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- PDB-1x9t: The crystal structure of human adenovirus 2 penton base in comple... -

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Basic information

Entry
Database: PDB / ID: 1x9t
TitleThe crystal structure of human adenovirus 2 penton base in complex with an ad2 N-terminal fibre peptide
Components
  • N-terminal peptide of Fiber protein
  • Penton protein
KeywordsVirus like Particle/peptide / jellyroll domain / insertion domain / anti-parallel beta sheets / Virus like Particle-peptide COMPLEX
Function / homology
Function and homology information


T=25 icosahedral viral capsid / adhesion receptor-mediated virion attachment to host cell / viral capsid / clathrin-dependent endocytosis of virus by host cell / cell adhesion / symbiont entry into 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 / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein ...Penton protein; domain 1 / adenovirus 2 penton base, domain 2 / adenovirus 2 penton base, domain 2 / Adenovirus penton base protein / Adenovirus penton base protein / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Jelly Rolls / Alpha-Beta Complex / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-C15 / Fiber protein / Penton protein
Similarity search - Component
Biological speciesHuman adenovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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:
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Assembly

Deposited unit
A: Penton protein
B: N-terminal peptide of Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4154
Polymers60,7412
Non-polymers6732
Water00
1
A: Penton protein
B: N-terminal peptide of Fiber protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)3,684,875240
Polymers3,644,488120
Non-polymers40,386120
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
B: N-terminal peptide of Fiber protein
hetero molecules
x 5


  • icosahedral pentamer
  • 307 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)307,07320
Polymers303,70710
Non-polymers3,36610
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Penton protein
B: N-terminal peptide of Fiber protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 368 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)368,48724
Polymers364,44912
Non-polymers4,03912
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
B: N-terminal peptide of Fiber protein
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 3.68 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)3,684,875240
Polymers3,644,488120
Non-polymers40,386120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)438.370, 299.825, 419.583
Angle α, β, γ (deg.)90.00, 103.22, 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(0.31911818, 0.48681032, -0.81312933), (-0.33759116, 0.86009954, 0.38244083), (0.8855483, 0.15246145, 0.43881626)142.48943, -9.50758, -20.15926
3generate(-0.78257174, 0.45008448, -0.43012259), (-0.05942366, 0.63373585, 0.77126371), (0.61971792, 0.62912864, -0.4691981)199.72409, -73.49794, 95.72627
4generate(-0.78257174, -0.05942366, 0.61971792), (0.45008448, 0.63373585, 0.62912864), (-0.43012259, 0.77126371, -0.4691981)92.60763, -103.53857, 187.50672
5generate(0.31911818, -0.33759116, 0.8855483), (0.48681032, 0.86009954, 0.15246145), (-0.81312933, 0.38244083, 0.43881626)-30.82865, -58.11435, 128.34463
6generate(-0.79986298, -0.59618992, -0.0691143), (-0.59618992, 0.7759954, 0.20588519), (-0.0691143, 0.20588519, -0.97613242)164.39348, 31.11223, 207.66218
7generate(-0.11518642, -0.9127015, 0.3920562), (-0.26990295, 0.40859144, 0.8718976), (-0.95597306, -0.00538636, -0.29340502)57.48308, -65.36687, 215.53476
8generate(0.61854658, -0.78131462, -0.08335222), (0.54803964, 0.35296854, 0.7583309), (-0.56307431, -0.51474331, 0.64651887)41.84425, -125.28671, 85.28474
9generate(0.38734195, -0.38360149, -0.83834128), (0.727269, 0.68599566, 0.02213041), (0.56660922, -0.61827166, 0.54469637)139.08933, -65.84011, -3.08677
10generate(-0.48928336, -0.26918814, -0.82954176), (0.02009624, 0.94744064, -0.31929982), (0.8718933, -0.17289876, -0.45815728)214.82892, 30.81974, 72.54664
11generate(0.10059943, 0.25807311, 0.96087357), (0.25807311, -0.93948595, 0.22530961), (0.96087357, 0.22530961, -0.16111348)-19.40492, -45.56698, 34.46516
12generate(0.79587987, 0.41743758, 0.4385443), (0.59904052, -0.64806775, -0.47027507), (0.08789593, 0.63698827, -0.7658461)-26.89471, -4.40412, 172.48527
13generate(0.50140866, 0.8133415, -0.29506772), (-0.00650463, -0.3374825, -0.94130933), (-0.86518614, 0.47389995, -0.16392616)73.70021, 96.59477, 194.39218
14generate(-0.375865, 0.89865911, -0.2261356), (-0.72171952, -0.43694844, -0.53683982), (-0.5812456, -0.03857283, 0.81281344)143.36108, 117.85266, 69.91129
15generate(-0.62357872, 0.55548437, 0.55007881), (-0.55820148, -0.80900704, 0.18417033), (0.54732137, -0.19221011, 0.81455177)85.81894, 29.99187, -28.92905
16generate(-0.30073645, 0.33811681, -0.89175928), (0.33811681, -0.83650945, -0.4311948), (-0.89175928, -0.4311948, 0.1372459)204.6993, 14.41735, 165.97922
17generate(-0.99981163, 0.0084536, -0.01747117), (0.0084536, -0.62062323, -0.78406336), (-0.01747117, -0.78406336, 0.62043486)176.61007, 79.24116, 40.24579
18generate(-0.3373835, -0.48211136, 0.80854252), (-0.48211136, -0.64922189, -0.58828528), (0.80854252, -0.58828528, -0.01339461)34.41931, 102.15247, 32.70337
19generate(0.77109478, -0.45563396, 0.44475896), (-0.45563396, -0.88278306, -0.11441922), (0.44475896, -0.11441922, -0.88831172)-25.37018, 51.48862, 153.77533
20generate(0.7937439, 0.05129493, -0.60608535), (0.05129493, -0.99853314, -0.01733196), (-0.60608535, -0.01733196, -0.79521076)79.86864, -2.73467, 236.14433
21generate(0.01692334, 0.71427037, -0.69966523), (0.71145501, 0.4830727, 0.51036509), (0.70252784, -0.50641742, -0.49999604)157.33366, -114.27246, 91.61846
22generate(-0.85531818, 0.5159101, -0.04761919), (0.5159101, 0.83964525, -0.16980171), (-0.04761919, -0.16980171, -0.98432708)167.05881, -27.77908, 206.6156
23generate(-0.48928336, 0.02009624, 0.8718933), (-0.26918814, 0.94744064, -0.17289876), (-0.82954176, -0.31929982, -0.45815728)41.23992, 41.17274, 221.28807
24generate(0.6091801, -0.08797331, 0.78813723), (-0.55886062, 0.6574893, 0.50535396), (-0.56264946, -0.74831044, 0.35136458)-46.24557, -2.70608, 115.35902
25generate(0.92203305, 0.3410499, -0.18313935), (0.04721018, 0.37049413, 0.92763425), (0.38422163, -0.86395547, 0.32550681)25.50431, -98.7765, 35.21879
26generate(-0.39102028, 0.4001303, 0.82885396), (-0.89234313, 0.0557765, -0.44789811), (-0.22544818, -0.91475938, 0.33524378)37.04428, 123.6991, 87.52341
27generate(0.47412809, 0.28016746, 0.83469081), (-0.70022798, -0.4547157, 0.5503766), (0.53374463, -0.84542287, -0.01941239)-39.18532, 5.04863, 57.33831
28generate(0.79587987, 0.59904052, 0.08789593), (0.41743758, -0.64806775, 0.63698827), (0.4385443, -0.47027508, -0.7658461)8.88246, -101.4984, 141.82054
29generate(0.12958504, 0.91607774, -0.37948555), (0.91607774, -0.2570737, -0.3077575), (-0.37948555, -0.3077575, -0.87251134)114.81959, -48.69761, 224.21853
30generate(-0.60395959, 0.79314447, 0.0784517), (0.10658875, 0.17792597, -0.97825415), (-0.78985546, -0.58246391, -0.19200037)132.22455, 90.4821, 190.66106
31generate(-0.48625338, -0.82432082, 0.28991867), (0.68663637, -0.15524245, 0.71023255), (-0.54045179, 0.54442168, 0.64149583)100.34405, -132.50054, 83.82942
32generate(0.37984811, -0.9015097, 0.20735397), (0.90047186, 0.3090208, -0.30603363), (0.2118156, 0.30296271, 0.92916508)33.05084, -47.5039, -11.28745
33generate(0.6091801, -0.55886062, -0.56264946), (-0.08797331, 0.6574893, -0.74831044), (0.78813723, 0.50535396, 0.35136458)91.56625, 84.0352, -2.71769
34generate(-0.11518642, -0.26990295, -0.95597306), (-0.9127015, 0.40859144, -0.00538636), (0.3920562, 0.8718976, -0.29340502)195.02398, 80.33418, 97.6956
35generate(-0.79220155, -0.43396639, -0.42905697), (-0.43396639, -0.09370441, 0.89604278), (-0.42905697, 0.89604278, -0.11409405)200.44896, -53.49227, 151.18465
36generate(0.86035032, -0.29007985, -0.4191074), (-0.50574826, -0.38360675, -0.77269953), (0.06337213, 0.87675512, -0.47674357)54.96586, 123.0365, 145.13527
37generate(0.00134198, 0.10543215, -0.99442559), (-0.71615397, -0.69395035, -0.07454126), (-0.69794104, 0.71226187, 0.07457438)188.76353, 70.19694, 155.4401
38generate(-0.91577661, -0.06027614, -0.39713977), (-0.06027614, -0.95686219, 0.28422093), (-0.39713977, 0.28422093, 0.8726388)207.99923, -23.74695, 47.71563
39generate(-0.62357872, -0.55820148, 0.54732137), (0.55548437, -0.80900704, -0.19221011), (0.55007881, 0.18417033, 0.81455177)86.08986, -28.9679, -29.16659
40generate(0.47412809, -0.70022798, 0.53374463), (0.28016746, -0.4547157, -0.84542287), (0.83469081, 0.5503766, -0.01941239)-8.48996, 61.74926, 31.04206
41generate(0.01692334, 0.71145501, 0.70252784), (0.71427037, 0.4830727, -0.50641742), (-0.69966523, 0.51036509, -0.49999604)14.27259, -10.77969, 214.21044
42generate(0.38734195, 0.727269, 0.56660922), (-0.38360149, 0.68599566, -0.61827166), (-0.83834128, 0.02213041, 0.54469637)-4.24266, 96.61244, 119.74275
43generate(0.37984811, 0.90047186, 0.2118156), (-0.9015097, 0.3090208, 0.30296271), (0.20735397, -0.30603363, 0.92916508)32.61248, 47.89502, -10.9031
44generate(0.00479804, 0.99170312, 0.12845969), (-0.12372271, -0.12688544, 0.98417111), (0.99230523, -0.02061548, 0.1220874)73.90547, -89.60613, 2.82101
45generate(-0.2195018, 0.87488429, 0.43173653), (0.87488429, -0.01931545, 0.48394668), (0.43173653, 0.48394668, -0.76118275)62.5708, -125.86909, 141.94883
46generate(-0.48625338, 0.68663637, -0.54045179), (-0.82432082, -0.15524245, 0.54442168), (0.28991867, 0.71023255, 0.64149583)185.07809, 16.50743, 11.23836
47generate(-0.86557083, 0.27146441, 0.42082563), (0.27146441, -0.45180852, 0.84980947), (0.42082563, 0.84980947, 0.31737935)120.15898, -110.44873, 32.86403
48generate(0.00479804, -0.12372271, 0.99230523), (0.99170312, -0.12688544, -0.02061548), (0.12845969, 0.98417111, 0.1220874)-14.24021, -84.60385, 78.34948
49generate(0.92203305, 0.04721018, 0.38422163), (0.3410499, 0.37049413, -0.86395547), (-0.18313935, 0.92763425, 0.32550681)-32.38438, 58.32533, 84.83535
50generate(0.61854658, 0.54803964, -0.56307431), (-0.78131462, 0.35296854, -0.51474331), (-0.08335222, 0.7583309, 0.64651887)90.80111, 120.81554, 43.3584
51generate(0.86035032, -0.50574826, 0.06337213), (-0.29007985, -0.38360675, 0.87675512), (-0.4191074, -0.77269953, -0.47674357)5.73807, -64.10597, 187.29915
52generate(0.50140866, -0.00650463, -0.86518614), (0.8133415, -0.3374825, 0.47389995), (-0.29506772, -0.94130933, -0.16392616)131.85981, -119.46684, 144.53807
53generate(-0.60395959, 0.10658875, -0.78985546), (0.79314447, 0.17792597, -0.58246391), (0.0784517, -0.97825415, -0.19200037)220.80859, -9.9191, 114.74824
54generate(-0.92817307, -0.32275934, 0.18525972), (-0.32275934, 0.45034166, -0.83247751), (0.18525972, -0.83247751, -0.52216859)149.66023, 113.146, 139.09819
55generate(-0.02317978, -0.70120442, 0.71258337), (-0.99222878, 0.10329535, 0.06936945), (-0.12224872, -0.70543776, -0.69814957)16.73934, 79.65667, 183.93712
56generate(-0.39102028, -0.89234313, -0.22544818), (0.4001303, 0.0557765, -0.91475938), (0.82885396, -0.44789811, 0.33524378)144.5991, 58.34082, -4.64139
57generate(-0.02317978, -0.99222878, -0.12224872), (-0.70120442, 0.10329535, -0.70543776), (0.71258337, 0.06936945, -0.69814957)101.91173, 133.26573, 110.9617
58generate(0.21931343, -0.88333789, -0.41426536), (-0.88333789, -0.36006132, 0.30011667), (-0.41426536, 0.30011667, -0.85925211)110.507, 46.59052, 225.91194
59generate(0.00134198, -0.71615397, -0.69794104), (0.10543215, -0.69395035, 0.71226187), (-0.99442559, -0.07454126, 0.07457438)158.50653, -81.90261, 181.35201
60generate(-0.375865, -0.72171952, -0.5812456), (0.89865911, -0.43694844, -0.03857283), (-0.2261356, -0.53683982, 0.81281344)179.57661, -74.64053, 38.86221
DetailsThe biological assembly is a pentamer generated by the following NCS transformations - transform 0.31890 0.49122 -0.81056 -0.33529 0.85838 0.38829 0.88650 0.14795 0.43844 142.48787 -10.25387 -20.5541 transform 0.31748 -0.33873 0.88570 0.49100 0.85779 0.15205 -0.81125 0.38661 0.43865 -30.76268 -58.66149 128.3920 transform -0.78147 0.45966 -0.42192 -0.04899 0.62893 0.77592 0.62201 0.62703 -0.46897 199.57140 -75.09582 95.14690 transform -0.78054 -0.05272 0.62288 0.45875 0.62856 0.62806 -0.42463 0.77597 -0.46643 92.59398-104.61158 186.86273

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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: Protein/peptide N-terminal peptide of Fiber protein


Mass: 2522.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / References: UniProt: P03275*PLUS
#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: 2

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 0.67 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.976 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 20, 2003 / Details: microgoniometer with beam size of 10 microns
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. all: 401225 / Num. obs: 354798 / % possible obs: 54 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 2.1 % / Biso Wilson estimate: 45.1 Å2 / Rmerge(I) obs: 0.19 / Rsym value: 0.19 / Net I/σ(I): 3.5
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 1 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.5 / Num. unique all: 18723 / Rsym value: 0.45 / % possible all: 29

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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: 3.5→29.98 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 21622171.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The working R is slightly higher due to a relatively high R for low resoution reflections. The lower resolution reflections were poorly measured. The test set has few of these reflections ...Details: The working R is slightly higher due to a relatively high R for low resoution reflections. The lower resolution reflections were poorly measured. The test set has few of these reflections and is thus slightly lower. The R-free, though chosen in thin shells, reflects the high correlation of reflections due to the 60-fold NCS and is basically the same as the R-working for this reason.
RfactorNum. reflection% reflectionSelection details
Rfree0.303 17745 5 %SHELLS
Rwork0.306 ---
obs0.306 354521 53.6 %-
all-372266 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 100 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 77.4 Å2
Baniso -1Baniso -2Baniso -3
1-19.59 Å20 Å220.13 Å2
2---11.56 Å20 Å2
3----8.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.58 Å
Luzzati d res low-5 Å
Luzzati sigma a0.92 Å0.93 Å
Refinement stepCycle: LAST / Resolution: 3.5→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3605 0 40 0 3645
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d1.13
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.408 2366 5.8 %
Rwork0.425 38373 -
obs--37.1 %
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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