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- PDB-6fla: 3H5 Fab bound to EDIII of DenV 2 Xtal form 1 -

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Basic information

Entry
Database: PDB / ID: 6fla
Title3H5 Fab bound to EDIII of DenV 2 Xtal form 1
Components
  • (Domain III of Dengue virus ...) x 2
  • Heavy chain
  • Light Chain of 3H5
KeywordsVIRAL PROTEIN / Dengue virus / antibody / macromolecular complex
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Immunoglobulin-like - #350 / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus ...Immunoglobulin-like - #350 / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Dengue virus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFlanagan, A. / Renner, M. / Grimes, J.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust204703/Z/16/Z United Kingdom
Wellcome Trust075491/Z/04 United Kingdom
CitationJournal: Nat. Immunol. / Year: 2018
Title: Characterization of a potent and highly unusual minimally enhancing antibody directed against dengue virus.
Authors: Renner, M. / Flanagan, A. / Dejnirattisai, W. / Puttikhunt, C. / Kasinrerk, W. / Supasa, P. / Wongwiwat, W. / Chawansuntati, K. / Duangchinda, T. / Cowper, A. / Midgley, C.M. / Malasit, P. / ...Authors: Renner, M. / Flanagan, A. / Dejnirattisai, W. / Puttikhunt, C. / Kasinrerk, W. / Supasa, P. / Wongwiwat, W. / Chawansuntati, K. / Duangchinda, T. / Cowper, A. / Midgley, C.M. / Malasit, P. / Huiskonen, J.T. / Mongkolsapaya, J. / Screaton, G.R. / Grimes, J.M.
History
DepositionJan 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heavy chain
B: Light Chain of 3H5
G: Domain III of Dengue virus 2
H: Heavy chain
I: Domain III of Dengue virus 2
L: Light Chain of 3H5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,55210
Polymers119,2976
Non-polymers2554
Water0
1
A: Heavy chain
B: Light Chain of 3H5
G: Domain III of Dengue virus 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5684
Polymers59,5333
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-47 kcal/mol
Surface area23420 Å2
MethodPISA
2
H: Heavy chain
I: Domain III of Dengue virus 2
L: Light Chain of 3H5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9846
Polymers59,7643
Non-polymers2203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-47 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.840, 263.870, 272.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Domain III of Dengue virus ... , 2 types, 2 molecules GI

#3: Protein Domain III of Dengue virus 2


Mass: 11063.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14340, UniProt: W5RZ25*PLUS
#4: Protein Domain III of Dengue virus 2


Mass: 11295.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P29991, UniProt: W5RZ25*PLUS

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Antibody , 2 types, 4 molecules AHBL

#1: Antibody Heavy chain


Mass: 24438.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#2: Antibody Light Chain of 3H5


Mass: 24030.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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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: 3.18 Å3/Da / Density % sol: 61.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% w/v PEG 3350, 0.2 M di-Sodium Tartrate at a protein concentration of 4.16 mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.951 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.951 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 33359 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 81.22 Å2 / Net I/σ(I): 20.5
Reflection shellResolution: 2.9→3 Å

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→39.59 Å / Cor.coef. Fo:Fc: 0.9296 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 1.897 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.75 / SU Rfree Blow DPI: 0.311 / SU Rfree Cruickshank DPI: 0.317
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 1689 5.06 %RANDOM
Rwork0.2032 ---
obs0.2042 33359 99.04 %-
Displacement parametersBiso mean: 67.62 Å2
Baniso -1Baniso -2Baniso -3
1--5.2265 Å20 Å20 Å2
2--4.6548 Å20 Å2
3---0.5717 Å2
Refine analyzeLuzzati coordinate error obs: 0.448 Å
Refinement stepCycle: 1 / Resolution: 2.9→39.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8129 0 14 0 8143
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018344HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2711350HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2784SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes188HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1201HARMONIC5
X-RAY DIFFRACTIONt_it8344HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion18.58
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1121SEMIHARMONIC5
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_contact8794SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.99 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.3302 148 5.57 %
Rwork0.3167 2508 -
all0.3175 2656 -
obs--99.04 %
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)
11.0805-0.1598-0.13111.5784-1.09672.7183-0.0117-0.07780.01520.1117-0.02070.03910.07220.14060.0325-0.11980.10580.02850.1247-0.1052-0.045531.8477-108.984-37.1755
20.0492-0.2328-0.73061.5629-1.74970.5844-0.0036-0.0042-0.0234-0.00160.0009-0.00890.0082-0.03850.00280.05420.04250.0467-0.01690.0559-0.014836.2878-135.162-38.6718
30.07540.2707-1.16073.2806-1.89342.028100.00360.01030.0535-0.0107-0.0054-0.04910.06670.01060.1175-0.01080.152-0.09080.152-0.036941.6845-137.025-46.9205
40.09990.358-0.31040.097-0.053300.00060.00230.00050.0044-0.00210.0008-0.00140.00150.00150.0041-0.00280.00790.01210.02790.000548.4796-142.945-42.9385
50.9571-0.64181.188700.16370.46950.0018-0.01670.0322-0.0531-0.02120.02060.04730.00160.01940.02610.0329-0.07840.0081-0.01740.006720.9308-113.3-61.783
601.1631-0.04052.26140.15393.3754-0.0025-0.00390.0798-0.1237-0.02990.04160.12080.03120.03240.02660.1103-0.0164-0.0577-0.0056-0.02927.8629-107.903-57.871
70.0084-1.9632-0.8391.67682.24490.89-0.00050.0066-0.08510.0058-0.0129-0.0280.0071-0.01030.01340.05730.01880.1265-0.10240.07760.010836.0604-144.886-53.3323
81.25070.436-1.36520.81730.26382.1173-0.0048-0.0291-0.12760.012-0.03340.0652-0.0037-0.11540.03820.08860.010.1416-0.14890.06190.047429.4337-146.85-55.2831
90.2251.5562-0.51381.107-0.96572.7513-0.0260.0896-0.0119-0.08480.0565-0.0311-0.0589-0.0532-0.03060.0444-0.02780.0527-0.01690.152-0.029241.2008-42.4102-33.2197
100.85671.13590.16280.7931-1.31671.0091-0.02280.01270.0098-0.07260.01440.00790.0405-0.08750.00840.04460.03250.05290.02540.152-0.037939.0363-46.0873-32.7518
110.04680.2862-0.79021.19940.31111.9983-0.0165-0.0221-0.05-0.17390.0907-0.0113-0.0134-0.0696-0.07430.057-0.04570.0350.00760.0118-0.071622.9007-68.4886-21.8833
120.15630.31840.81430.03770.38340.4809-0.0004-0.0142-0.0048-0.03110.0088-0.0102-0.0271-0.0139-0.00840.0679-0.0148-0.06360.03520.0687-0.066316.9825-66.2508-27.5875
131.5026-0.3840.34881.496-1.62441.207-0.0039-0.0361-0.04540.01450.0133-0.016-0.07810.049-0.00940.001-0.04410.0346-0.02530.12660.032546.6964-44.1047-11.3186
140.107-0.1140.38350-0.32130.09030.0009-0.0055-0.00350.00550.0043-0.00610.0010.0002-0.0052-0.011-0.0275-0.0480.01260.05040.019254.3247-40.2741-7.6368
151.23940.328-0.41481.3881-0.26910.3474-0.0059-0.0071-0.0582-0.0231-0.0404-0.06280.07330.00180.0463-0.0102-0.02090.0268-0.04350.0534-0.021236.6333-62.9187-14.0372
161.0092-0.81860.69120.99350.29440.4822-0.00940.0362-0.0895-0.0409-0.0121-0.04080.09380.0250.02150.0585-0.07740.152-0.08580.01860.053131.0806-80.8024-16.1386
170-0.0477-0.07460.13730.015700.0012-0.01050.0013-0.0068-0.0007-0.0010.00190.0019-0.00040.0052-0.00520.0089-0.0181-0.05880.006933.1417-89.5216-45.9387
1800.01490.42810.03570.3750.1460.00010.0038-0.00360.00110.00620.0027-0.0032-0.0006-0.00630.0253-0.01730.0155-0.00640.0021-0.010124.6932-73.6257-38.9867
190.79691.5662-0.13470.6785-0.15540.14970.00280.001-0.0073-0.00360.002-0.0023-0.01240.0104-0.0048-0.0088-0.01590.03220.0167-0.02740.035531.3165-80.2873-43.6469
2000.1612-0.01750.57410.73460.27780.0002-0.0013-0.004-0.01070.0010.0029-0.0090.0008-0.00120.00690.00690.0137-0.0042-0.03430.015122.9806-85.469-49.7236
210.0465-0.19910.17730.25840.02920.0808-0.00030.0052-0.0054-0.005-0.00420.0081-0.0017-0.00060.00450.00850.0108-0.0131-0.00120.00320.013919.7418-80.9873-52.8727
220.02040.02240.122600.080900.0004-0.00270.0010.0084-0.0032-0.01070.00010.00750.0029-0.0061-0.02630.012-0.0019-0.02410.015238.6932-81.5733-45.4967
230.45170.65060.71280.4940.718500.00040.0142-0.0017-0.00690.01060.011-0.0099-0.0206-0.0110.0226-0.00350.0356-0.019-0.04650.035420.5594-81.4855-45.9406
240.18190.2865-0.47810.1271-0.03770-0.00130.00790.00320.00020.00610.006-0.0013-0.0108-0.0048-0.00240.00950.0719-0.0043-0.02640.023617.6134-80.9863-41.4593
250-0.03480.11250.30450.12570.05510.0006-0.0006-0.0004-0.00060.0003-0.0006-0.0033-0.0001-0.00090.03460.00470.0314-0.01460.04450.001745.9753-23.2323-24.8699
2600.13910.12370.0684-0.36500.0001-0.0058-0.00560.00180.00350.0056-0.00420.0132-0.00360.0021-0.00160.02340.00710.03730.00158.8613-10.3001-30.6245
270.3635-1.1798-0.13060.7009-0.22360.0557-0.0012-0.00670.00340.01250.0097-0.0148-0.013-0.0051-0.00850.010.01660.0414-0.00910.05910.018450.443-15.2206-26.5205
280.07060.3582-0.15820.8228-0.33150.30820.0007-0.0022-0.00090.0048-0.0054-0.006-0.0097-0.00890.0048-0.00490.01730.0267-0.0110.04370.028452.501-21.2845-19.1756
290.0046-0.01510.000800.01480-0.0001-0.0016-0.00170.002-0.0003-0.00210.00130.00570.0004-0.01050.02030.00710.00080.01570.02366.876-29.3854-19.4748
3000.27320.090-0.151200.00160.00010.01060.01310.00620.0001-0.0113-0.0009-0.00780.0281-0.01960.0422-0.01870.01540.003251.3917-14.7752-18.5629
310.15210.2814-0.3871.4555-0.21760.236-0.00070.0051-0.0084-0.0080.0084-0.01250.00170.0057-0.00770.0026-0.00250.0103-0.00710.02550.037958.526-15.7255-24.2513
320.153-0.47680.04520.5206-0.35460.04280.00220.00080.0074-0.00420.0133-0.02630.01460.0112-0.0155-0.0018-0.03520.0521-0.00260.05910.016459.1563-22.7641-27.0037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|2 - A|108 }
2X-RAY DIFFRACTION2{ A|109 - A|137 }
3X-RAY DIFFRACTION3{ A|138 - A|207 }
4X-RAY DIFFRACTION4{ A|208 - A|217 }
5X-RAY DIFFRACTION5{ B|1 - B|26 }
6X-RAY DIFFRACTION6{ B|27 - B|110 }
7X-RAY DIFFRACTION7{ B|111 - B|142 }
8X-RAY DIFFRACTION8{ B|143 - B|215 }
9X-RAY DIFFRACTION9{ H|2 - H|71 }
10X-RAY DIFFRACTION10{ H|72 - H|119 }
11X-RAY DIFFRACTION11{ H|120 - H|194 }
12X-RAY DIFFRACTION12{ H|195 - H|217 }
13X-RAY DIFFRACTION13{ L|1 - L|67 }
14X-RAY DIFFRACTION14{ L|68 - L|77 }
15X-RAY DIFFRACTION15{ L|78 - L|151 }
16X-RAY DIFFRACTION16{ L|152 - L|215 }
17X-RAY DIFFRACTION17{ G|300 - G|307 }
18X-RAY DIFFRACTION18{ G|308 - G|316 }
19X-RAY DIFFRACTION19{ G|317 - G|331 }
20X-RAY DIFFRACTION20{ G|332 - G|343 }
21X-RAY DIFFRACTION21{ G|344 - G|355 }
22X-RAY DIFFRACTION22{ G|356 - G|365 }
23X-RAY DIFFRACTION23{ G|366 - G|384 }
24X-RAY DIFFRACTION24{ G|385 - G|394 }
25X-RAY DIFFRACTION25{ I|300 - I|308 }
26X-RAY DIFFRACTION26{ I|309 - I|316 }
27X-RAY DIFFRACTION27{ I|317 - I|330 }
28X-RAY DIFFRACTION28{ I|331 - I|341 }
29X-RAY DIFFRACTION29{ I|342 - I|346 }
30X-RAY DIFFRACTION30{ I|347 - I|361 }
31X-RAY DIFFRACTION31{ I|362 - I|378 }
32X-RAY DIFFRACTION32{ I|379 - I|394 }

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