[English] 日本語
Yorodumi
- PDB-2wzp: Structures of Lactococcal Phage p2 Baseplate Shed Light on a Nove... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wzp
TitleStructures of Lactococcal Phage p2 Baseplate Shed Light on a Novel Mechanism of Host Attachment and Activation in Siphoviridae
Components
  • CAMELID VHH5
  • LACTOCOCCAL PHAGE P2 ORF15
  • LACTOCOCCAL PHAGE P2 ORF16
  • PUTATIVE RECEPTOR BINDING PROTEINReceptor (biochemistry)
KeywordsVIRAL PROTEIN / BASEPLATE
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, long flexible tail mechanism / virus tail, baseplate / virus tail / entry receptor-mediated virion attachment to host cell / cell adhesion / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Laminin - #60 / Rhinovirus 14, subunit 4 - #40 / Phage tail base-plate attachment protein, domain D1/D2 / Elongation Factor Tu (Ef-tu); domain 3 - #210 / Jelly Rolls - #880 / Phage tail base-plate attachment protein, domain D3 / Phage tail base-plate attachment protein, domain D4 / Phage tail proteins - horseshoe like beta roll fold / : / : ...Laminin - #60 / Rhinovirus 14, subunit 4 - #40 / Phage tail base-plate attachment protein, domain D1/D2 / Elongation Factor Tu (Ef-tu); domain 3 - #210 / Jelly Rolls - #880 / Phage tail base-plate attachment protein, domain D3 / Phage tail base-plate attachment protein, domain D4 / Phage tail proteins - horseshoe like beta roll fold / : / : / : / Phage tail base-plate attachment protein C-terminal insertion domain / Phage tail base-plate attachment protein N0 domain / Phage tail base-plate attachment protein C-terminal barrel domain / Phage tail base-plate attachment protein ORF16 / Baseplate protein Gp15-like / Baseplate protein Gp16, domain D4 / Baseplate protein Gp16, domain 1 and 2 / : / Distal tail protein, N-terminal domain / Phage tail base-plate attachment protein N-terminal barrel domain / Dit, C-terminal domain / Triple-stranded beta-helix / Phage fibre proteins / Phage tail base-plate Siphoviridae RBP, head domain / : / : / Lactophage receptor-binding protein N-terminal shoulder domain / Lactococcus phage p2, Receptor binding protein, neck domain / Rhinovirus 14, subunit 4 / Receptor-binding protein of phage tail base-plate Siphoviridae, head / Lactophage receptor-binding protein C-terminal head domain / Phage tail protein beta-alpha-beta fold / Phage tail proteins - 2 layer sandwich fold / Adenovirus pIV-like, attachment domain / 3-Layer(bab) Sandwich / Other non-globular / Laminin / Elongation Factor Tu (Ef-tu); domain 3 / Special / Ribbon / Roll / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Baseplate protein gp16 / Distal tail protein / Receptor binding protein / Receptor binding protein
Similarity search - Component
Biological speciesLACTOCOCCUS PHAGE P2 (virus)
LAMA GLAMA (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSciara, G. / Bebeacua, C. / Bron, P. / Tremblay, D. / Ortiz-Lombardia, M. / Lichiere, J. / van Heel, M. / Campanacci, V. / Moineau, S. / Cambillau, C.
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2010
Title: Structure of lactococcal phage p2 baseplate and its mechanism of activation.
Authors: Giuliano Sciara / Cecilia Bebeacua / Patrick Bron / Denise Tremblay / Miguel Ortiz-Lombardia / Julie Lichière / Marin van Heel / Valérie Campanacci / Sylvain Moineau / Christian Cambillau /
Abstract: Siphoviridae is the most abundant viral family on earth which infects bacteria as well as archaea. All known siphophages infecting gram+ Lactococcus lactis possess a baseplate at the tip of their ...Siphoviridae is the most abundant viral family on earth which infects bacteria as well as archaea. All known siphophages infecting gram+ Lactococcus lactis possess a baseplate at the tip of their tail involved in host recognition and attachment. Here, we report analysis of the p2 phage baseplate structure by X-ray crystallography and electron microscopy and propose a mechanism for the baseplate activation during attachment to the host cell. This approximately 1 MDa, Escherichia coli-expressed baseplate is composed of three protein species, including six trimers of the receptor-binding protein (RBP). RBPs host-recognition domains point upwards, towards the capsid, in agreement with the electron-microscopy map of the free virion. In the presence of Ca(2+), a cation mandatory for infection, the RBPs rotated 200 degrees downwards, presenting their binding sites to the host, and a channel opens at the bottom of the baseplate for DNA passage. These conformational changes reveal a novel siphophage activation and host-recognition mechanism leading ultimately to DNA ejection.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Lactococcal Bacteriophage P2 Receptor-Binding Protein Structure Suggests a Common Ancestor Gene with Bacterial and Mammalian Viruses.
Authors: Spinelli, S. / Desmyter, A. / Verrips, C.T. / De Haard, H.J.W. / Moineau, S. / Cambillau, C.
History
DepositionDec 1, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet
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 / _struct_sheet.number_strands
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PUTATIVE RECEPTOR BINDING PROTEIN
B: PUTATIVE RECEPTOR BINDING PROTEIN
C: PUTATIVE RECEPTOR BINDING PROTEIN
D: CAMELID VHH5
E: CAMELID VHH5
F: CAMELID VHH5
G: PUTATIVE RECEPTOR BINDING PROTEIN
H: PUTATIVE RECEPTOR BINDING PROTEIN
I: PUTATIVE RECEPTOR BINDING PROTEIN
J: CAMELID VHH5
K: CAMELID VHH5
L: CAMELID VHH5
P: LACTOCOCCAL PHAGE P2 ORF15
Q: LACTOCOCCAL PHAGE P2 ORF15
R: LACTOCOCCAL PHAGE P2 ORF16


Theoretical massNumber of molelcules
Total (without water)372,97015
Polymers372,97015
Non-polymers00
Water36,1922009
1
A: PUTATIVE RECEPTOR BINDING PROTEIN
B: PUTATIVE RECEPTOR BINDING PROTEIN
C: PUTATIVE RECEPTOR BINDING PROTEIN
D: CAMELID VHH5
E: CAMELID VHH5
F: CAMELID VHH5
G: PUTATIVE RECEPTOR BINDING PROTEIN
H: PUTATIVE RECEPTOR BINDING PROTEIN
I: PUTATIVE RECEPTOR BINDING PROTEIN
J: CAMELID VHH5
K: CAMELID VHH5
L: CAMELID VHH5
P: LACTOCOCCAL PHAGE P2 ORF15
Q: LACTOCOCCAL PHAGE P2 ORF15
R: LACTOCOCCAL PHAGE P2 ORF16

A: PUTATIVE RECEPTOR BINDING PROTEIN
B: PUTATIVE RECEPTOR BINDING PROTEIN
C: PUTATIVE RECEPTOR BINDING PROTEIN
D: CAMELID VHH5
E: CAMELID VHH5
F: CAMELID VHH5
G: PUTATIVE RECEPTOR BINDING PROTEIN
H: PUTATIVE RECEPTOR BINDING PROTEIN
I: PUTATIVE RECEPTOR BINDING PROTEIN
J: CAMELID VHH5
K: CAMELID VHH5
L: CAMELID VHH5
P: LACTOCOCCAL PHAGE P2 ORF15
Q: LACTOCOCCAL PHAGE P2 ORF15
R: LACTOCOCCAL PHAGE P2 ORF16

A: PUTATIVE RECEPTOR BINDING PROTEIN
B: PUTATIVE RECEPTOR BINDING PROTEIN
C: PUTATIVE RECEPTOR BINDING PROTEIN
D: CAMELID VHH5
E: CAMELID VHH5
F: CAMELID VHH5
G: PUTATIVE RECEPTOR BINDING PROTEIN
H: PUTATIVE RECEPTOR BINDING PROTEIN
I: PUTATIVE RECEPTOR BINDING PROTEIN
J: CAMELID VHH5
K: CAMELID VHH5
L: CAMELID VHH5
P: LACTOCOCCAL PHAGE P2 ORF15
Q: LACTOCOCCAL PHAGE P2 ORF15
R: LACTOCOCCAL PHAGE P2 ORF16


Theoretical massNumber of molelcules
Total (without water)1,118,90945
Polymers1,118,90945
Non-polymers00
Water75742
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area188190 Å2
ΔGint-900.5 kcal/mol
Surface area372360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.881, 202.881, 760.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein
PUTATIVE RECEPTOR BINDING PROTEIN / Receptor (biochemistry)


Mass: 28881.230 Da / Num. of mol.: 6 / Fragment: RESIDUES 2-264
Source method: isolated from a genetically manipulated source
Details: LACTOCOCCAL PHAGE P2 ORF18 / Source: (gene. exp.) LACTOCOCCUS PHAGE P2 (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q1RNF7, UniProt: Q71AW2*PLUS
#2: Antibody
CAMELID VHH5


Mass: 13499.944 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LAMA GLAMA (llama) / Organ: LYMPHOCYTESLymphocyte / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
#3: Protein LACTOCOCCAL PHAGE P2 ORF15


Mass: 37899.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS PHAGE P2 (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: D3WAD3*PLUS
#4: Protein LACTOCOCCAL PHAGE P2 ORF16


Mass: 42883.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS PHAGE P2 (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: D3KFX4*PLUS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2009 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAINS P AND Q: PHAGE P2 SEQUENCE IS DEPOSITED IN GENBANK, NR GQ253898

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.87 Å3/Da / Density % sol: 68.2 % / Description: NONE
Crystal growpH: 7
Details: 4 MG/ML OF COMPLEX, 25% PEG 2000 MME, 0.1 M NA-HEPES PH 7.5.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9708
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9708 Å / Relative weight: 1
ReflectionResolution: 2.6→48.7 Å / Num. obs: 184640 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 59.46 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.1
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
BUSTER2.9.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZRU

1zru


Resolution: 2.6→38.07 Å / Cor.coef. Fo:Fc: 0.8463 / Cor.coef. Fo:Fc free: 0.8227 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE BIOLOGICAL UNIT, THE BASEPLATE SHOULD BE RECONSTITUTED USING THE 3-FOLD CRYSTALLOGRAPHIC SYMMETRY
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 3689 2.01 %RANDOM
Rwork0.1789 ---
obs0.1794 183300 --
Displacement parametersBiso mean: 64.43 Å2
Baniso -1Baniso -2Baniso -3
1--17.5803 Å20 Å20 Å2
2---17.5803 Å20 Å2
3---35.1607 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25638 0 0 2009 27647
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00926166HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1535533HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8918SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes700HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3789HARMONIC5
X-RAY DIFFRACTIONt_it26166HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion18.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3510SEMIHARMONIC5
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_contact29933SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2918 254 1.88 %
Rwork0.2593 13268 -
all0.2599 13522 -
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)
10.68591.66551.02753.0943-1.03861.30810.0084-0.0464-0.0190.0233-0.04410.01850.06470.02130.03570.1115-0.11870.0359-0.07910.0654-0.05715.648249.1337344.07
2-0.65631.2749-1.18032.06381.22050.11550.0057-0.01980.01260.01590.00680.0054-0.0331-0.0103-0.01250.1309-0.13270.0569-0.0668-0.1155-0.056534.5701100.3068357.464
31.8443-0.07021.5332-0.6959-0.91030.5376-0.01810.013-0.00730.01250.01540.00370.02740.0240.0028-0.0031-0.0157-0.09260.08310.1204-0.093967.376754.8076365.42
42.7919-0.8042-0.2137-1.38810.09281.1996-0.00650.01910.0212-0.01950.01340.0514-0.0189-0.0076-0.0069-0.11380.09880.20590.1191-0.05270.0337-55.172158.8868337.41
5-0.20330.9583-0.2913.83581.03061.2025-0.003-0.01420.02790.0105-0.0032-0.0217-0.01740.01970.00620.21840.0064-0.0551-0.14-0.2063-0.0749-6.393980.006355.134
6-0.4141-0.1373-0.52592.8905-1.05852.5302-0.0016-0.0255-0.06010.02340.0050.01420.04920.0018-0.00340.1786-0.05240.14430.04910.0524-0.2444-19.513924.7348364.761
73.0635-1.56141.01680.5112-0.74790.12460.0542-0.1527-0.08230.0696-0.0891-0.10930.17080.19780.0349-0.27370.1603-0.1551-0.10770.08590.298274.900467.5522304.098
81.38480.06510.13980.7227-0.24330.44860.0558-0.2533-0.02940.1275-0.1009-0.1748-0.03640.240.0452-0.3070.0499-0.1523-0.02660.02980.289263.772789.4044301.751
91.640.10650.59141.1767-0.1280.25580.0545-0.0844-0.13620.0052-0.1308-0.11290.29520.13230.0763-0.240.1659-0.0334-0.12920.08740.30152.894768.9088293.142
100.2860.3130.08731.1746-0.52231.28250.0314-0.1354-0.01240.1658-0.0375-0.13860.1959-0.11570.0061-0.0793-0.0265-0.0123-0.2511-0.02210.29321.367325.0297304.967
110.470.24890.11751.05240.44481.02110.0102-0.15620.09360.20270.0032-0.1431-0.18970.0525-0.0134-0.0745-0.0108-0.0413-0.258-0.04410.29211.439647.21303.039
120.9166-0.220.22080.4511-0.23511.37490.0878-0.05770.01060.156-0.09190.0933-0.0923-0.41360.0041-0.16030.02720.045-0.1878-0.06770.2882-10.722642.7348292.908
132.80821.16772.29720.41231.34230.70550.028-0.04540.04380.0057-0.02530.0013-0.00460.0203-0.00270.022-0.2056-0.19970.07510.0602-0.125549.980979.7531346.858
142.16830.6255-0.02390.0154-0.50951.43280.0524-0.0590.02920.0659-0.09230.02330.00460.02670.03990.0258-0.1335-0.08650.02920.0294-0.040932.998869.9866338.652
153.3404-0.89152.4736-1.8167-1.68411.60850.0135-0.01750.0150.0341-0.0383-0.01190.0440.01610.0248-0.0796-0.0093-0.05630.18090.1407-0.068450.012258.623344.322
160.5699-0.2501-0.2282.17281.75421.8063-0.0003-0.10790.01310.0677-0.0055-0.0262-0.0641-0.00040.00580.1459-0.01660.105-0.0343-0.1133-0.1019-10.056554.0318345.792
171.9183-0.9385-1.48361.81020.37880.26150.0188-0.02240.0361-0.00280.01690.0214-0.0443-0.0861-0.03570.00970.22570.19380.0222-0.0624-0.0143-27.470559.6617335.232
180.43570.7969-0.83930.9111-0.31641.6970.0269-0.0769-0.01370.0333-0.0113-0.00210.0279-0.1325-0.0156-0.0373-0.00370.2020.1291-0.0558-0.0512-25.362539.7802342.28
191.22060.72910.17170.83210.11760.5419-0.0052-0.0488-0.02560.2048-0.0558-0.1088-0.0006-0.01010.061-0.12130.042-0.0124-0.21650.01260.29416.569992.7617302.288
200.47130.4803-0.07561.937-0.41210.1851-0.03360.0581-0.0036-0.06580.01670.03210.062-0.04130.0169-0.12430.0329-0.0114-0.25210.0040.293713.932964.1891280.199
21-0.14910.0668-0.03752.99080.51020.5471-0.0935-0.04980.02860.20180.0073-0.1206-0.00290.11480.0862-0.1542-0.0142-0.0505-0.1615-0.00930.251429.4919119.1671302.187
221.3638-0.09660.06461.0781-0.39050.6568-0.04210.0346-0.0683-0.06750.01140.018-0.050.28690.0307-0.30160.0295-0.0518-0.10080.00140.297151.4648101.3219279.319
230.85060.10590.32641.174-0.50271.01530.03680.0552-0.02050.0184-0.065-0.18040.04590.17580.0282-0.23650.01580.0222-0.1906-0.01370.301425.4239109.6835254.761
240.76180.12520.39360.5640.14661.50210.0192-0.0168-0.0676-0.014-0.0073-0.0460.1141-0.0195-0.0119-0.17350.01170.0137-0.2418-0.0110.3016.14594.0541251.472
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN D AND RESID 2:123)
2X-RAY DIFFRACTION2(CHAIN E AND RESID 2:123)
3X-RAY DIFFRACTION3(CHAIN F AND RESID 2:123)
4X-RAY DIFFRACTION4(CHAIN J AND RESID 2:123)
5X-RAY DIFFRACTION5(CHAIN K AND RESID 2:123)
6X-RAY DIFFRACTION6(CHAIN L AND RESID 2:123)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 2:161)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 2:161)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 2:161)
10X-RAY DIFFRACTION10(CHAIN G AND RESID 2:161)
11X-RAY DIFFRACTION11(CHAIN H AND RESID 2:161)
12X-RAY DIFFRACTION12(CHAIN I AND RESID 2:161)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 162:267)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 162:267)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 162:267)
16X-RAY DIFFRACTION16(CHAIN G AND RESID 162:267)
17X-RAY DIFFRACTION17(CHAIN H AND RESID 162:267)
18X-RAY DIFFRACTION18(CHAIN I AND RESID 162:267)
19X-RAY DIFFRACTION19(CHAIN P AND RESID 1:135)
20X-RAY DIFFRACTION20(CHAIN P AND RESID 136:298)
21X-RAY DIFFRACTION21(CHAIN Q AND RESID 1:135)
22X-RAY DIFFRACTION22(CHAIN Q AND RESID 136:298)
23X-RAY DIFFRACTION23(CHAIN R AND RESID 1:213)
24X-RAY DIFFRACTION24(CHAIN R AND RESID 214:375)

+
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