[English] 日本語
Yorodumi
- PDB-4y7l: T6SS protein TssM C-terminal domain (869-1107) from EAEC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y7l
TitleT6SS protein TssM C-terminal domain (869-1107) from EAEC
ComponentsType VI secretion protein IcmF
KeywordsMEMBRANE PROTEIN / Type 6 secretion system / Alpha-beta fold / periplasmic protein
Function / homology: / : / Type VI secretion protein IcmF helical domain / Type VI secretion system IcmF, C-terminal / Type VI secretion protein IcmF C2-like domain / metal ion binding / : / Type VI secretion protein IcmF
Function and homology information
Biological speciesEscherichia coli 2-156-04_S3_C3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsNguyen, V.S. / Spinelli, S. / Durand, E. / Roussel, A. / Cambillau, C.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE14-0006-02 France
French National Research AgencyANR-10-JCJC-1303-03 France
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 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Type VI secretion protein IcmF
B: Type VI secretion protein IcmF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5549
Polymers53,0162
Non-polymers5387
Water9,656536
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-127 kcal/mol
Surface area21280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.030, 64.030, 249.660
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 / TssM


Mass: 26508.033 Da / Num. of mol.: 2 / Fragment: C-terminal domain, UNP residues 868-1107
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 2-156-04_S3_C3 (bacteria)
Gene: AC43_2230 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A070IVV8, UniProt: A0A0M3KL15*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 536 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.1M NaAc pH 4.0 and 0.2M ZnCl2. / PH range: 3.8 - 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.51→30 Å / Num. all: 82164 / Num. obs: 82164 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 23.72 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 19.2
Reflection shellResolution: 1.51→1.55 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3 / % possible all: 97

-
Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y7M
Resolution: 1.51→22.11 Å / Cor.coef. Fo:Fc: 0.9574 / Cor.coef. Fo:Fc free: 0.9561 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.08 / SU Rfree Blow DPI: 0.074 / SU Rfree Cruickshank DPI: 0.07
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 4107 5 %RANDOM
Rwork0.1913 ---
obs0.1919 82127 99.23 %-
Displacement parametersBiso mean: 29.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.2734 Å20 Å20 Å2
2---0.2734 Å20 Å2
3---0.5468 Å2
Refine analyzeLuzzati coordinate error obs: 0.215 Å
Refinement stepCycle: 1 / Resolution: 1.51→22.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3784 0 22 536 4342
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013909HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.035357HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1306SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes83HARMONIC2
X-RAY DIFFRACTIONt_gen_planes591HARMONIC5
X-RAY DIFFRACTIONt_it3909HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.03
X-RAY DIFFRACTIONt_other_torsion14.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion511SEMIHARMONIC5
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_contact4757SEMIHARMONIC4
LS refinement shellResolution: 1.51→1.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2761 268 5 %
Rwork0.2399 5091 -
all0.2417 5359 -
obs--99.23 %
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)
10.068-0.0575-0.09760.004-0.17050.00090.00250.0029-0.0005-0.0033-0.00470.00240.0013-0.00690.0021-0.01190.02370.07160.00630.07890.0081-25.9776-7.6937-4.2747
20.35360.16890.12870.83720.41920.3546-0.0108-0.0396-0.00170.00940.01150.0224-0.02750.021-0.00060.07160.0011-0.0131-0.01260.0079-0.0585-11.11848.4254-9.8272
30.06370.02140.08830.0851-0.1710.0878-0.0010.002-0.00370.0006-0.0026-0.0044-0.00230.00170.00360.0170.00930.00510.01660.0229-0.0284-6.6459-1.7286-9.9816
40.107-0.10090.07520.168-0.12240.00840.0008-0.0007-0.0083-0.00040.00610.0092-0.00180.0077-0.0069-0.01540.02480.0225-0.00840.04250.0291-11.5492-9.6505-7.9991
500.0262-0.007700.040200.00010.0022-0.0023-0.00380.00110.0030.00250.001-0.0013-0.0092-0.0114-0.0015-0.00760.00980.0181-18.232-15.5388-13.5737
60.0089-0.0176-0.0260.02040.04470.01510.00040.00030.00010-0.00020.00030.0010.0004-0.00020.005-0.00980.001-0.0051-0.01050.0036-17.2044-13.7837-20.8587
70.00650.00170.00450.0028-0.00270-0.00010.00030.00020.0005-0.00010.00010.000500.0001-0.0018-0.00380.0008-0.00010.00410.0034-31.2221-12.3916-12.8203
80.12-0.77110.23870.9168-0.61490.1861-0.00320.0028-0.008-0.00070.03490.00050.0009-0.0151-0.03170.0493-0.0404-0.0184-0.04320.0023-0.0113-12.0186-3.8683-17.9771
90.00150.1675-0.04520.28480.34070.1290.0016-0.0009-0.0036-0.00390.0015-0.0075-0.00160.0005-0.00310.0429-0.03720.0495-0.0377-0.0026-0.00625.32784.8486-31.3354
100.03330.34710.00380.77980.72650.25180.00380.0075-0.0118-0.0091-0.0027-0.0154-0.0012-0.0048-0.00110.064-0.01080.0559-0.04030.0306-0.02477.525517.8274-34.0415
110.00180.1089-0.07080.320.19220.03470.0002-0.0011-0.0048-0.00470.0018-0.00680.00010.0024-0.0020.0294-0.00810.0463-0.02930.03230.001112.517514.1054-32.0363
120.0003-0.0439-0.11340.04240.077200.00010.0008000.0005-0.00020.00250.0001-0.00070.01320.00060.0257-0.014-0.00640.005311.48137.1278-38.9497
1300.17490.0130.2476-0.16290.049600.0015-0.0045-0.0026-0.002-0.01410.0020.00080.00190.0353-0.026-0.009-0.03460.0117-0.00287.68636.478-21.1258
140.0990.0937-0.1220.82220.82610.23830.0047-0.0113-0.0002-0.01080.0041-0.0314-0.00370.0005-0.00880.0711-0.00680.0439-0.05040.0371-0.02236.594420.4979-27.3615
150-0.0657-0.1940.35960.35580.09480.0014-0.0002-0.00050.0037-0.0012-0.00090.0044-0.0019-0.00020.0622-0.01580.0427-0.05030.022-0.00824.922726.3308-30.8465
160.10270.2495-0.01660.3722-0.02330.18080.00130.00350.0067-0.00020.00120.0012-0.0015-0.0051-0.00250.1065-0.04680.0084-0.02540.0131-0.0738-2.456413.6321-21.5759
1700.00660.00650.022-0.03550.0380.00030.001-0.0040-0.0018-0.0016-0.00030.00260.00150.0077-0.0207-0.01030.0028-0.0023-0.0071-6.24647.198-38.2697
180.0014-0.0343-0.20890.11570.09880.74570.00080.0119-0.007400.00060.0024-0.0098-0.0143-0.00140.0565-0.01510.0221-0.01770.0277-0.037-1.951715.5077-36.6557
1900.2861-0.37320.3470.87650.7099-0.0001-0.0058-0.0212-0.00950.0076-0.0057-0.01620.0052-0.00750.0777-0.0580.0505-0.0357-0.0016-0.0424-0.54944.8535-31.498
200.14370.02070.55580.21520.13710.2428-0.0077-0.0056-0.0261-0.01620.00690.0387-0.03710.0010.00080.0438-0.0104-0.0062-0.02240.0521-0.0191-19.11381.9964-15.5557
210.1106-0.075-0.09360.11250.29750.2495-0.0017-0.00080.0042-0.0013-0.007-0.0050.00120.00510.0088-0.0684-0.0214-0.02480.0353-0.05580.039228.57610.7385.9565
221.021-0.20470.21390.29440.39940.0068-0.0024-0.04610.00770.0039-0.0105-0.01620.03-0.0120.01290.0031-0.01650.00630.02180.005-0.021216.1031-7.63860.6201
230.06170.11830.04580.05410.11690.0534-0.0012-0.00530.0014-0.00290.0010.0021-0.00360.00110.0002-0.0032-0.0110.00270.0213-0.0254-0.012713.04911.3646-5.6735
240.09760.01180.10730.1882-0.14510.0141-0.00150.00240.0070.00060.0009-0.0025-0.0012-0.0030.0006-0.0064-0.0027-0.0598-0.0122-0.01770.021516.61719.5622-4.2878
250.00030.133-0.05750.03490.03250.00060.00040.00270.003-0.0025-0.0021-0.0033-0.00070.00010.0017-0.0012-0.0223-0.0077-0.0099-0.00750.009925.74914.3411-8.0873
260.00690.0207-0.01280-0.02860.02880.00050.0012-0.0003-0.0029-0.00090.0002-0.0006-0.00060.00040.0038-0.01360.0120.00070.0060.000327.3079.3906-14.2512
270.02350.0015-0.01260.001-0.0091000.0005-0.001-0.0007-0.00050-0.0014-0.00150.0005-0.0032-0.01210.0010.0005-0.00210.005538.129515.9087-2.7751
280.1329-0.1223-0.10810.16550.30040.1416-0.0012-0.00670.0144-0.04380.0115-0.02790.01080.0168-0.01030.0152-0.02290.0229-0.01940.00040.011421.48670.9757-10.6695
290.06840.2456-0.34290.221-0.41690.328700.00250.0005-0.0006-0.00020.00010-0.00060.00020.0522-0.00790.0358-0.0352-0.0381-0.016111.0606-14.791-25.4105
300.1060.3474-0.40480.3911-0.38070.2647-0.00260.001-0.0083-0.0064-0.0066-0.00850.00030.00120.00930.02310.00580.0196-0.0585-0.06820.03669.3453-28.562-23.0626
310.20270.3652-0.09510.14980.01150.037-0.0005-0.00110.0001-0.00750.0009-0.00080.0037-0.0048-0.00030.024-0.00060.0027-0.0348-0.06950.01524.747-24.3928-24.5884
320.00110.00290.01560.017-0.04390.08080.00050.0006-0.0006-0.00120.00080.0002-0.00220-0.00130.02980.00680.0023-0.014-0.0246-0.01138.6932-21.6981-33.3627
330.03930.0078-0.22540.258-0.15280.01320.00060.0011-0.0113-0.00750.00410.0117-0.00220.0032-0.00470.0298-0.00390.0278-0.0196-0.0201-0.01034.9863-12.0253-18.0196
340.4010.3393-0.3020.1984-0.27270.0968-0.0024-0.0001-0.0178-0.00680.0111-0.00250.0011-0.0225-0.00870.0185-0.00150.0263-0.0671-0.03820.04847.5535-28.3555-16.5631
350.12290.0412-0.21520.1195-0.06010.09960.00190.00270.00020.00030.00030.0012-0.0019-0.0003-0.00220.0146-0.03020.0306-0.0506-0.00110.040910.201-33.2417-14.7924
360.04840.0691-0.11180.43090.03860.0133-0.002-0.0038-0.01350.00540.0033-0.007-0.0089-0.0042-0.00120.025-0.01940.0338-0.0345-0.00750.016113.4711-17.6331-10.6444
370.0291-0.0316-0.01220.0280.01370.00860.00020.0010.0008-0.0026-0.00110.0008-0.0006-0.00010.0009-0.0054-0.01340.02750.00210.00880.008124.1776-18.7911-23.693
380.3375-0.3362-0.62210.12790.23980.14960.00050.0178-0.0116-0.0033-0.00020.0028-0.00370.0154-0.00030.0015-0.00640.0496-0.0386-0.02210.041119.2996-24.426-22.1867
390.12290.2479-0.5250.0947-0.10870.4492-0.00010.0029-0.001-0.0041-0.0040.00090.00490.00370.00410.0431-0.02810.0532-0.0442-0.02530.004216.4836-14.02-23.0959
400.6351-0.083-0.09360.12140.20010-0.0043-0.0221-0.0126-0.00380.0022-0.00810.01470.0150.0021-0.011-0.01190.0253-0.0253-0.00530.041125.9585-3.0112-3.3944
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|948 - 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|868 - 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|942}
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}

+
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