[English] 日本語
Yorodumi
- PDB-9f4a: Interface between baseplate cup and extended tail tube/sheath of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9f4a
TitleInterface between baseplate cup and extended tail tube/sheath of Klebsiella phage KP1 variant vB_Kpn_Lilla1
Components
  • (Baseplate wedge ...) x 6
  • Baseplate central spike protein
  • Baseplate subunit
  • Baseplate tail tube cap
  • IraD/Gp25-like domain-containing protein
  • Long tail fiber proximal subunit
  • Putative baseplate hub subunit
  • Tail sheath protein
  • Tail tube protein
KeywordsVIRUS / Baseplate cup / baseplate wedge / fibers
Function / homology
Function and homology information


virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / symbiont entry into host cell via disruption of host cell envelope / viral tail assembly / viral release from host cell / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme ...virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / symbiont entry into host cell via disruption of host cell envelope / viral tail assembly / viral release from host cell / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / structural molecule activity / membrane
Similarity search - Function
Baseplate tail-tube protein gp48, T4-like virus / Tail-tube assembly protein / : / Long-tail fiber proximal subunit, C-terminal, second / Baseplate wedge protein gp53, bacteriophage T4 / Baseplate wedge protein gp7 / : / : / : / Base plate wedge protein 53 ...Baseplate tail-tube protein gp48, T4-like virus / Tail-tube assembly protein / : / Long-tail fiber proximal subunit, C-terminal, second / Baseplate wedge protein gp53, bacteriophage T4 / Baseplate wedge protein gp7 / : / : / : / Base plate wedge protein 53 / Baseplate wedge protein gp7, domain V / Baseplate wedge protein gp7, helical domain / Baseplate wedge protein gp7, domain VI / Bacteriophage T4, Gp27, baseplate hub, C-terminal / Bacteriophage T4, Gp27, baseplate hub, N-terminal / Gp27, baseplate hub, domain 3 / Gp27, baseplate hub, domain 4 / Gp27, baseplate hub, domain 2 / Baseplate structural protein, domain 2 / Baseplate structural protein, domain 1 / : / Tail sheath protein Gp18-like domain I / Baseplate wedge protein gp10 / Baseplate wedge protein gp6 / : / : / : / : / : / : / Baseplate wedge protein gp6-like, helical domain / Baseplate structural protein gp6, C-terminal domain I / Baseplate structural protein gp6, C-terminal domain II / Baseplate wedge protein gp6, domain II / Baseplate structural protein gp6, C-terminal domain III / Baseplate wedge protein gp10 domain 3 / Baseplate structural protein Gp9 C-terminal domain superfamily / Bacteriophage T4, Gp8 / Bacteriophage T4, Gp8 superfamily / Bacteriophage T4, Gp8 / : / Baseplate structural protein Gp10, C-terminal domain / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / : / Bacteriophage T4 gp9/10-like protein, N-terminal / Bacteriophage T4 gp9/10-like protein, C-terminal / Protein Gp5, N-terminal OB-fold domain / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / : / Bacteriophage T4 gp5 C-terminal trimerisation domain / : / Tail sheath protein Gp18 domain III N-terminal region / IraD/Gp25-like / Phage tail sheath protein, beta-sandwich domain / Baseplate wedge protein gp25 / Phage tail sheath protein beta-sandwich domain / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Lysozyme-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold
Similarity search - Domain/homology
IraD/Gp25-like domain-containing protein / Baseplate wedge protein gp6 / Baseplate wedge subunit / Baseplate wedge tail fiber connector / Tail sheath protein / Baseplate wedge protein gp10 / Tail tube protein / Baseplate wedge protein gp7 / Baseplate tail tube cap / Baseplate wedge subunit ...IraD/Gp25-like domain-containing protein / Baseplate wedge protein gp6 / Baseplate wedge subunit / Baseplate wedge tail fiber connector / Tail sheath protein / Baseplate wedge protein gp10 / Tail tube protein / Baseplate wedge protein gp7 / Baseplate tail tube cap / Baseplate wedge subunit / Long tail fiber proximal subunit / Baseplate subunit / Putative baseplate hub subunit / Baseplate central spike protein
Similarity search - Component
Biological speciesKlebsiella phage KP1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsOrlova, E.V. / Isupov, M.N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Baseplate cup of Klebsiella phage KP1 variant vB_Kpn_Lilla1
Authors: Orlova, E.V. / Isupov, M.N.
History
DepositionApr 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
Le: Long tail fiber proximal subunit
Lf: Long tail fiber proximal subunit
Lg: Long tail fiber proximal subunit
Lh: Long tail fiber proximal subunit
Li: Long tail fiber proximal subunit
Lj: Long tail fiber proximal subunit
LS: Long tail fiber proximal subunit
LT: Long tail fiber proximal subunit
LU: Long tail fiber proximal subunit
LV: Long tail fiber proximal subunit
LW: Long tail fiber proximal subunit
LX: Long tail fiber proximal subunit
LY: Long tail fiber proximal subunit
LZ: Long tail fiber proximal subunit
La: Long tail fiber proximal subunit
Lb: Long tail fiber proximal subunit
Lc: Long tail fiber proximal subunit
Ld: Long tail fiber proximal subunit
BM: Baseplate tail tube cap
BK: Baseplate tail tube cap
BO: Baseplate tail tube cap
BP: Baseplate tail tube cap
BL: Baseplate tail tube cap
BN: Baseplate tail tube cap
BQ: Baseplate subunit
BV: Baseplate subunit
BS: Baseplate subunit
BR: Baseplate subunit
BT: Baseplate subunit
BU: Baseplate subunit
AX: Baseplate wedge protein gp6
AW: Baseplate wedge protein gp6
AT: Baseplate wedge protein gp6
AS: Baseplate wedge protein gp6
AV: Baseplate wedge protein gp6
AU: Baseplate wedge protein gp6
AR: Baseplate wedge protein gp6
AQ: Baseplate wedge protein gp6
AN: Baseplate wedge protein gp6
AM: Baseplate wedge protein gp6
AP: Baseplate wedge protein gp6
AO: Baseplate wedge protein gp6
AY: Baseplate wedge protein gp7
AZ: Baseplate wedge protein gp7
A0: Baseplate wedge protein gp7
A1: Baseplate wedge protein gp7
A2: Baseplate wedge protein gp7
A3: Baseplate wedge protein gp7
A4: Baseplate wedge subunit
A9: Baseplate wedge subunit
A6: Baseplate wedge subunit
A5: Baseplate wedge subunit
A8: Baseplate wedge subunit
A7: Baseplate wedge subunit
Ad: Baseplate wedge subunit
Ac: Baseplate wedge subunit
Af: Baseplate wedge subunit
Ae: Baseplate wedge subunit
Ab: Baseplate wedge subunit
Aa: Baseplate wedge subunit
LN: Baseplate wedge tail fiber connector
LO: Baseplate wedge tail fiber connector
LM: Baseplate wedge tail fiber connector
LQ: Baseplate wedge tail fiber connector
LR: Baseplate wedge tail fiber connector
LP: Baseplate wedge tail fiber connector
LB: Baseplate wedge tail fiber connector
LC: Baseplate wedge tail fiber connector
LA: Baseplate wedge tail fiber connector
LE: Baseplate wedge tail fiber connector
LF: Baseplate wedge tail fiber connector
LD: Baseplate wedge tail fiber connector
LH: Baseplate wedge tail fiber connector
LI: Baseplate wedge tail fiber connector
LG: Baseplate wedge tail fiber connector
LK: Baseplate wedge tail fiber connector
LL: Baseplate wedge tail fiber connector
LJ: Baseplate wedge tail fiber connector
FA: Baseplate wedge protein gp10
FB: Baseplate wedge protein gp10
FC: Baseplate wedge protein gp10
FJ: Baseplate wedge protein gp10
FK: Baseplate wedge protein gp10
FL: Baseplate wedge protein gp10
FS: Baseplate wedge protein gp10
FT: Baseplate wedge protein gp10
FU: Baseplate wedge protein gp10
Fb: Baseplate wedge protein gp10
Fc: Baseplate wedge protein gp10
Fd: Baseplate wedge protein gp10
Fk: Baseplate wedge protein gp10
Fl: Baseplate wedge protein gp10
Fm: Baseplate wedge protein gp10
Ft: Baseplate wedge protein gp10
Fu: Baseplate wedge protein gp10
Fv: Baseplate wedge protein gp10
SA: Tail sheath protein
SB: Tail sheath protein
SC: Tail sheath protein
SD: Tail sheath protein
SE: Tail sheath protein
SF: Tail sheath protein
SK: Tail sheath protein
SG: Tail sheath protein
SL: Tail sheath protein
SH: Tail sheath protein
SI: Tail sheath protein
SJ: Tail sheath protein
SQ: Tail sheath protein
SP: Tail sheath protein
SM: Tail sheath protein
SN: Tail sheath protein
SO: Tail sheath protein
SR: Tail sheath protein
SW: Tail sheath protein
SS: Tail sheath protein
ST: Tail sheath protein
SU: Tail sheath protein
SV: Tail sheath protein
SX: Tail sheath protein
SY: Tail sheath protein
SZ: Tail sheath protein
Sa: Tail sheath protein
Sb: Tail sheath protein
Sc: Tail sheath protein
Sd: Tail sheath protein
Se: Tail sheath protein
Sf: Tail sheath protein
Sg: Tail sheath protein
Sh: Tail sheath protein
Si: Tail sheath protein
Sj: Tail sheath protein
Sk: Tail sheath protein
Sl: Tail sheath protein
Sm: Tail sheath protein
Sn: Tail sheath protein
So: Tail sheath protein
Sp: Tail sheath protein
TM: Tail tube protein
TN: Tail tube protein
TO: Tail tube protein
TP: Tail tube protein
TQ: Tail tube protein
TR: Tail tube protein
TW: Tail tube protein
TS: Tail tube protein
TT: Tail tube protein
TU: Tail tube protein
TV: Tail tube protein
TX: Tail tube protein
TY: Tail tube protein
TZ: Tail tube protein
Ta: Tail tube protein
Tb: Tail tube protein
Tc: Tail tube protein
Td: Tail tube protein
Te: Tail tube protein
Tf: Tail tube protein
Tg: Tail tube protein
Th: Tail tube protein
Ti: Tail tube protein
Tj: Tail tube protein
Tk: Tail tube protein
Tl: Tail tube protein
Tm: Tail tube protein
Tn: Tail tube protein
To: Tail tube protein
Tp: Tail tube protein
Tq: Tail tube protein
Tr: Tail tube protein
Ts: Tail tube protein
Tt: Tail tube protein
Tu: Tail tube protein
Tv: Tail tube protein
AA: IraD/Gp25-like domain-containing protein
AB: IraD/Gp25-like domain-containing protein
AD: IraD/Gp25-like domain-containing protein
AC: IraD/Gp25-like domain-containing protein
AE: IraD/Gp25-like domain-containing protein
AF: IraD/Gp25-like domain-containing protein
BE: Putative baseplate hub subunit
BF: Putative baseplate hub subunit
BG: Putative baseplate hub subunit
AL: Baseplate wedge subunit
AI: Baseplate wedge subunit
AG: Baseplate wedge subunit
AK: Baseplate wedge subunit
AH: Baseplate wedge subunit
AJ: Baseplate wedge subunit
BB: Baseplate central spike protein
BC: Baseplate central spike protein
BD: Baseplate central spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,021,558193
Polymers11,021,523192
Non-polymers351
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 8 types, 120 molecules LeLfLgLhLiLjLSLTLULVLWLXLYLZLaLbLcLdBMBKBOBPBLBNBQBVBSBRBTBU...

#1: Protein
Long tail fiber proximal subunit


Mass: 138688.438 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A5B9NKG2
#2: Protein
Baseplate tail tube cap


Mass: 38263.664 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V618
#3: Protein
Baseplate subunit


Mass: 33716.129 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A7I8V4E3
#9: Protein ...
Tail sheath protein


Mass: 71695.094 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V5S7
#10: Protein ...
Tail tube protein


Mass: 18633.738 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V5T6
#11: Protein
IraD/Gp25-like domain-containing protein


Mass: 15382.360 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A0K1Y5J2
#12: Protein Putative baseplate hub subunit


Mass: 43526.016 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A7T3TJP2
#14: Protein Baseplate central spike protein / Peptidoglycan hydrolase


Mass: 63317.457 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A976LXP5, lysozyme

-
Baseplate wedge ... , 6 types, 72 molecules AXAWATASAVAUARAQANAMAPAOAYAZA0A1A2A3A4A9A6A5A8A7AdAcAfAeAbAa...

#4: Protein
Baseplate wedge protein gp6


Mass: 73689.242 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V5R4
#5: Protein
Baseplate wedge protein gp7


Mass: 119645.719 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V5T9
#6: Protein
Baseplate wedge subunit


Mass: 38704.387 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2Z4QAY9
#7: Protein
Baseplate wedge tail fiber connector


Mass: 32380.195 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V5S1
#8: Protein
Baseplate wedge protein gp10


Mass: 66712.070 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V5S8
#13: Protein
Baseplate wedge subunit


Mass: 24693.420 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V5R5

-
Non-polymers , 1 types, 1 molecules

#15: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: vB_Kpn_Lilla1 / Type: VIRUS / Entity ID: #3-#10, #12, #2, #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: vB_Kpn_Lilla1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Klebsiella
Buffer solutionpH: 7.5 / Details: 100mM NaCl, 8mM MgSO4, 50mM Tris-HCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Klebsiella phage KP1 variant vB_Kpn_Lilla1
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 92 % / Chamber temperature: 281 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Details: Alignment procedure: EPU Autocoma and Autosrigmate Residual tilt (if alignment procedure is coma free, mrad): 68 Software used to collect images EPU 2.4, Tomo 5.13 Film/CCD/Direct electron ...Details: Alignment procedure: EPU Autocoma and Autosrigmate Residual tilt (if alignment procedure is coma free, mrad): 68 Software used to collect images EPU 2.4, Tomo 5.13 Film/CCD/Direct electron detector model*: post GIF K3
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Calibrated magnification: 83505 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: OTHER
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 93.6 K / Temperature (min): 78.7 K / Residual tilt: 68 mradians
Image recordingAverage exposure time: 2 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 4
Image scansSampling size: 5 µm / Width: 4092 / Height: 5760

-
Processing

EM softwareName: REFMAC / Version: 5.8.0258 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 34529
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2415 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementResolution: 3.95→546.304 Å / Cor.coef. Fo:Fc: 0.862 / WRfactor Rwork: 0.45 / SU B: 91.285 / SU ML: 1.147 / Average fsc overall: 0.5353 / Average fsc work: 0.5353 / ESU R: 0.783
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.4502 5540952 -
all0.45 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 161.415 Å2
Baniso -1Baniso -2Baniso -3
1--3.567 Å20.001 Å2-0.005 Å2
2---3.559 Å2-0.003 Å2
3---7.126 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.012617673
ELECTRON MICROSCOPYr_angle_refined_deg1.6161.639839550
ELECTRON MICROSCOPYr_dihedral_angle_1_deg9.653577358
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.9522.84533063
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.47415101298
ELECTRON MICROSCOPYr_dihedral_angle_4_deg20.856153864
ELECTRON MICROSCOPYr_chiral_restr0.110.283688
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.02478928
ELECTRON MICROSCOPYr_nbd_refined0.2070.201536822
ELECTRON MICROSCOPYr_nbtor_refined0.2960.202862928
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.0770.244032
ELECTRON MICROSCOPYr_mcbond_it10.88715.452310035
ELECTRON MICROSCOPYr_mcangle_it18.09523.144387192
ELECTRON MICROSCOPYr_scbond_it14.3616.596307638
ELECTRON MICROSCOPYr_scangle_it23.64724.431452358
ELECTRON MICROSCOPYr_lrange_it35.887290.0742396147
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
3.95-4.0530.6364100200.6364100200.2870.636
4.053-4.1640.5674004030.5674004030.320.567
4.164-4.2840.5313886400.5313886400.3860.531
4.284-4.4160.5193774380.5193774380.4210.519
4.416-4.5610.4983651980.4983651980.4930.498
4.561-4.7210.4943541980.4943541980.5280.494
4.721-4.8990.4863416420.4863416420.5420.486
4.899-5.0990.4773277380.4773277380.5820.477
5.099-5.3260.4773160610.4773160610.5820.477
5.326-5.5860.4743006570.4743006570.5750.474
5.586-5.8880.4742864310.4742864310.5770.474
5.888-6.2450.4722703630.4722703630.5690.472
6.245-6.6760.4762549340.4762549340.5650.476
6.676-7.2110.4622363860.4622363860.6060.462
7.211-7.8990.4372178160.4372178160.6710.437
7.899-8.8320.4141971340.4141971340.7350.414
8.832-10.1970.3791735520.3791735520.7970.379
10.197-12.4880.3411470320.3411470320.8390.341
12.488-17.6560.3361132610.3361132610.8450.336
17.656-546.3040.334620480.334620480.9180.334

+
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