASNSERSER2GG62 - 915 - 34
81ASNASNSERSER2HH62 - 915 - 34
12GLUGLUARGARG2AA101 - 11944 - 62
22GLUGLUARGARG2BB101 - 11944 - 62
32GLUGLUARGARG2CC101 - 11944 - 62
42GLUGLUARGARG2DD101 - 11944 - 62
52GLUGLUARGARG2EE101 - 11944 - 62
62GLUGLUARGARG2FF101 - 11944 - 62
72GLUGLUARGARG2GG101 - 11944 - 62
82GLUGLUARGARG2HH101 - 11944 - 62
13PROPROPHEPHE6AA92 - 10035 - 43
23PROPROPHEPHE6BB92 - 10035 - 43
33PROPROPHEPHE6CC92 - 10035 - 43
43PROPROPHEPHE6DD92 - 10035 - 43
53PROPROPHEPHE6EE92 - 10035 - 43
63PROPROPHEPHE6FF92 - 10035 - 43
73PROPROPHEPHE6GG92 - 10035 - 43
83PROPROPHEPHE6HH92 - 10035 - 43
14VALVALPHEPHE3SI711 - 7174 - 10
24VALVALPHEPHE3TJ711 - 7174 - 10
34VALVALPHEPHE3UK711 - 7174 - 10
44VALVALPHEPHE3VL711 - 7174 - 10
54VALVALPHEPHE3WM711 - 7174 - 10
64VALVALPHEPHE3XN711 - 7174 - 10
74VALVALPHEPHE3YO711 - 7174 - 10
84VALVALPHEPHE3ZP711 - 7174 - 10

NCS ensembles :
IDDetails
1A B C D E F G H
4S T U V W X Y Z
2A B C D E F G H
3A B C D E F G H

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Components

#1: Protein
Relaxosome protein TraM /


Mass: 7980.898 Da / Num. of mol.: 8 / Fragment: UNP database residues 58-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: traM, ECOK12F071 / Production host: Escherichia coli (E. coli) / References: UniProt: P10026
#2: Protein/peptide
Protein traD


Mass: 1079.029 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: traD, ECOK12F102 / Production host: Escherichia coli (E. coli) / References: UniProt: P09130*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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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: 1.91 Å3/Da / Density % sol: 35.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 2000, 100 mM tris HCl pH 8.5, 200 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 2.55→71.07 Å / Num. all: 17494 / Num. obs: 17494 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.55→2.56 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G07
Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.906 / Highest resolution: 2.55 Å / SU B: 20.356 / SU ML: 0.27 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25746 884 5.1 %RANDOM
Rwork0.21767 ---
all0.21973 17453 --
obs0.21973 16609 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.975 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.06 Å20 Å2
2--0.13 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Highest resolution: 2.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 0 12 4468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224528
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0581.9696083
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4015545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77525.733225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93415825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9791516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023416
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.22037
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23183
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2125
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3921.52884
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.68224528
X-RAY DIFFRACTIONr_scbond_it0.99731804
X-RAY DIFFRACTIONr_scangle_it1.5754.51555
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A120tight positional0.040.05
12B120tight positional0.030.05
13C120tight positional0.030.05
14D120tight positional0.030.05
15E120tight positional0.030.05
16F120tight positional0.030.05
17G120tight positional0.030.05
18H120tight positional0.030.05
21A76tight positional0.030.05
22B76tight positional0.040.05
23C76tight positional0.030.05
24D76tight positional0.030.05
25E76tight positional0.020.05
26F76tight positional0.040.05
27G76tight positional0.030.05
28H76tight positional0.020.05
41S28tight positional0.040.05
42T28tight positional0.030.05
43U28tight positional0.040.05
44V28tight positional0.030.05
45W28tight positional0.030.05
46X28tight positional0.040.05
47Y28tight positional0.030.05
48Z28tight positional0.030.05
11A109medium positional0.280.5
12B109medium positional0.340.5
13C109medium positional0.290.5
14D109medium positional0.310.5
15E109medium positional0.340.5
16F109medium positional0.490.5
17G109medium positional0.310.5
18H109medium positional0.370.5
21A83medium positional0.420.5
22B83medium positional0.540.5
23C83medium positional0.610.5
24D83medium positional0.550.5
25E83medium positional0.430.5
26F83medium positional0.510.5
27G83medium positional0.390.5
28H83medium positional0.620.5
31A68loose positional0.455
32B68loose positional0.265
33C68loose positional0.245
34D68loose positional0.35
35E68loose positional0.335
36F68loose positional0.455
37G68loose positional0.315
38H68loose positional0.445
41S27loose positional0.575
42T27loose positional0.585
43U27loose positional0.585
44V27loose positional0.375
45W27loose positional0.465
46X27loose positional0.735
47Y27loose positional0.655
48Z27loose positional0.65
11A120tight thermal0.060.5
12B120tight thermal0.080.5
13C120tight thermal0.060.5
14D120tight thermal0.090.5
15E120tight thermal0.060.5
16F120tight thermal0.050.5
17G120tight thermal0.060.5
18H120tight thermal0.060.5
21A76tight thermal0.050.5
22B76tight thermal0.090.5
23C76tight thermal0.060.5
24D76tight thermal0.080.5
25E76tight thermal0.080.5
26F76tight thermal0.060.5
27G76tight thermal0.050.5
28H76tight thermal0.050.5
41S28tight thermal0.10.5
42T28tight thermal0.140.5
43U28tight thermal0.050.5
44V28tight thermal0.060.5
45W28tight thermal0.060.5
46X28tight thermal0.10.5
47Y28tight thermal0.060.5
48Z28tight thermal0.10.5
11A109medium thermal0.432
12B109medium thermal0.52
13C109medium thermal0.442
14D109medium thermal0.482
15E109medium thermal0.322
16F109medium thermal0.342
17G109medium thermal0.362
18H109medium thermal0.322
21A83medium thermal0.332
22B83medium thermal0.562
23C83medium thermal0.542
24D83medium thermal0.362
25E83medium thermal0.332
26F83medium thermal0.382
27G83medium thermal0.312
28H83medium thermal0.332
31A68loose thermal1.5710
32B68loose thermal4.710
33C68loose thermal2.2610
34D68loose thermal6.4210
35E68loose thermal4.5910
36F68loose thermal4.1410
37G68loose thermal3.1310
38H68loose thermal2.8110
41S27loose thermal2.2510
42T27loose thermal2.0610
43U27loose thermal0.8410
44V27loose thermal1.0810
45W27loose thermal1.5410
46X27loose thermal1.4810
47Y27loose thermal1.310
48Z27loose thermal1.8210
LS refinement shellResolution: 2.55→2.614 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 64 -
Rwork0.257 1239 -
obs--100 %
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)
111.1312-11.255-3.225221.36585.08243.23290.2635-0.53020.05650.1522-0.26890.8754-0.0775-0.31680.0054-0.33550.04590.0713-0.2722-0.0645-0.003-22.3820.697-21.738
29.1086-10.8818-4.830223.68097.925513.8421-0.3052-1.61440.58212.2590.1889-0.96840.3157-0.29070.11630.0301-0.0395-0.13750.1218-0.06640.0466-9.13817.772-10.333
35.2837-0.5708-2.0643.76280.33526.43230.0843-0.84170.89310.75010.1081-0.1004-0.3270.184-0.1924-0.2125-0.0019-0.0018-0.2581-0.14180.1113-12.47727.761-21.838
421.1455-10.6566-15.823412.15367.527414.9390.54380.14210.6154-0.7291-0.58630.695-0.6477-1.11110.0425-0.3060.0227-0.0935-0.1995-0.06310.2541-24.41628.749-35.057
513.9036-5.0026-4.22247.60961.5784.4579-0.2382-1.0799-0.09081.1466-0.05210.4387-0.1257-0.06630.2902-0.1497-0.00460.0531-0.1696-0.1107-0.0593-15.4121.325-16.836
614.8936-13.74-5.014342.713812.5276.7843-0.49950.14642.31891.24310.8818-0.1114-0.26740.738-0.3824-0.1966-0.0702-0.035-0.21030.00930.394-5.30333.58-24.915
75.2205-4.3454-1.892415.99216.42796.76910.0445-0.50.8164-0.250.21420.0217-0.516-0.0387-0.2587-0.35170.01370.0346-0.3676-0.06320.1198-19.52627.113-26.72
812.6636-8.8209-13.434713.819316.995627.1930.1723-0.15260.04221.4128-0.23250.96770.8364-1.05770.0602-0.0642-0.07710.2238-0.21730.02650.2953-28.16412.885-20.263
913.0273-13.542-5.425926.96823.72567.3331-0.0730.2478-0.1296-0.19840.03510.01510.6451-0.31010.0379-0.1283-0.01420.0247-0.1067-0.0591-0.0421-58.95512.755-40.003
1017.8064-10.8611-20.971518.06699.756225.50460.82122.45511.0712-1.1401-0.5066-0.4208-0.8334-1.7776-0.31460.1070.0498-0.02430.40640.24730.1186-56.87925.365-52.344
111.58230.2083-1.573310.57588.948117.6356-0.00770.1433-0.1609-0.5420.0505-0.6627-0.68231.154-0.0428-0.20960.00580.0618-0.1020.02780.0462-48.75219.79-40.249
124.9407-14.7107-9.592155.210721.623722.83950.0254-0.139203.239-0.1693-1.71012.385-0.06880.14390.2645-0.1327-0.2428-0.21280.07850.259-52.19.352-26.352
133.3230.4715-1.339915.9988.908111.2312-0.12361.03710.1024-0.3668-0.04140.1310.0687-0.28470.165-0.17330.02640.06660.015-0.0064-0.0228-55.76518.833-45.255
1421.3143-13.5326-10.957323.67710.815512.68720.6398-0.01470.2960.15640.4448-2.1681-0.38661.3894-1.0846-0.0121-0.1224-0.01620.1126-0.00280.3346-41.08224.799-37.11
1521.3125-8.3827-12.435914.1866.515112.37480.2934-0.5992-0.28560.2411-0.3052-1.21950.3830.62370.0118-0.17490.0101-0.0208-0.23370.03250.0839-51.92213.76-34.996
168.5201-0.1587-7.080614.825615.71822.2734-0.47821.6159-0.37660.2810.250.65641.1862-1.37260.2282-0.0561-0.0736-0.01880.3448-0.02180.1491-67.9019.687-41.637
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA60 - 913 - 34
2X-RAY DIFFRACTION2AA101 - 12244 - 65
3X-RAY DIFFRACTION3BB60 - 913 - 34
4X-RAY DIFFRACTION4BB101 - 12244 - 65
5X-RAY DIFFRACTION5CC60 - 913 - 34
6X-RAY DIFFRACTION6CC101 - 12244 - 65
7X-RAY DIFFRACTION7DD60 - 913 - 34
8X-RAY DIFFRACTION8DD101 - 12244 - 65
9X-RAY DIFFRACTION9EE60 - 913 - 34
10X-RAY DIFFRACTION10EE101 - 12244 - 65
11X-RAY DIFFRACTION11FF60 - 913 - 34
12X-RAY DIFFRACTION12FF101 - 12244 - 65
13X-RAY DIFFRACTION13GG60 - 913 - 34
14X-RAY DIFFRACTION14GG101 - 12244 - 65
15X-RAY DIFFRACTION15HH60 - 913 - 34
16X-RAY DIFFRACTION16HH101 - 12244 - 65

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  • 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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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

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