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- PDB-3s84: Dimeric apoA-IV -

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Basic information

Entry
Database: PDB / ID: 3s84
TitleDimeric apoA-IV
ComponentsApolipoprotein A-IV
KeywordsTRANSPORT PROTEIN / four helix bundle
Function / homology
Function and homology information


protein-lipid complex assembly / : / chylomicron assembly / negative regulation of plasma lipoprotein oxidation / positive regulation of triglyceride catabolic process / chylomicron remodeling / response to lipid hydroperoxide / protein metabolic process => GO:0019538 / response to stilbenoid / regulation of intestinal cholesterol absorption ...protein-lipid complex assembly / : / chylomicron assembly / negative regulation of plasma lipoprotein oxidation / positive regulation of triglyceride catabolic process / chylomicron remodeling / response to lipid hydroperoxide / protein metabolic process => GO:0019538 / response to stilbenoid / regulation of intestinal cholesterol absorption / Assembly of active LPL and LIPC lipase complexes / regulation of cholesterol transport / positive regulation of lipoprotein lipase activity / phosphatidylcholine metabolic process / very-low-density lipoprotein particle remodeling / Chylomicron remodeling / phosphatidylcholine-sterol O-acyltransferase activator activity / lipid transporter activity / Chylomicron assembly / lipoprotein metabolic process / positive regulation of fatty acid biosynthetic process / chylomicron / phosphatidylcholine binding / high-density lipoprotein particle remodeling / phospholipid efflux / very-low-density lipoprotein particle / reverse cholesterol transport / cholesterol transfer activity / high-density lipoprotein particle assembly / high-density lipoprotein particle / triglyceride homeostasis / lipid transport / retinoid metabolic process / cholesterol efflux / leukocyte cell-cell adhesion / cholesterol binding / cholesterol biosynthetic process / lipid homeostasis / antioxidant activity / positive regulation of lipid biosynthetic process / lipid catabolic process / Retinoid metabolism and transport / removal of superoxide radicals / cholesterol metabolic process / innate immune response in mucosa / cholesterol homeostasis / hydrogen peroxide catabolic process / phospholipid binding / collagen-containing extracellular matrix / early endosome / blood microparticle / copper ion binding / Amyloid fiber formation / endoplasmic reticulum lumen / lipid binding / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2890 / Apolipoprotein / Apolipoprotein A/E / Apolipoprotein A1/A4/E domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsDeng, X. / Davidson, W.S. / Thompson, T.B.
CitationJournal: Structure / Year: 2012
Title: The Structure of Dimeric Apolipoprotein A-IV and Its Mechanism of Self-Association.
Authors: Deng, X. / Morris, J. / Dressmen, J. / Tubb, M.R. / Tso, P. / Jerome, W.G. / Davidson, W.S. / Thompson, T.B.
History
DepositionMay 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apolipoprotein A-IV
B: Apolipoprotein A-IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3314
Polymers63,1392
Non-polymers1922
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-88 kcal/mol
Surface area25870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.825, 70.825, 512.383
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Apolipoprotein A-IV / Apo-AIV / ApoA-IV / Apolipoprotein A4


Mass: 31569.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOA4 / Production host: Escherichia coli (E. coli) / References: UniProt: P06727
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 293 K / Method: batch plate / pH: 7.5
Details: Crystal grew in pH 8.5 PEG and AmSO4, Dehydration in 60% PEG, Batch plate, temperature 293K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9794947, 0.9796317, 0.9494888
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2010
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing. Design parameters for this beamline are: Monochromator energy range 3.5 35 keV ...Monochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing. Design parameters for this beamline are: Monochromator energy range 3.5 35 keV monochromator energy resolution E/E < 2x10-4 over full energy range
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97949471
20.97963171
30.94948881
ReflectionResolution: 2.39→18.86 Å / Num. obs: 31511 / % possible obs: 99.9 % / Biso Wilson estimate: 74.37 Å2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
CRANKphasing
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→18.86 Å / Cor.coef. Fo:Fc: 0.9505 / Cor.coef. Fo:Fc free: 0.9325 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 1583 5.09 %RANDOM
Rwork0.2002 ---
obs0.2016 31126 99.1 %-
Displacement parametersBiso mean: 95.78 Å2
Baniso -1Baniso -2Baniso -3
1--4.3438 Å20 Å20 Å2
2---4.3438 Å20 Å2
3---8.6877 Å2
Refine analyzeLuzzati coordinate error obs: 0.565 Å
Refinement stepCycle: LAST / Resolution: 2.4→18.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3906 0 10 22 3938
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013992HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.125363HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1561SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes157HARMONIC2
X-RAY DIFFRACTIONt_gen_planes560HARMONIC5
X-RAY DIFFRACTIONt_it3992HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion20.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion506SEMIHARMONIC5
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_contact5126SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.48 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2414 131 4.74 %
Rwork0.23 2634 -
all0.2306 2765 -
obs--99.1 %
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)
13.6036-1.1422-1.1394-2.52012.47670.41570.0441-0.36440.00270.38280.11370.00640.0423-0.1485-0.15780.0948-0.27610.16820.1412-0.0592-0.19564.213375.0675-60.3926
21.92980.3733-1.483119.04150.776700.14490.25850.0492-1.7735-0.37780.09820.035-0.45810.2330.2069-0.2339-0.034-0.0785-0.0169-0.44996.847460.0783-77.981
33.83145.03360.21286.688-1.30570.24780.2645-0.4312-0.30430.2566-0.557-0.16430.8769-0.50820.29250.3448-0.48060.16020.0295-0.0565-0.19860.954929.4412-58.5373
44.8626.3444-2.21137.704-3.84652.3671-0.49270.1136-0.5752-0.1342-0.0477-0.7602-0.50620.43790.54050.4773-0.41070.1095-0.10140.0046-0.185-8.97736.1706-35.9207
56.70581.2674-6.09266.735-5.83351.6588-0.0592-0.1968-0.00890.0472-0.1092-0.32280.1390.73460.16840.1741-0.13330.001-0.31760.0034-0.3212-24.2404-11.6116-13.1957
63.95653.0202-1.76823.5138-2.19240-0.0885-0.3871-0.39010.06580.11190.27210.36880.2458-0.02330.23020.07180.1161-0.09150.1442-0.0671-39.8169-28.368910.508
74.28154.9772-4.66164.3201-2.81157.4033-0.44610.2993-0.33750.0899-0.0870.21830.6391-0.14450.53310.2868-0.01510.1745-0.10480.0442-0.0083-48.2854-30.86326.0568
82.18671.4088-1.53140.8978-1.21563.287-0.07330.20930.2925-0.27510.33710.496-0.0145-0.5297-0.26380.2219-0.0558-0.0007-0.27360.0251-0.2718-31.9468-7.0414-16.5118
92.76230.2165-1.3399-0.36094.83684.3852-0.28530.48770.2987-0.2130.4963-0.0705-0.4227-0.0864-0.2110.4455-0.2218-0.0707-0.2810.0592-0.1999-22.4996.9895-23.1395
103.74125.2052-3.81424.7634-5.16863.72730.3691-0.18120.60090.28530.03790.8801-0.6845-0.0925-0.4070.54740.05530.208-0.23560.0352-0.0947-43.5931-12.15974.3945
11-1.9331.1165.57581.933-2.60600.00790.09950.2149-0.0285-0.08310.1979-0.2740.10110.07530.3184-0.0710.14810.30470.0097-0.1382-67.3033-25.47691.8447
1219.23779.9373-5.22915.2007-3.17371.66470.6193-0.8752-0.1960.4366-0.5953-0.0754-0.39380.3668-0.0240.08550.09320.093-0.27960.0488-0.3294-48.0071-25.716317.1267
135.88233.7904-2.61832.416-2.71898.971-0.0558-0.2902-0.1069-0.23130.0335-0.2335-1.37740.50720.02230.4495-0.15740.006-0.20140.0227-0.2965-24.1991-5.3766-4.1314
145.22155.85170.70815.0175-0.41500.1073-0.5638-0.37180.2561-0.8774-0.7478-0.65751.01730.77010.3946-0.34760.0445-0.2570.0735-0.3015-6.08319.8445-26.2233
15-1.87442.4255-1.088510.01821.236300.2978-0.142-0.20140.0412-0.2789-1.00290.2410.3392-0.01890.3879-0.7196-0.07610.16580.1518-0.34814.329728.0145-43.6805
160.36360.534-0.885516.2842-6.39764.88530.137-0.0613-0.0543-0.3375-0.4326-0.8404-0.04650.12650.2955-0.1605-0.30670.0754-0.3205-0.0374-0.460712.818253.2137-68.9824
170.59191.99580.57165.7179-3.08074.82470.3134-0.05620.22910.9248-0.1740.37440.4103-0.7994-0.13940.31-0.37760.1923-0.1061-0.1016-0.29385.286352.4844-58.178
18-1.55231.61131.00334.2395-0.758918.1608-0.41570.7062-0.13020.05090.64520.1931-0.232-0.4585-0.22950.4112-0.65320.12560.12030.0032-0.318-9.774123.0982-38.314
19-0.33251.40940.58074.74140.07250.1011-0.15540.01560.7271-0.15560.51851.3475-0.1582-0.8917-0.3631-0.0878-0.3862-0.0094-0.06160.04-0.1848-3.540544.7587-62.6734
205.4145-2.12014.4003-4.2529-0.379800.14950.1313-0.0215-0.4291-0.16230.7553-0.1468-0.15330.01280.1897-0.2177-0.4157-0.26920.06740.0740.17166.1794-77.0273
213.6036-1.1422-1.1394-2.52012.47670.41570.0441-0.36440.00270.38280.11370.00640.0423-0.1485-0.15780.0948-0.27610.16820.1412-0.0592-0.19564.213375.0675-60.3926
221.92980.3733-1.483119.04150.776700.14490.25850.0492-1.7735-0.37780.09820.035-0.45810.2330.2069-0.2339-0.034-0.0785-0.0169-0.44996.847460.0783-77.981
233.83145.03360.21286.688-1.30570.24780.2645-0.4312-0.30430.2566-0.557-0.16430.8769-0.50820.29250.3448-0.48060.16020.0295-0.0565-0.19860.954929.4412-58.5373
244.8626.3444-2.21137.704-3.84652.3671-0.49270.1136-0.5752-0.1342-0.0477-0.7602-0.50620.43790.54050.4773-0.41070.1095-0.10140.0046-0.185-8.97736.1706-35.9207
256.70581.2674-6.09266.735-5.83351.6588-0.0592-0.1968-0.00890.0472-0.1092-0.32280.1390.73460.16840.1741-0.13330.001-0.31760.0034-0.3212-24.2404-11.6116-13.1957
263.95653.0202-1.76823.5138-2.19240-0.0885-0.3871-0.39010.06580.11190.27210.36880.2458-0.02330.23020.07180.1161-0.09150.1442-0.0671-39.8169-28.368910.508
274.28154.9772-4.66164.3201-2.81157.4033-0.44610.2993-0.33750.0899-0.0870.21830.6391-0.14450.53310.2868-0.01510.1745-0.10480.0442-0.0083-48.2854-30.86326.0568
282.18671.4088-1.53140.8978-1.21563.287-0.07330.20930.2925-0.27510.33710.496-0.0145-0.5297-0.26380.2219-0.0558-0.0007-0.27360.0251-0.2718-31.9468-7.0414-16.5118
292.76230.2165-1.3399-0.36094.83684.3852-0.28530.48770.2987-0.2130.4963-0.0705-0.4227-0.0864-0.2110.4455-0.2218-0.0707-0.2810.0592-0.1999-22.4996.9895-23.1395
303.74125.2052-3.81424.7634-5.16863.72730.3691-0.18120.60090.28530.03790.8801-0.6845-0.0925-0.4070.54740.05530.208-0.23560.0352-0.0947-43.5931-12.15974.3945
31-1.9331.1165.57581.933-2.60600.00790.09950.2149-0.0285-0.08310.1979-0.2740.10110.07530.3184-0.0710.14810.30470.0097-0.1382-67.3033-25.47691.8447
3219.23779.9373-5.22915.2007-3.17371.66470.6193-0.8752-0.1960.4366-0.5953-0.0754-0.39380.3668-0.0240.08550.09320.093-0.27960.0488-0.3294-48.0071-25.716317.1267
335.88233.7904-2.61832.416-2.71898.971-0.0558-0.2902-0.1069-0.23130.0335-0.2335-1.37740.50720.02230.4495-0.15740.006-0.20140.0227-0.2965-24.1991-5.3766-4.1314
345.22155.85170.70815.0175-0.41500.1073-0.5638-0.37180.2561-0.8774-0.7478-0.65751.01730.77010.3946-0.34760.0445-0.2570.0735-0.3015-6.08319.8445-26.2233
35-1.87442.4255-1.088510.01821.236300.2978-0.142-0.20140.0412-0.2789-1.00290.2410.3392-0.01890.3879-0.7196-0.07610.16580.1518-0.34814.329728.0145-43.6805
360.36360.534-0.885516.2842-6.39764.88530.137-0.0613-0.0543-0.3375-0.4326-0.8404-0.04650.12650.2955-0.1605-0.30670.0754-0.3205-0.0374-0.460712.818253.2137-68.9824
370.59191.99580.57165.7179-3.08074.82470.3134-0.05620.22910.9248-0.1740.37440.4103-0.7994-0.13940.31-0.37760.1923-0.1061-0.1016-0.29385.286352.4844-58.178
38-1.55231.61131.00334.2395-0.758918.1608-0.41570.7062-0.13020.05090.64520.1931-0.232-0.4585-0.22950.4112-0.65320.12560.12030.0032-0.318-9.774123.0982-38.314
39-0.33251.40940.58074.74140.07250.1011-0.15540.01560.7271-0.15560.51851.3475-0.1582-0.8917-0.3631-0.0878-0.3862-0.0094-0.06160.04-0.1848-3.540544.7587-62.6734
405.4145-2.12014.4003-4.2529-0.379800.14950.1313-0.0215-0.4291-0.16230.7553-0.1468-0.15330.01280.1897-0.2177-0.4157-0.26920.06740.0740.17166.1794-77.0273
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|94 - A|105 }A94 - 105
2X-RAY DIFFRACTION2{ A|106 - A|138 }A106 - 138
3X-RAY DIFFRACTION3{ A|139 - A|159 }A139 - 159
4X-RAY DIFFRACTION4{ A|160 - A|184 }A160 - 184
5X-RAY DIFFRACTION5{ A|185 - A|201 }A185 - 201
6X-RAY DIFFRACTION6{ A|202 - A|227 }A202 - 227
7X-RAY DIFFRACTION7{ A|228 - A|252 }A228 - 252
8X-RAY DIFFRACTION8{ A|253 - A|276 }A253 - 276
9X-RAY DIFFRACTION9{ A|277 - A|297 }A277 - 297
10X-RAY DIFFRACTION10{ A|298 - A|332 }A298 - 332
11X-RAY DIFFRACTION11{ B|92 - B|104 }B92 - 104
12X-RAY DIFFRACTION12{ B|105 - B|140 }B105 - 140
13X-RAY DIFFRACTION13{ B|141 - B|161 }B141 - 161
14X-RAY DIFFRACTION14{ B|162 - B|182 }B162 - 182
15X-RAY DIFFRACTION15{ B|183 - B|196 }B183 - 196
16X-RAY DIFFRACTION16{ B|197 - B|231 }B197 - 231
17X-RAY DIFFRACTION17{ B|232 - B|266 }B232 - 266
18X-RAY DIFFRACTION18{ B|267 - B|298 }B267 - 298
19X-RAY DIFFRACTION19{ B|299 - B|324 }B299 - 324
20X-RAY DIFFRACTION20{ B|325 - B|332 }B325 - 332
21X-RAY DIFFRACTION21{ A|94 - A|105 }A94 - 105
22X-RAY DIFFRACTION22{ A|106 - A|138 }A106 - 138
23X-RAY DIFFRACTION23{ A|139 - A|159 }A139 - 159
24X-RAY DIFFRACTION24{ A|160 - A|184 }A160 - 184
25X-RAY DIFFRACTION25{ A|185 - A|201 }A185 - 201
26X-RAY DIFFRACTION26{ A|202 - A|227 }A202 - 227
27X-RAY DIFFRACTION27{ A|228 - A|252 }A228 - 252
28X-RAY DIFFRACTION28{ A|253 - A|276 }A253 - 276
29X-RAY DIFFRACTION29{ A|277 - A|297 }A277 - 297
30X-RAY DIFFRACTION30{ A|298 - A|332 }A298 - 332
31X-RAY DIFFRACTION31{ B|92 - B|104 }B92 - 104
32X-RAY DIFFRACTION32{ B|105 - B|140 }B105 - 140
33X-RAY DIFFRACTION33{ B|141 - B|161 }B141 - 161
34X-RAY DIFFRACTION34{ B|162 - B|182 }B162 - 182
35X-RAY DIFFRACTION35{ B|183 - B|196 }B183 - 196
36X-RAY DIFFRACTION36{ B|197 - B|231 }B197 - 231
37X-RAY DIFFRACTION37{ B|232 - B|266 }B232 - 266
38X-RAY DIFFRACTION38{ B|267 - B|298 }B267 - 298
39X-RAY DIFFRACTION39{ B|299 - B|324 }B299 - 324
40X-RAY DIFFRACTION40{ B|325 - B|332 }B325 - 332

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