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- PDB-1x9p: The crystal structure of human adenovirus 2 penton base -

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Basic information

Entry
Database: PDB / ID: 1x9p
TitleThe crystal structure of human adenovirus 2 penton base
ComponentsPenton protein
KeywordsVIRUS LIKE PARTICLE / jellyroll domain / anti-parallel beta sheet / insertion domain
Function / homology
Function and homology information


T=25 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / host cell nucleus / virion attachment to host cell / structural molecule activity
Similarity search - Function
Penton protein; domain 1 / adenovirus 2 penton base, domain 2 / adenovirus 2 penton base, domain 2 / Adenovirus penton base protein / Adenovirus penton base protein / Jelly Rolls / Alpha-Beta Complex / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-C15 / Penton protein
Similarity search - Component
Biological speciesHuman adenovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsZubieta, C. / Schoehn, G. / Chroboczek, J. / Cusack, S.
CitationJournal: Mol.Cell / Year: 2005
Title: The structure of the human adenovirus 2 penton
Authors: Zubieta, C. / Schoehn, G. / Chroboczek, J. / Cusack, S.
History
DepositionAug 24, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penton protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9884
Polymers58,2191
Non-polymers7693
Water00
1
A: Penton protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)3,539,271240
Polymers3,493,12160
Non-polymers46,150180
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Penton protein
hetero molecules
x 5


  • icosahedral pentamer
  • 295 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)294,93920
Polymers291,0935
Non-polymers3,84615
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Penton protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 354 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)353,92724
Polymers349,3126
Non-polymers4,61518
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: Penton protein
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 3.54 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)3,539,271240
Polymers3,493,12160
Non-polymers46,150180
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)435.984, 300.168, 420.621
Angle α, β, γ (deg.)90.00, 104.36, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.37082958, 0.90742971, 0.19762777), (-0.90761253, 0.30901713, 0.28416175), (0.19678645, -0.28474502, 0.93818728)30.92245, 44.70173, -9.67161
3generate(-0.64718954, 0.56063958, 0.5165549), (-0.56111822, -0.80901664, 0.17503835), (0.51603493, -0.17656538, 0.83817219)81.04172, 27.70143, -25.38887
4generate(-0.64718954, -0.56111822, 0.51603493), (0.56063958, -0.80901664, -0.17656538), (0.5165549, 0.17503835, 0.83817219)81.09467, -27.50707, -25.43106
5generate(0.37082958, -0.90761253, 0.19678645), (0.90742971, 0.30901713, -0.28474502), (0.19762777, 0.28416175, 0.93818728)31.00814, -44.6275, -9.73988
6generate(-0.87474169, -0.26331655, 0.40680631), (-0.26331655, -0.44645906, -0.85518343), (0.40680631, -0.85518343, 0.32120074)110.6886, 108.49405, 36.14401
7generate(-0.00533673, -0.990972, 0.13396277), (0.13927776, -0.13339553, -0.98122747), (0.99023897, 0.01342149, 0.13873225)67.93426, 88.66517, 7.38875
8generate(0.92380165, -0.34921526, -0.15696886), (-0.0203725, 0.36456291, -0.93095588), (0.38232902, 0.86321642, 0.32966943)22.17543, 96.49902, 37.26757
9generate(0.62863578, 0.77506767, -0.06393095), (-0.5216361, 0.35925462, -0.77384229), (-0.57681266, 0.51981364, 0.63014358)36.64926, 121.16949, 84.48896
10generate(-0.48292513, 0.82815599, 0.28450127), (-0.67178377, -0.14198452, -0.72701235), (-0.56168486, -0.54221587, 0.62490965)91.35341, 128.58283, 83.79456
11generate(-0.94622077, 0.27889476, 0.16396331), (0.27889476, 0.44632579, 0.85030054), (0.16396331, 0.85030054, -0.50010502)141.22994, -109.26078, 139.52524
12generate(-0.57174928, -0.81913332, 0.04608002), (-0.13434083, 0.14888086, 0.97968721), (-0.80935487, 0.55394503, -0.19516557)122.85176, -88.90891, 187.44212
13generate(0.54050205, -0.78506957, -0.30252821), (0.00784548, -0.35485918, 0.93488684), (-0.84130612, -0.50768173, -0.18564287)68.10952, -95.88298, 189.06475
14generate(0.85343968, 0.33401107, -0.40009664), (0.50895704, -0.36874272, 0.77781202), (0.1122651, -0.86744764, -0.48469695)52.65514, -120.54506, 142.15072
15generate(-0.06540556, 0.99157719, -0.11178903), (0.67647471, 0.12641682, 0.72553481), (0.73355578, -0.02816844, -0.67904525)97.84604, -128.813, 111.53362
16generate(0.82096246, -0.01557821, -0.57076962), (-0.01557821, -0.99986673, 0.0048829), (-0.57076962, 0.0048829, -0.82109573)72.6788, 0.76666, 231.85086
17generate(0.20625642, 0.9026756, -0.37767055), (0.9026756, -0.32450246, -0.2826215), (-0.37767055, -0.2826215, -0.88175396)102.88887, -44.45806, 222.36086
18generate(-0.81711416, 0.57364524, -0.05705783), (0.57364524, 0.79931291, -0.17896931), (-0.05705783, -0.17896931, -0.98219875)153.27067, -28.31753, 206.57667
19generate(-0.83488592, -0.54796053, -0.05200735), (-0.54796053, 0.81850474, 0.17259565), (-0.05200735, 0.17259565, -0.98361882)154.19827, 26.88258, 206.31151
20generate(0.1775011, -0.91212065, -0.36949869), (-0.91212065, -0.29344943, 0.28622257), (-0.36949869, 0.28622257, -0.88405167)104.38976, 44.8576, 221.93182
21generate(-0.35422555, 0.71614595, -0.60138111), (-0.8956603, -0.44473414, -0.00204329), (-0.26891801, 0.53790939, 0.79895969)171.16324, 72.89038, 42.30452
22generate(-0.89968401, 0.07110686, -0.43071162), (0.07110686, -0.94959742, -0.30530077), (-0.43071162, -0.30530077, 0.84928143)198.03901, 25.33374, 50.30717
23generate(-0.48292513, -0.67178377, -0.56168486), (0.82815599, -0.14198452, -0.54221587), (0.28450127, -0.72701235, 0.62490965)177.56285, -11.96336, 15.12711
24generate(0.32010448, -0.48587634, -0.81330025), (0.32927093, 0.86201098, -0.38537998), (0.88832076, -0.14443427, 0.43591853)138.03212, 12.5424, -14.61801
25generate(0.3996452, 0.37191141, -0.83783389), (-0.73610612, 0.67490142, -0.05153497), (0.54628884, 0.63733036, 0.54348737)134.07694, 64.9849, 2.17855
26generate(-0.12336286, 0.28783476, -0.9497014), (0.89974603, 0.43614516, 0.0153127), (0.41861519, -0.85260105, -0.3127823)187.91576, -74.57386, 99.77594
27generate(-0.4938774, 0.2474255, -0.83358607), (-0.05918503, 0.94687239, 0.31611675), (0.86751498, 0.20545874, -0.45299499)206.15294, -27.40316, 77.63291
28generate(-0.57174928, -0.13434083, -0.80935487), (-0.81913332, 0.14888086, 0.55394503), (0.04608002, 0.97968721, -0.19516557)210.00351, 10.03617, 118.02416
29generate(-0.2493622, -0.32987613, -0.9104945), (-0.32987613, -0.85503227, 0.40012693), (-0.9104945, 0.40012693, 0.10439447)194.14611, -13.99575, 165.13035
30generate(0.02775585, -0.06895727, -0.99723343), (0.73244974, -0.67749317, 0.06723385), (-0.6802551, -0.73228949, 0.03170333)180.49514, -66.28762, 153.85233
31generate(0.43630049, -0.29051192, 0.851613), (0.72312333, -0.4500287, -0.52399125), (0.53547599, 0.84443886, 0.01372821)-41.01852, -5.29676, 57.02789
32generate(0.59305129, 0.0636463, 0.8026452), (0.57349283, 0.66632092, -0.47657361), (-0.56515143, 0.74294386, 0.35866178)-48.7499, 2.01477, 111.20123
33generate(0.32010448, 0.32927093, 0.88832076), (-0.48587634, 0.86201098, -0.14443427), (-0.81330025, -0.38537998, 0.43591853)-35.32907, 54.14351, 123.46741
34generate(-0.00533673, 0.13927776, 0.99023897), (-0.990972, -0.13339553, 0.01342149), (0.13396277, -0.98122747, 0.13873225)-19.30317, 79.04932, 76.87498
35generate(0.06647636, -0.24376911, 0.96755233), (-0.24376911, -0.94428064, -0.22115762), (0.96755233, -0.22115762, -0.12219571)-22.81944, 42.31321, 35.8131
36generate(0.04128792, -0.71346879, 0.69946951), (-0.72720906, 0.45861768, 0.51072184), (-0.68517318, -0.52974721, -0.4999056)6.53686, 6.98017, 208.41177
37generate(0.80051012, -0.38217866, 0.46165249), (-0.58541466, -0.66359589, 0.46575763), (0.12834807, -0.64310183, -0.75494822)-30.8447, 0.05458, 168.3788
38generate(0.73456993, 0.47685367, 0.48271897), (0.47685367, -0.86890732, 0.13270512), (0.48271897, 0.13270512, -0.86566261)-27.63994, -52.21639, 150.90144
39generate(-0.06540556, 0.67647471, 0.73355578), (0.99157719, 0.12641682, -0.02816844), (-0.11178903, 0.72553481, -0.67904525)11.72228, -77.59604, 180.1328
40generate(-0.4938774, -0.05918503, 0.86751498), (0.2474255, 0.94687239, 0.20545874), (-0.83358607, 0.31611675, -0.45299499)32.84471, -41.01056, 215.67613
41generate(-0.35422555, -0.8956603, -0.26891801), (0.71614595, -0.44473414, 0.53790939), (-0.60138111, -0.00204329, 0.79895969)137.29186, -112.91702, 69.28367
42generate(0.62863578, -0.5216361, -0.57681266), (0.77506767, 0.35925463, 0.51981364), (-0.06393095, -0.77384229, 0.63014358)88.90164, -115.85487, 42.86892
43generate(0.59305129, 0.57349283, -0.56515143), (0.0636463, 0.66632092, 0.74294386), (0.8026452, -0.47657361, 0.35866178)90.60127, -80.856, 0.20542
44generate(-0.41180246, 0.87629553, -0.25004975), (-0.434958, 0.05210955, 0.89894167), (0.80076855, 0.47894754, 0.35969291)140.04192, -56.28767, 0.25268
45generate(-0.99725174, -0.03169104, -0.06696743), (-0.03169104, -0.63456024, 0.7722234), (-0.06696743, 0.7722234, 0.63181198)168.8983, -76.10246, 42.94538
46generate(0.43630049, 0.72312333, 0.53547599), (-0.29051192, -0.4500287, 0.84443886), (0.851613, -0.52399125, 0.01372821)-8.81046, -62.45663, 31.37356
47generate(-0.38914825, 0.4668954, 0.79408585), (0.4668954, -0.64313549, 0.60694763), (0.79408585, 0.60694763, 0.03228374)31.82698, -99.72412, 34.15143
48generate(-0.41180246, -0.434958, 0.80076855), (0.87629553, 0.05210955, 0.47894754), (-0.25004975, 0.89894167, 0.35969291)32.9845, -119.90601, 85.52589
49generate(0.3996452, -0.73610612, 0.54628884), (0.37191141, 0.67490142, 0.63733036), (-0.83783389, -0.05153497, 0.54348737)-6.93754, -95.1116, 114.49918
50generate(0.92380165, -0.0203725, 0.38232902), (-0.34921526, 0.36456291, 0.86321642), (-0.15696886, -0.93095588, 0.32966943)-32.76825, -59.60594, 81.0312
51generate(0.04128792, -0.72720906, -0.68517318), (-0.71346879, 0.45861768, -0.52974721), (0.69946951, 0.51072184, -0.4999056)147.6043, 111.86817, 96.04895
52generate(0.54050205, 0.00784548, -0.84130612), (-0.78506957, -0.35485918, -0.50768173), (-0.30252821, 0.93488684, -0.18564287)123.00025, 115.43048, 145.34331
53generate(0.02775585, 0.73244974, -0.6802551), (-0.06895727, -0.67749317, -0.73228949), (-0.99723343, 0.06723385, 0.03170333)148.20139, 80.20148, 179.57492
54generate(-0.78835286, 0.44522525, -0.42458715), (0.44522525, -0.06341508, -0.8931702), (-0.42458715, -0.8931702, -0.14823207)188.38061, 54.86645, 151.43687
55generate(-0.77998958, -0.4568935, -0.42762669), (0.04689522, 0.63874005, -0.76799218), (0.62403293, -0.61907955, -0.47678446)188.01158, 74.43754, 99.81498
56generate(-0.12336286, 0.89974603, 0.41861519), (0.28783476, 0.43614516, -0.85260105), (-0.9497014, 0.0153127, -0.3127823)48.51164, 63.50541, 210.81394
57generate(-0.77998958, 0.04689522, 0.62403293), (-0.4568935, 0.63874005, -0.61907955), (-0.42762669, -0.76799218, -0.47678446)80.86848, 100.14844, 185.15645
58generate(-0.20900468, -0.87098456, 0.44463798), (-0.87098456, -0.0409373, -0.48960191), (0.44463798, -0.48960191, -0.75005802)52.81018, 120.56046, 142.21388
59generate(0.80051012, -0.58541466, 0.12834807), (-0.38217866, -0.66359589, -0.64310183), (0.46165249, 0.46575763, -0.75494822)3.11236, 96.53275, 141.33139
60generate(0.85343968, 0.50895704, 0.1122651), (0.33401107, -0.36874272, -0.86744764), (-0.40009664, 0.77781202, -0.48469695)0.45571, 61.27079, 183.72856
DetailsThe biological assembly is a pentamer generated from the NCS operations transform -0.786808 0.446245 -0.426379 0.446245 -0.065939 -0.892478 -0.426379 -0.892478 -0.147254 188.40018 54.79469 151.5200 transform -0.779791 0.044970 0.624423 -0.457367 0.640150 -0.617271 -0.427483 -0.766933 -0.478615 80.93045 100.10513 185.2010 transform 0.319237 -0.486126 -0.813492 0.330668 0.861597 -0.385109 0.888114 -0.146055 0.435800 138.05939 12.51177 -14.6326 transform 0.321485 0.329827 0.887615 -0.485796 0.862065 -0.144382 -0.812803 -0.384783 0.437370 -35.30357 54.13622 123.5062

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Components

#1: Protein Penton protein / Virion component III / Penton base protein


Mass: 58218.684 Da / Num. of mol.: 1 / Fragment: residues 49-571
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 2 / Genus: Mastadenovirus / Species: Human adenovirus C / Gene: penton base / Plasmid: Htb / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03276
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-C15 / N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE


Mass: 336.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H38NO3S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.4 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M Ammonium sulfate, 10% dioxane, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-110.934
SYNCHROTRONESRF ID14-220.933
SYNCHROTRONESRF ID14-430.933
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMay 19, 2003
ADSC QUANTUM 42CCDMay 19, 2003
ADSC QUANTUM 43CCDMay 20, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1diamond (111), Ge (220)SINGLE WAVELENGTHMx-ray1
2diamond (111), Ge (220)SINGLE WAVELENGTHMx-ray1
3Si (111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
20.9331
ReflectionResolution: 3.3→25 Å / Num. all: 657395 / Num. obs: 447016 / % possible obs: 57.3 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 1.6 / Redundancy: 1.5 % / Biso Wilson estimate: 118.2 Å2 / Rmerge(I) obs: 0.21 / Rsym value: 0.21 / Net I/σ(I): 2.9
Reflection shellResolution: 3.3→3.39 Å / Redundancy: 1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.6 / Num. unique all: 12708 / Rsym value: 0.47 / % possible all: 22

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RAVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: electron microscopy map of ad3 dodecahedron

Resolution: 3.3→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1824525.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.307 22325 5 %SHELLS
Rwork0.307 ---
obs0.307 445700 57.1 %-
all-460825 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 100 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 62.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.51 Å20 Å217.68 Å2
2--0.05 Å20 Å2
3----3.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.62 Å
Luzzati d res low-5 Å
Luzzati sigma a1.03 Å1.05 Å
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3632 0 45 0 3677
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d1.31
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.842
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it3.212.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.403 1786 6.5 %
Rwork0.405 25642 -
obs--21.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ZWIT_PARA.TXTZWIT_TOPO.TXT
X-RAY DIFFRACTION4SULFATE_PARA.TXTSULFATE_TOPO.TXT

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