[English] 日本語
Yorodumi
- PDB-2aen: Crystal structure of the rotavirus strain DS-1 VP8* core -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2aen
TitleCrystal structure of the rotavirus strain DS-1 VP8* core
ComponentsOuter capsid protein VP4, VP8* core
KeywordsVIRAL PROTEIN / Rotavirus / VP4 / VP8* / Neutralization antigen / Spike protein
Function / homology
Function and homology information


host cell rough endoplasmic reticulum / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ETHANOL / : / Outer capsid protein VP4
Similarity search - Component
Biological speciesHuman rotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.604 Å
AuthorsMonnier, N. / Higo-Moriguchi, K. / Sun, Z.-Y.J. / Prasad, B.V.V. / Taniguchi, K. / Dormitzer, P.R.
CitationJournal: J.Virol. / Year: 2006
Title: High-resolution molecular and antigen structure of the VP8* core of a sialic acid-independent human rotavirus strain
Authors: Monnier, N. / Higo-Moriguchi, K. / Sun, Z.-Y.J. / Prasad, B.V.V. / Taniguchi, K. / Dormitzer, P.R.
History
DepositionJul 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 20, 2017Group: Database references / Category: pdbx_database_related
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Aug 23, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer capsid protein VP4, VP8* core
B: Outer capsid protein VP4, VP8* core
C: Outer capsid protein VP4, VP8* core
D: Outer capsid protein VP4, VP8* core
E: Outer capsid protein VP4, VP8* core
F: Outer capsid protein VP4, VP8* core
G: Outer capsid protein VP4, VP8* core
H: Outer capsid protein VP4, VP8* core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,95018
Polymers150,2138
Non-polymers73710
Water31,0581724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.421, 84.123, 90.769
Angle α, β, γ (deg.)90.03, 90.02, 75.54
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

-
Components

#1: Protein
Outer capsid protein VP4, VP8* core / Hemagglutinin / Outer capsid protein VP4 [Contains: tryptic fragment VP8* / tryptic fragment VP5*]


Mass: 18776.646 Da / Num. of mol.: 8 / Fragment: VP8* core, residues 60-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rotavirus A / Species: Rotavirus A / Strain: DS-1 / Gene: GENOME SEGEMENT 4 / Variant: SEROTYPE 2 / Plasmid: pGEX_DS-1_VP8_60_223 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: GenBank: 75270083, UniProt: P11196*PLUS
#2: Chemical
ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1724 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.72 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, sodium chloride, sodium citrate, ethanol, tris, EDTA, sodium azide, benzamidine, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.916 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 13, 2003 / Details: Mirrors
RadiationMonochromator: Horizontal Bent Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.6→14.88 Å / Num. all: 153466 / Num. obs: 153466 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.95 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.05 / Net I/σ(I): 17.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.72 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 15018 / Rsym value: 0.376 / % possible all: 94.7

-
Processing

Software
NameVersionClassification
REFMAC5.2refinement
SCALEPACKdata scaling
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1KQR

1kqr


Resolution: 1.604→14.88 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.263 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ATOM RECORDS CONTAIN THE SUM OF TLS AND RESIDUAL B FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.19173 7761 5.1 %RANDOM
Rwork0.1579 ---
all0.15961 145697 --
obs0.15961 145697 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.907 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å2-0.06 Å20.07 Å2
2---0.13 Å20 Å2
3----0.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.604→14.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10616 0 48 1724 12388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02211089
X-RAY DIFFRACTIONr_bond_other_d0.0020.029308
X-RAY DIFFRACTIONr_angle_refined_deg1.311.91915077
X-RAY DIFFRACTIONr_angle_other_deg1.506321835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68451310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54324.876605
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.706151786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.2431556
X-RAY DIFFRACTIONr_chiral_restr0.0840.21596
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212455
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022313
X-RAY DIFFRACTIONr_nbd_refined0.1920.21715
X-RAY DIFFRACTIONr_nbd_other0.1850.29152
X-RAY DIFFRACTIONr_nbtor_refined0.1820.25270
X-RAY DIFFRACTIONr_nbtor_other0.0840.26441
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.21155
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.244
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.2285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.2112
X-RAY DIFFRACTIONr_mcbond_it0.7941.58490
X-RAY DIFFRACTIONr_mcbond_other0.1771.52668
X-RAY DIFFRACTIONr_mcangle_it1.019210781
X-RAY DIFFRACTIONr_scbond_it1.78935390
X-RAY DIFFRACTIONr_scangle_it2.4954.54295
LS refinement shellResolution: 1.604→1.645 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 549 -
Rwork0.192 10013 -
obs--100 %
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)
13.55950.39341.42936.5380.31882.8580.1524-0.2695-0.34060.1238-0.01380.18070.3269-0.1347-0.1386-0.17920.0033-0.0387-0.16320.0383-0.191910.286212.200721.9078
21.2135-0.3365-0.20089.50383.27252.48360.0188-0.0798-0.19910.0041-0.19250.5550.1715-0.33310.1737-0.2059-0.0055-0.0247-0.14640.0168-0.1641-0.023818.022716.9393
33.2243-1.89431.01893.2085-0.40342.0817-0.0217-0.20160.1808-0.03450.0265-0.1063-0.219-0.1912-0.0048-0.1880.0051-0.0091-0.17560.0042-0.1885-3.959130.955513.0294
42.1667-0.38090.18751.1470.24031.19340.0055-0.01240.1206-0.05720.0058-0.0902-0.020.1609-0.0113-0.1895-0.0078-0.0032-0.16860.0074-0.195315.232524.43216.0823
54.51891.50091.69458.2057-0.29181.48140.1498-0.2614-0.39460.0370.01060.35840.3505-0.1064-0.1604-0.1281-0.0186-0.0457-0.15180.0592-0.157744.0787-28.439121.1789
62.2207-0.1064-0.30528.24093.12152.55510.1002-0.214-0.35830.1001-0.16610.49610.2267-0.36380.0659-0.1929-0.0311-0.0348-0.13750.0508-0.115633.6974-22.757816.0972
72.1047-1.0153-0.04931.9074-0.18651.47830.0412-0.1034-0.0213-0.06030.01660.0755-0.0101-0.1888-0.0578-0.1931-0.0045-0.0176-0.15610.0166-0.186729.5991-10.020112.3445
81.718-0.7042-0.01831.24460.31231.5210.0508-0.13640.03620.07950.0146-0.13120.03020.1644-0.0654-0.1882-0.0136-0.0071-0.1734-0.0028-0.165248.8955-16.025415.5923
97.1344-0.1192-0.52743.7515-1.50033.0937-0.05590.24770.0302-0.62710.22460.42360.287-0.4687-0.16870.0344-0.0656-0.0944-0.09060.0473-0.151825.181647.68433.8919
108.7226-2.1281-2.40653.13381.72192.9665-0.2460.0763-0.414-0.38970.07140.38780.3428-0.35760.1747-0.0347-0.0544-0.0383-0.14490.0061-0.155428.916136.57739.2087
110.3603-1.2073-0.13254.04590.3883.2378-0.0889-0.0674-0.1413-0.33390.2143-0.11490.18260.07-0.1254-0.1368-0.04360.0089-0.1456-0.007-0.175840.659530.3243.3079
120.60050.7127-0.19343.4831-0.01510.6013-0.15320.09330.0387-0.58740.1994-0.1805-0.0625-0.0415-0.0462-0.0568-0.04290.0334-0.1381-0.0157-0.177238.153650.293139.6032
137.32980.25410.32184.3267-1.23112.654-0.0571-0.1477-0.1338-0.11840.08430.42180.0688-0.3138-0.0273-0.16780.0152-0.0546-0.17680.0163-0.197114.86638.529234.4816
147.2342-1.7847-1.9642.91371.32282.2293-0.12640.0323-0.3903-0.0847-0.03130.41160.2739-0.31530.1576-0.1531-0.0012-0.0225-0.15830.0173-0.167617.4948-3.247439.0574
150.535-0.46540.66353.2334-0.60130.823-0.0533-0.0034-0.0877-0.10370.049-0.08420.1305-0.00120.0043-0.18720.02360.0139-0.16980.0211-0.185728.8183-10.98142.2707
160.4899-0.5046-0.1822.79020.03811.5569-0.0304-0.05320.0722-0.09810.0197-0.2181-0.18660.10580.0106-0.1848-0.0006-0.0049-0.15950.0006-0.184228.3419.402639.6929
176.85610.6974-0.14954.0941.14022.9116-0.061-0.11670.1444-0.13560.0768-0.4285-0.08170.2813-0.0158-0.15810.0190.0546-0.1805-0.0218-0.195-0.73534.859279.8586
187.4248-2.0612.58783.0748-1.37752.8645-0.10410.03920.4123-0.079-0.0387-0.4255-0.27430.35140.1428-0.1533-0.00370.0226-0.1571-0.0222-0.161-3.352846.638484.4347
190.4482-0.2462-0.71843.6530.96021.2424-0.083-0.02960.1266-0.10410.0680.0474-0.1914-0.00050.0151-0.18870.0266-0.0133-0.1547-0.0272-0.1878-14.539954.321187.7637
200.5471-0.61480.19432.81720.07571.6566-0.0288-0.055-0.0829-0.09280.02460.20510.1768-0.10690.0043-0.185-0.00060.0014-0.1584-0.0021-0.1831-14.198433.979885.0721
218.43470.09491.193.93361.45933.5634-0.05380.30680.0966-0.55090.1812-0.3061-0.25590.4834-0.12740.0257-0.05860.0731-0.0749-0.0519-0.16629.95977.145279.2892
229.4179-1.90632.34152.5151-1.78162.8742-0.26020.04430.4219-0.42380.0793-0.3982-0.33860.34880.1809-0.0216-0.0510.0279-0.1425-0.0228-0.14356.232988.291384.5901
230.8231-1.39720.70614.227-0.2513.14810.0041-0.08370.12-0.33840.19920.1166-0.1891-0.0625-0.2033-0.1274-0.0392-0.0087-0.1394-0.0075-0.1756-5.506894.519388.7145
240.6450.76140.18183.5857-0.00160.6232-0.15560.1081-0.0312-0.60910.18010.17970.06360.0301-0.0245-0.0497-0.0454-0.0419-0.13580.0094-0.1756-3.004974.55684.9829
254.6071.3436-1.23217.80340.18481.59890.1263-0.25930.39450.09690.0083-0.2991-0.33790.1293-0.1346-0.1324-0.01960.0405-0.1471-0.0654-0.163733.895-9.62266.5455
262.0566-0.14660.24238.4218-3.03932.56960.1079-0.17830.31720.0893-0.1868-0.4826-0.2230.36790.0789-0.1931-0.03160.0255-0.1391-0.0474-0.130144.3012-15.302161.4588
272.2006-0.8438-0.16281.47030.03991.56390.0047-0.13310.0113-0.02320.0011-0.0739-0.00190.1698-0.0058-0.1961-0.00380.0139-0.1698-0.0163-0.180948.4086-28.016157.7247
281.5715-0.66420.00031.2169-0.29441.39640.0481-0.1227-0.0330.09090.00680.1159-0.0316-0.1492-0.0548-0.1902-0.016-0.0004-0.17280.0014-0.165429.1072-22.045860.984
293.3990.7534-1.62276.4592-0.39073.06860.173-0.25780.3130.1192-0.0613-0.1569-0.32860.1372-0.1117-0.18370.00150.0325-0.1614-0.0416-0.18723.859331.201267.2803
301.3469-0.53680.35619.1224-3.16452.60190.0251-0.08220.1881-0.0107-0.2126-0.6149-0.20560.31610.1875-0.1998-0.00830.0223-0.1524-0.0244-0.162314.179425.405462.3621
313.1759-2.3325-0.6482.56450.47472.2153-0.0305-0.1406-0.1478-0.04330.02310.03540.18820.23330.0074-0.19250.00920.0031-0.1809-0.0021-0.18318.182512.693658.3055
322.2365-0.406-0.17351.0965-0.3611.29750.0037-0.0202-0.1325-0.05830.00370.09550.0153-0.1651-0.0074-0.1924-0.0086-0.0026-0.1736-0.0118-0.1969-1.068118.977961.4638
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA167 - 176108 - 117
2X-RAY DIFFRACTION1AA185 - 194126 - 135
3X-RAY DIFFRACTION2AA139 - 15780 - 98
4X-RAY DIFFRACTION2AA96 - 10537 - 46
5X-RAY DIFFRACTION3AA111 - 13552 - 76
6X-RAY DIFFRACTION4AA60 - 951 - 36
7X-RAY DIFFRACTION4AA106 - 11047 - 51
8X-RAY DIFFRACTION4AA136 - 13877 - 79
9X-RAY DIFFRACTION4AA158 - 16699 - 107
10X-RAY DIFFRACTION4AA177 - 184118 - 125
11X-RAY DIFFRACTION4AA195 - 223136 - 164
12X-RAY DIFFRACTION5BB167 - 176108 - 117
13X-RAY DIFFRACTION5BB185 - 194126 - 135
14X-RAY DIFFRACTION6BB139 - 15780 - 98
15X-RAY DIFFRACTION6BB96 - 10537 - 46
16X-RAY DIFFRACTION7BB111 - 13552 - 76
17X-RAY DIFFRACTION8BB60 - 951 - 36
18X-RAY DIFFRACTION8BB106 - 11047 - 51
19X-RAY DIFFRACTION8BB136 - 13877 - 79
20X-RAY DIFFRACTION8BB158 - 16699 - 107
21X-RAY DIFFRACTION8BB177 - 184118 - 125
22X-RAY DIFFRACTION8BB195 - 223136 - 164
23X-RAY DIFFRACTION9CC167 - 176108 - 117
24X-RAY DIFFRACTION9CC185 - 194126 - 135
25X-RAY DIFFRACTION10CC139 - 15780 - 98
26X-RAY DIFFRACTION10CC96 - 10537 - 46
27X-RAY DIFFRACTION11CC111 - 13552 - 76
28X-RAY DIFFRACTION12CC60 - 951 - 36
29X-RAY DIFFRACTION12CC106 - 11047 - 51
30X-RAY DIFFRACTION12CC136 - 13877 - 79
31X-RAY DIFFRACTION12CC158 - 16699 - 107
32X-RAY DIFFRACTION12CC177 - 184118 - 125
33X-RAY DIFFRACTION12CC195 - 223136 - 164
34X-RAY DIFFRACTION13DD167 - 176108 - 117
35X-RAY DIFFRACTION13DD185 - 194126 - 135
36X-RAY DIFFRACTION14DD139 - 15780 - 98
37X-RAY DIFFRACTION14DD96 - 10537 - 46
38X-RAY DIFFRACTION15DD111 - 13552 - 76
39X-RAY DIFFRACTION16DD60 - 951 - 36
40X-RAY DIFFRACTION16DD106 - 11047 - 51
41X-RAY DIFFRACTION16DD136 - 13877 - 79
42X-RAY DIFFRACTION16DD158 - 16699 - 107
43X-RAY DIFFRACTION16DD177 - 184118 - 125
44X-RAY DIFFRACTION16DD195 - 223136 - 164
45X-RAY DIFFRACTION17EE167 - 176108 - 117
46X-RAY DIFFRACTION17EE185 - 194126 - 135
47X-RAY DIFFRACTION18EE139 - 15780 - 98
48X-RAY DIFFRACTION18EE96 - 10537 - 46
49X-RAY DIFFRACTION19EE111 - 13552 - 76
50X-RAY DIFFRACTION20EE60 - 951 - 36
51X-RAY DIFFRACTION20EE106 - 11047 - 51
52X-RAY DIFFRACTION20EE136 - 13877 - 79
53X-RAY DIFFRACTION20EE158 - 16699 - 107
54X-RAY DIFFRACTION20EE177 - 184118 - 125
55X-RAY DIFFRACTION20EE195 - 223136 - 164
56X-RAY DIFFRACTION21FF167 - 176108 - 117
57X-RAY DIFFRACTION21FF185 - 194126 - 135
58X-RAY DIFFRACTION22FF139 - 15780 - 98
59X-RAY DIFFRACTION22FF96 - 10537 - 46
60X-RAY DIFFRACTION23FF111 - 13552 - 76
61X-RAY DIFFRACTION24FF60 - 951 - 36
62X-RAY DIFFRACTION24FF106 - 11047 - 51
63X-RAY DIFFRACTION24FF136 - 13877 - 79
64X-RAY DIFFRACTION24FF158 - 16699 - 107
65X-RAY DIFFRACTION24FF177 - 184118 - 125
66X-RAY DIFFRACTION24FF195 - 223136 - 164
67X-RAY DIFFRACTION25GG167 - 176108 - 117
68X-RAY DIFFRACTION25GG185 - 194126 - 135
69X-RAY DIFFRACTION26GG139 - 15780 - 98
70X-RAY DIFFRACTION26GG96 - 10537 - 46
71X-RAY DIFFRACTION27GG111 - 13552 - 76
72X-RAY DIFFRACTION28GG60 - 951 - 36
73X-RAY DIFFRACTION28GG106 - 11047 - 51
74X-RAY DIFFRACTION28GG136 - 13877 - 79
75X-RAY DIFFRACTION28GG158 - 16699 - 107
76X-RAY DIFFRACTION28GG177 - 184118 - 125
77X-RAY DIFFRACTION28GG195 - 223136 - 164
78X-RAY DIFFRACTION29HH167 - 176108 - 117
79X-RAY DIFFRACTION29HH185 - 194126 - 135
80X-RAY DIFFRACTION30HH139 - 15780 - 98
81X-RAY DIFFRACTION30HH96 - 10537 - 46
82X-RAY DIFFRACTION31HH111 - 13552 - 76
83X-RAY DIFFRACTION32HH60 - 951 - 36
84X-RAY DIFFRACTION32HH106 - 11047 - 51
85X-RAY DIFFRACTION32HH136 - 13877 - 79
86X-RAY DIFFRACTION32HH158 - 16699 - 107
87X-RAY DIFFRACTION32HH177 - 184118 - 125
88X-RAY DIFFRACTION32HH195 - 223136 - 164

+
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