[English] 日本語
Yorodumi
- PDB-4y7o: T6SS protein TssM C-terminal domain (869-1107) from EAEC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y7o
TitleT6SS protein TssM C-terminal domain (869-1107) from EAEC
Components
  • Type VI secretion protein IcmF
  • Type VI secretion system protein VasD
KeywordsSIGNALING PROTEIN / Type 6 secretion system / Alpha-beta fold / periplasmic protein
Function / homology
Function and homology information


Type VI secretion system, lipoprotein SciN / Type VI secretion system IcmF, C-terminal / Type VI secretion protein IcmF C2-like domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Type VI secretion protein IcmF / :
Similarity search - Component
Biological speciesEscherichia coli 1-176-05_S3_C1 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsNguyen, V.S. / Spinelli, S. / Durand, E. / Roussel, A. / Cambillau, C.
CitationJournal: Nature / Year: 2015
Title: Biogenesis and structure of a type VI secretion membrane core complex.
Authors: Eric Durand / Van Son Nguyen / Abdelrahim Zoued / Laureen Logger / Gérard Péhau-Arnaudet / Marie-Stéphanie Aschtgen / Silvia Spinelli / Aline Desmyter / Benjamin Bardiaux / Annick ...Authors: Eric Durand / Van Son Nguyen / Abdelrahim Zoued / Laureen Logger / Gérard Péhau-Arnaudet / Marie-Stéphanie Aschtgen / Silvia Spinelli / Aline Desmyter / Benjamin Bardiaux / Annick Dujeancourt / Alain Roussel / Christian Cambillau / Eric Cascales / Rémi Fronzes /
Abstract: Bacteria share their ecological niches with other microbes. The bacterial type VI secretion system is one of the key players in microbial competition, as well as being an important virulence ...Bacteria share their ecological niches with other microbes. The bacterial type VI secretion system is one of the key players in microbial competition, as well as being an important virulence determinant during bacterial infections. It assembles a nano-crossbow-like structure in the cytoplasm of the attacker cell that propels an arrow made of a haemolysin co-regulated protein (Hcp) tube and a valine-glycine repeat protein G (VgrG) spike and punctures the prey's cell wall. The nano-crossbow is stably anchored to the cell envelope of the attacker by a membrane core complex. Here we show that this complex is assembled by the sequential addition of three type VI subunits (Tss)-TssJ, TssM and TssL-and present a structure of the fully assembled complex at 11.6 Å resolution, determined by negative-stain electron microscopy. With overall C5 symmetry, this 1.7-megadalton complex comprises a large base in the cytoplasm. It extends in the periplasm via ten arches to form a double-ring structure containing the carboxy-terminal domain of TssM (TssMct) and TssJ that is anchored in the outer membrane. The crystal structure of the TssMct-TssJ complex coupled to whole-cell accessibility studies suggest that large conformational changes induce transient pore formation in the outer membrane, allowing passage of the attacking Hcp tube/VgrG spike.
History
DepositionFeb 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Type VI secretion protein IcmF
B: Type VI secretion protein IcmF
C: Type VI secretion system protein VasD
D: Type VI secretion system protein VasD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2288
Polymers86,9674
Non-polymers2624
Water6,828379
1
A: Type VI secretion protein IcmF
C: Type VI secretion system protein VasD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6805
Polymers43,4832
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-58 kcal/mol
Surface area17140 Å2
MethodPISA
2
B: Type VI secretion protein IcmF
D: Type VI secretion system protein VasD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5493
Polymers43,4832
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-37 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.470, 85.470, 256.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Type VI secretion protein IcmF


Mass: 26508.033 Da / Num. of mol.: 2 / Fragment: UNP residues 868-1107
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 1-176-05_S3_C1 (bacteria)
Gene: AB98_0769 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A017IZH1, UniProt: A0A0M3KL17*PLUS
#2: Protein Type VI secretion system protein VasD


Mass: 16975.258 Da / Num. of mol.: 2 / Fragment: UNP residues 25-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EA 17.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H4VA93
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.75 / Details: 0.05M ZnCl2, 15% PEG6000 and 0.1 NaAc pH 4.75.

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 1 crystal
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. all: 46408 / Num. obs: 46408 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 54.15 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 21.5
Reflection shellResolution: 2.24→2.3 Å / Redundancy: 10 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 3.1 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y7L
Resolution: 2.24→49.34 Å / Cor.coef. Fo:Fc: 0.9344 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.246 / SU Rfree Blow DPI: 0.182 / SU Rfree Cruickshank DPI: 0.179
RfactorNum. reflection% reflectionSelection details
Rfree0.2244 2321 5 %RANDOM
Rwork0.2036 ---
obs0.2047 46407 99.2 %-
Displacement parametersBiso mean: 61.99 Å2
Baniso -1Baniso -2Baniso -3
1--4.9137 Å20 Å20 Å2
2---4.9137 Å20 Å2
3---9.8273 Å2
Refine analyzeLuzzati coordinate error obs: 0.321 Å
Refinement stepCycle: 1 / Resolution: 2.24→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5518 0 4 379 5901
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015643HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.197711HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1848SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes128HARMONIC2
X-RAY DIFFRACTIONt_gen_planes828HARMONIC5
X-RAY DIFFRACTIONt_it5643HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.61
X-RAY DIFFRACTIONt_other_torsion19.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion758SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6450SEMIHARMONIC4
LS refinement shellResolution: 2.24→2.3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2527 151 5.01 %
Rwork0.2209 2864 -
all0.2224 3015 -
obs--99.2 %
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)
10.1563-0.2830.07750.40030.130700.00010.0043-0.0058-0.00280.00270.00110.0062-0.0016-0.0028-0.0664-0.0564-0.0073-0.0304-0.06960.089622.0968-24.0964-0.7914
20.90860.16680.0490.21310.22480.04090.0051-0.0072-0.05740.02410.00120.00350.0173-0.0028-0.0063-0.0308-0.1399-0.0292-0.05720.03530.109234.77-14.407315.0379
300.05750.10640.04570.15130.0206-0.0016-0.00410.0012-0.00490.0050.0016-0.0003-0.0008-0.0034-0.0106-0.04980.0409-0.0602-0.05310.064138.397-11.97764.8041
40.12530.0697-0.15840.00540.22960.0261-0.00050.01100.0033-0.0047-0.00940.0071-0.00170.0052-0.0763-0.1070.0620.0054-0.05340.059333.8428-15.3321-3.257
50.06740.05870.10900.015800.00050.0056-0.0031-0.00490.0002-0.002-0.0042-0.0009-0.0007-0.0197-0.0404-0.01540.008-0.02650.003524.7222-13.0637-8.526
600.08650.01460.1534-0.26720.06390.00060.00010.0019-0.0001-0.0005-0.0012-0.0067-0.0011-0.0001-0.007-0.0408-0.0314-0.00360.00840.013123.901-5.2759-6.1704
70.00180.19570.12840-0.007900.00170.0023-0.0004-0.0116-0.00350.0028-0.0032-0.00170.0017-0.0246-0.0238-0.0180.0081-0.01790.024514.349-15.1016-9.6681
80.2473-0.44760.93731.18980.66650.50180.00170.0027-0.023-0.00220.01510.0417-0.02870.0164-0.0168-0.068-0.1233-0.00540.0112-0.03540.052530.2129-6.38343.5547
90.04210.0779-0.28960.148-0.27750.1494-0.00370.0102-0.01590.00760.0008-0.0086-0.0227-0.00850.00290.0272-0.0620.0750.0255-0.0125-0.058341.994911.564313.1666
100.60870.2655-0.19870.1577-0.18440.0096-0.0036-0.0013-0.00980.03120.01080.0044-0.0435-0.018-0.00710.0647-0.04840.0744-0.0064-0.076-0.058844.295913.59626.3005
1100.3492-0.55480.0853-0.2820.2227-0.00030.0052-0.01790.0036-0.001-0.0154-0.0180.00930.00120.0284-0.0580.0444-0.0044-0.0191-0.028948.788113.825122.1219
120.0270.1888-0.20640.0428-0.11840.25240.00060.0071-0.001-0.0019-0.002-0.004-0.0055-0.00020.00130.0642-0.03340.0418-0.0241-0.0218-0.038544.942621.521616.4454
130-0.3844-0.05440.07220.06640.3238-0.0017-0.0026-0.01690.00030.0022-0.0029-0.0150.0065-0.00050.0013-0.01150.080.0302-0.0596-0.030647.69623.745512.8464
140.81330.7440.03290.00510.20110.08090.0023-0.0054-0.01930.0071-0.004-0.0102-0.01340.00680.00160.0106-0.03250.02980.0309-0.034-0.044846.14297.182228.0102
1500.421-0.21480.0423-0.42030.37250.0017-0.00770.00150.00360.0018-0.0041-0.00090.0049-0.00350.0375-0.00880.05460.0289-0.0055-0.066443.18468.724734.3091
160.13280.1383-0.443300.18730.21980.0011-0.0109-0.015-0.0099-0.001-0.00060.00720.0024-0.0001-0.0214-0.06560.06050.02530.02730.001338.8615-0.672721.1907
170.1345-0.108-0.24070.03240.04490.0311-0.0010.00230.0014-0.0054-0.00120.0036-0.0048-0.00080.00220.00920.01370.03010.00180.01240.001228.807513.137215.994
180.4338-0.1366-0.17690.7572-0.08760.10180.0083-0.02010.00660.0031-0.0210.0287-0.0074-0.00190.01270.05450.00280.09680.0373-0.0235-0.094334.269612.674623.9579
190.0814-0.12660.19570.4027-0.01650.2713-0.00280.0095-0.01810.00890.01080.0176-0.0239-0.0092-0.0080.0375-0.00560.02790.01330.0201-0.053936.48119.503813.4385
200.814-0.1902-0.70370.16870.16820.0034-0.001-0.006-0.03630.01620.00430.0393-0.0078-0.016-0.0033-0.0605-0.13080.00270.01380.00410.048725.1457-11.40449.6873
210.0685-0.14690.31850.37360.018500.0002-0.0087-0.00030.0046-0.00460.0037-0.00080.01530.0044-0.02860.0546-0.019-0.03920.010.069979.8432-5.752811.0533
220.1219-0.08290.4440.31570.33550.0013-0.00270.0128-0.0509-0.0512-0.0135-0.01850.050.0180.01620.0252-0.00210.0896-0.0501-0.06370.0464.192-7.4617-4.7289
230.0293-0.16950.2480.0699-0.09510.0909-0.00340.00820.0029-0.00040.0009-0.0099-0.0059-0.00430.0024-0.0193-0.00130.0807-0.0286-0.01240.046359.5915-5.49825.1748
240.03010.0564-0.05250.2304-0.14380.10810.0004-0.0069-0.0040.0133-0.0010.00020.00420.00050.0006-0.03180.00060.0451-0.0120.02630.05664.7079-4.313813.3296
250.15940.09220.160.04710.10860.0003-0.0008-0.0056-0.0050.0044-0.0022-0.0036-0.0040.00010.003-0.016-0.0212-0.0348-0.00080.00290.014670.49373.359317.2337
2600.04640.21140.3912-0.14590-0.0005-0.0065-0.00140.004-0.00110.0038-0.00620.00470.0016-0.0132-0.0543-0.0345-0.0253-0.01540.026367.53659.316414.2855
270.05320.06050.048200.02370.0164-0.001-0.00080.00170.00410.00160.002300.0007-0.0006-0.0001-0.0044-0.02090.010.01380.010681.74945.700717.6642
280.0941-0.2377-0.29291.89650.48720.6148-0.0039-0.00060.0210.0238-0.0494-0.07810.0264-0.06710.0532-0.0528-0.0840.0338-0.0573-0.04380.082663.45453.72614.7203
290.0034-0.23080.12380.10170.1140.0824-0.0039-0.0007-0.0137-0.0098-0.00530.0114-0.0052-0.00530.00920.0042-0.01270.02180.0438-0.1083-0.056543.85739.9907-6.8375
300.1032-0.01180.17730.033-0.371700.00710.0060.003-0.0374-0.01990.0041-0.0326-0.02190.0128-0.0122-0.0139-0.02190.0602-0.121-0.040241.24127.8035-19.8734
310-0.3380.240900.10980.03920.0010.011-0.0187-0.0013-0.01340.0041-0.003-0.02530.0124-0.0180.0065-0.03020.0508-0.112-0.033337.33986.6858-15.5302
320.0399-0.1365-0.193300.12380.16020.0003-0.0008-0.0030.00440.00070.0063-0.0041-0.003-0.0010.00340.04630.00540.0271-0.0532-0.033635.651815.559-11.5173
330-0.1248-0.17860.09290.13040.0811-0.0017-0.0114-0.0097-0.00180-0.0006-0.0009-0.01070.0017-0.0095-0.09870.05920.007-0.0453-0.015443.64120.6294-4.754
340.2802-0.6716-0.26890.1580.47540.3050.0033-0.0036-0.00440.0086-0.00820.00680.0037-0.01150.0049-0.0195-0.0538-0.01120.0353-0.1349-0.022743.44171.2597-20.3355
350-0.3895-0.15540.05360.77230.22380.00160.00730.005-0.0060.00490.01-0.0023-0.0075-0.00650.02130.0071-0.03770.0349-0.1226-0.050645.05513.3079-27.4343
360.01850.1097-0.077700.06920.19850.00170.0008-0.01840.0004-0.00770.0090.0052-0.00660.0060.0106-0.06690.06040.0061-0.1241-0.012353.64230.3793-12.9893
370.12130.1654-0.14480.0959-0.21840.126-0.0007-0.00040.003-0.0011-0.00170.0013-0.0011-0.00190.00250.02550.00110.0134-0.0194-0.02610.004653.299217.9825-11.5952
380.4252-0.2830.35211.1189-0.49740.10080.00310.01790.0166-0.0249-0.0032-0.0016-0.0047-0.00190.00020.0493-0.020.02830.0159-0.0932-0.071549.927613.3537-18.2019
390.0802-0.98480.30760.53450.84530.13620.0044-0.004-0.0151-0.0225-0.0189-0.0046-0.0104-0.01060.01450.0146-0.01730.0120.0275-0.1178-0.036949.594411.3801-7.2314
400.0310.16070.02550.4205-0.13310-0.00270.0123-0.0171-0.0225-0.0154-0.03570.00290.00630.0181-0.0390.00880.0547-0.0057-0.02260.048570.49681.1392-0.904
410.14850.8032-0.44050.81150.58920.6499-0.0018-0.00450.0019-0.0030.01350.0058-0.01220.0196-0.01170.0675-0.0856-0.0147-0.0303-0.1156-0.071951.310832.12131.8503
420.01660.3437-0.535700.2560.4541-0.00190.00860.00210.0012-0.0072-0.00430.00920.00420.00910.0168-0.07410.05280.0129-0.0316-0.033359.699132.403817.2409
430.09140.79970.19980.01981.06710.2954-0.00020.00450.0039-0.0015-0.0085-0.03390.00240.01190.00880.0255-0.0534-0.0027-0.0104-0.0863-0.045559.222128.930132.2216
4400.8446-0.03370.04510.05970.19340.00150.00150.0285-0.00570.0065-0.01050.00690.0118-0.0080.088-0.0828-0.0231-0.0431-0.0218-0.066553.361835.251121.8616
4500.48250.22190.57610.27510-0.0021-0.01220.0108-0.01470.00190.0067-0.0130.03080.00020.0424-0.1077-0.0496-0.0816-0.063-0.004757.053540.906131.6122
460.1889-0.4211-0.11470.00090.26260.0012-0.00030.00990.0089-0.0171-0.00130.00150.0023-0.00920.00160.00720.10750.0260.0206-0.005-0.0426.458216.8529-27.2666
470.05730.1997-0.167200.05070.1880.001-0.0052-0.00520.00450.00490.010.0132-0.0023-0.0059-0.01040.03680.020.0306-0.009-0.01416.766512.7871-12.2173
480.02880.33060.15560-0.33930.27270.00120.0003-0.0024-0.0066-0.00920.01610.0079-0.00080.008-0.00340.0152-0.00380.02150.0092-0.033621.12129.3242-28.3568
490.1751-0.60.23480.00920.927800.0003-0.00010.00870.00190.01130.01590.0102-0.0071-0.0116-0.01030.09620.0050.0035-0.0448-0.013921.262920.0331-19.1613
500.2837-0.67980.204100.10560-0.00260.0079-0.0017-0.00930.00150.01060.0091-0.01410.0011-0.00650.0656-0.03170.0089-0.0055-0.014615.205319.6217-29.4514
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|869 - A|880}
2X-RAY DIFFRACTION2{A|881 - A|907}
3X-RAY DIFFRACTION3{A|908 - A|915}
4X-RAY DIFFRACTION4{A|916 - A|926}
5X-RAY DIFFRACTION5{A|927 - A|934}
6X-RAY DIFFRACTION6{A|935 - A|943}
7X-RAY DIFFRACTION7{A|944 - A|950}
8X-RAY DIFFRACTION8{A|951 - A|976}
9X-RAY DIFFRACTION9{A|977 - A|984}
10X-RAY DIFFRACTION10{A|985 - A|997}
11X-RAY DIFFRACTION11{A|998 - A|1005}
12X-RAY DIFFRACTION12{A|1006 - A|1010}
13X-RAY DIFFRACTION13{A|1011 - A|1019}
14X-RAY DIFFRACTION14{A|1020 - A|1031}
15X-RAY DIFFRACTION15{A|1032 - A|1040}
16X-RAY DIFFRACTION16{A|1041 - A|1054}
17X-RAY DIFFRACTION17{A|1055 - A|1061}
18X-RAY DIFFRACTION18{A|1062 - A|1077}
19X-RAY DIFFRACTION19{A|1078 - A|1092}
20X-RAY DIFFRACTION20{A|1093 - A|1107}
21X-RAY DIFFRACTION21{B|869 - B|880}
22X-RAY DIFFRACTION22{B|881 - B|907}
23X-RAY DIFFRACTION23{B|908 - B|915}
24X-RAY DIFFRACTION24{B|916 - B|926}
25X-RAY DIFFRACTION25{B|927 - B|934}
26X-RAY DIFFRACTION26{B|935 - B|943}
27X-RAY DIFFRACTION27{B|944 - B|950}
28X-RAY DIFFRACTION28{B|951 - B|976}
29X-RAY DIFFRACTION29{B|977 - B|984}
30X-RAY DIFFRACTION30{B|985 - B|997}
31X-RAY DIFFRACTION31{B|998 - B|1005}
32X-RAY DIFFRACTION32{B|1006 - B|1010}
33X-RAY DIFFRACTION33{B|1011 - B|1019}
34X-RAY DIFFRACTION34{B|1020 - B|1031}
35X-RAY DIFFRACTION35{B|1032 - B|1040}
36X-RAY DIFFRACTION36{B|1041 - B|1054}
37X-RAY DIFFRACTION37{B|1055 - B|1061}
38X-RAY DIFFRACTION38{B|1062 - B|1077}
39X-RAY DIFFRACTION39{B|1078 - B|1092}
40X-RAY DIFFRACTION40{B|1093 - B|1107}
41X-RAY DIFFRACTION41{C|23 - C|53}
42X-RAY DIFFRACTION42{C|54 - C|70}
43X-RAY DIFFRACTION43{C|78 - C|101}
44X-RAY DIFFRACTION44{C|102 - C|123}
45X-RAY DIFFRACTION45{C|124 - C|152}
46X-RAY DIFFRACTION46{D|25 - D|53}
47X-RAY DIFFRACTION47{D|54 - D|79}
48X-RAY DIFFRACTION48{D|80 - D|101}
49X-RAY DIFFRACTION49{D|104 - D|123}
50X-RAY DIFFRACTION50{D|124 - D|150}

+
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://pdbjlvh1.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