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- PDB-4ar2: Dodecahedron formed of penton base protein from adenovirus Ad3 -

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Basic information

Entry
Database: PDB / ID: 4ar2
TitleDodecahedron formed of penton base protein from adenovirus Ad3
Components
  • FIBER PROTEIN
  • L2 PROTEIN III (PENTON BASE)
KeywordsVIRAL PROTEIN / CAPSID PROTEIN / DSDNA VIRUS / DODECAHEDRON / VIRUS-LIKE PARTICLE / STRAND SWAPPING
Function / homology
Function and homology information


T=25 icosahedral viral capsid / adhesion receptor-mediated virion attachment to host cell / viral capsid / cell adhesion / endocytosis involved in viral entry into host cell / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / metal ion binding
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
Fiber protein / Penton protein
Similarity search - Component
Biological speciesHUMAN ADENOVIRUS 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsBurmeister, W.P. / Szolajska, E. / Zochowska, M. / Nerlo, B. / Andreev, I. / Schoehn, G. / Andrieu, J.-P. / Fender, P. / Naskalska, A. / Zubieta, C. ...Burmeister, W.P. / Szolajska, E. / Zochowska, M. / Nerlo, B. / Andreev, I. / Schoehn, G. / Andrieu, J.-P. / Fender, P. / Naskalska, A. / Zubieta, C. / Cusack, S. / Chroboczek, J.
CitationJournal: Plos One / Year: 2012
Title: The Structural Basis for the Integrity of Adenovirus Ad3 Dodecahedron.
Authors: Szolajska, E. / Burmeister, W.P. / Zochowska, M. / Nerlo, B. / Andreev, I. / Schoehn, G. / Andrieu, J.P. / Fender, P. / Naskalska, A. / Zubieta, C. / Cusack, S. / Chroboczek, J.
History
DepositionApr 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L2 PROTEIN III (PENTON BASE)
P: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6133
Polymers60,5732
Non-polymers401
Water00
1
A: L2 PROTEIN III (PENTON BASE)
P: FIBER PROTEIN
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)3,636,792180
Polymers3,634,387120
Non-polymers2,40560
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: L2 PROTEIN III (PENTON BASE)
P: FIBER PROTEIN
hetero molecules
x 5


  • icosahedral pentamer
  • 303 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)303,06615
Polymers302,86610
Non-polymers2005
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: L2 PROTEIN III (PENTON BASE)
P: FIBER PROTEIN
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 364 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)363,67918
Polymers363,43912
Non-polymers2406
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
Unit cell
Length a, b, c (Å)346.040, 348.550, 372.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.962216, 0.267978, 0.048253), (-0.135196, 0.31637, 0.938953), (0.236353, -0.909999, 0.340645)6.70836, 24.67315, -42.46407
3generate(0.902065, 0.296198, 0.31392), (0.047831, -0.791466, 0.609339), (0.428942, -0.534649, -0.728121)17.56766, -8.13896, -77.5548
4generate(0.901355, 0.045433, 0.430692), (0.295091, -0.792325, -0.533987), (0.316987, 0.608405, -0.727573)17.84501, -53.02705, -57.46813
5generate(0.96155, -0.139217, 0.236728), (0.269737, 0.316774, -0.909338), (0.051606, 0.938229, 0.342146)6.90382, -48.443, -9.428
6generate(0.105088, 0.98983, 0.09588), (0.006935, -0.097141, 0.995246), (0.994439, -0.103923, -0.017072)154.36816, -0.11099, -172.50928
7generate(0.152, 0.92072, 0.359402), (0.923105, -0.262199, 0.281299), (0.353233, 0.289008, -0.889776)146.6971, -158.41914, -64.01796
8generate(0.41517, 0.827779, 0.377381), (0.602769, 0.060405, -0.795626), (-0.681398, 0.557793, -0.473881)101.71443, -105.56051, 114.42274
9generate(0.528803, 0.839333, 0.126048), (-0.506512, 0.431245, -0.746642), (-0.681038, 0.330982, 0.653176)81.68137, 85.31494, 116.42027
10generate(0.338189, 0.939746, -0.050051), (-0.871782, 0.332874, 0.359433), (0.354436, -0.077923, 0.931828)114.13251, 150.03575, -61.038
11generate(0.37167, 0.381178, -0.846501), (0.036367, 0.905142, 0.423551), (0.927652, -0.188206, 0.322552)105.96649, -5.16959, -160.41843
12generate(0.414204, 0.600254, -0.684201), (0.831578, 0.056026, 0.552575), (0.370018, -0.797845, -0.475952)99.22054, -141.89063, -67.22337
13generate(0.640673, 0.552914, -0.532751), (0.554626, -0.813083, -0.176877), (-0.530969, -0.182157, -0.827581)60.67596, -96.8388, 86.97224
14generate(0.738881, 0.301741, -0.602501), (-0.411093, -0.506605, -0.757862), (-0.533908, 0.807653, -0.250277)43.41902, 67.45765, 89.81385
15generate(0.573272, 0.19611, -0.79555), (-0.731775, 0.559324, -0.389437), (0.368598, 0.805417, 0.464153)71.27521, 124.45345, -63.38511
16generate(-0.617184, 0.654758, -0.436321), (0.440895, 0.747093, 0.497457), (0.651686, 0.114651, -0.749773)277.54901, -74.96735, -116.14239
17generate(-0.497604, 0.556195, -0.66561), (-0.621238, 0.307012, 0.720976), (0.605354, 0.772263, 0.192759)256.40256, 108.49042, -105.57785
18generate(-0.246881, 0.677028, -0.693312), (-0.882248, -0.452995, -0.128197), (-0.40086, 0.580024, 0.709143)212.88651, 151.56535, 69.35555
19generate(-0.212281, 0.851925, -0.478707), (0.01751, -0.486477, -0.873518), (-0.977052, -0.193813, 0.088353)207.47379, -5.75655, 167.09059
20generate(-0.44272, 0.836983, -0.32165), (0.834686, 0.253646, -0.488838), (-0.327564, -0.484895, -0.810912)247.76434, -145.57658, 52.27922
21generate(0.573537, -0.757954, -0.310743), (-0.569782, -0.096566, -0.816103), (0.588561, 0.64512, -0.487253)72.09933, 95.66355, -103.98481
22generate(0.424451, -0.723319, -0.544657), (0.293438, 0.678953, -0.672991), (0.856583, 0.125829, 0.500432)97.2008, -52.27591, -147.84995
23generate(0.531224, -0.504802, -0.680423), (0.838214, 0.430007, 0.335397), (0.123277, -0.748511, 0.651563)78.74267, -143.7225, -21.96442
24generate(0.742638, -0.405977, -0.532609), (0.30981, -0.496815, 0.810674), (-0.593723, -0.767045, -0.243178)42.78558, -52.18308, 99.38449
25generate(0.769246, -0.56164, -0.304666), (-0.559984, -0.822221, 0.101838), (-0.307699, 0.09227, -0.946999)38.56958, 95.80709, 48.95875
26generate(-0.444761, -0.116029, -0.888102), (0.646466, 0.644698, -0.407978), (0.619895, -0.75558, -0.211728)246.11836, -112.84386, -109.32576
27generate(-0.223207, 0.025391, -0.97444), (0.847746, -0.488378, -0.206912), (-0.481149, -0.872263, 0.087484)207.77013, -147.11508, 81.16329
28generate(-0.005979, -0.150011, -0.988666), (-0.154579, -0.976661, 0.149124), (-0.987962, 0.153719, -0.017349)170.28395, 26.48606, 168.54303
29generate(-0.097489, -0.399979, -0.911325), (-0.975385, -0.143578, 0.167358), (-0.197786, 0.905208, -0.376136)186.29697, 168.1362, 31.32974
30generate(-0.368437, -0.37762, -0.849504), (-0.478956, 0.860283, -0.174684), (0.796778, 0.342515, -0.497823)233.15274, 81.5655, -140.47789
31generate(-0.493216, -0.869722, -0.017914), (-0.250642, 0.161797, -0.954463), (0.833017, -0.466266, -0.29779)256.48788, 40.73499, -146.16367
32generate(-0.502083, -0.814776, -0.28992), (0.769826, -0.268318, -0.579115), (0.394058, -0.513951, 0.761953)257.44717, -134.28981, -68.26599
33generate(-0.253753, -0.881341, -0.398557), (0.682073, -0.4552, 0.572337), (-0.685847, -0.126612, 0.716647)214.55997, -116.99256, 117.66512
34generate(-0.092129, -0.976654, -0.194059), (-0.393062, -0.143392, 0.908262), (-0.914885, 0.159954, -0.370675)187.03157, 69.00961, 155.16948
35generate(-0.240461, -0.969846, 0.039712), (-0.970342, 0.239136, -0.03537), (0.024807, -0.047039, -0.998585)213.09647, 166.76401, -8.36142
36generate(-0.985392, 0.119989, -0.12085), (0.111593, -0.081102, -0.990439), (-0.128643, -0.989457, 0.066527)341.62534, -21.79301, 19.88815
37generate(-0.993689, -0.107601, 0.031706), (-0.111166, 0.906775, -0.406696), (0.015011, -0.407654, -0.913013)343.31073, 18.2358, -6.71749
38generate(-0.937086, -0.322831, -0.132856), (-0.316586, 0.625486, 0.713121), (-0.147118, 0.710316, -0.688337)333.11688, 55.88904, 22.33233
39generate(-0.893772, -0.227994, -0.386252), (-0.216645, -0.534597, 0.816866), (-0.39273, 0.813772, 0.428414)325.22342, 38.22278, 67.10452
40generate(-0.923817, 0.046562, -0.379992), (0.047544, -0.970939, -0.234558), (-0.37987, -0.234755, 0.894756)330.48013, -9.59416, 65.27094
41generate(0.583355, -0.563708, 0.584748), (-0.750916, -0.099929, 0.652794), (-0.309552, -0.819907, -0.481592)72.33907, 130.48666, 50.19634
42generate(0.341693, -0.60887, 0.715907), (-0.60611, -0.724935, -0.32726), (0.718245, -0.322096, -0.616748)114.43113, 103.07596, -127.22364
43generate(0.199314, -0.796418, 0.570957), (0.438812, -0.448428, -0.778689), (0.876195, 0.405747, 0.2601)138.59297, -77.85259, -152.28111
44generate(0.35443, -0.866306, 0.351984), (0.933723, 0.348178, -0.083275), (-0.050412, 0.358171, 0.932294)111.45085, -161.60065, 8.82545
45generate(0.587994, -0.723897, 0.360884), (0.202363, 0.563624, 0.80086), (-0.783143, -0.397871, 0.477897)71.12305, -33.51637, 133.95815
46generate(-0.709789, -0.239557, 0.662428), (-0.230328, -0.809777, -0.539639), (0.665694, -0.535605, 0.519595)295.69705, 37.23017, -115.54214
47generate(-0.711077, -0.474827, 0.518564), (0.650082, -0.72498, 0.227588), (0.267884, 0.498942, 0.824193)295.32019, -112.42587, -45.75154
48generate(-0.495452, -0.630347, 0.597654), (0.55057, 0.304289, 0.777355), (-0.671862, 0.714193, 0.19629)258.08008, -93.02379, 114.91512
49generate(-0.360306, -0.489683, 0.793971), (-0.389247, 0.852421, 0.349091), (-0.847742, -0.183271, -0.49774)235.55167, 68.25406, 142.70815
50generate(-0.494882, -0.246079, 0.833389), (-0.868693, 0.163908, -0.467448), (-0.02157, -0.95529, -0.294882)259.19614, 147.9456, 0.43946
51generate(0.201005, 0.440155, 0.875135), (-0.793886, -0.450176, 0.408762), (0.573884, -0.77692, 0.258945)139.14883, 137.24168, -100.47661
52generate(0.003436, 0.261235, 0.965269), (0.262719, -0.931602, 0.251188), (0.964866, 0.252731, -0.071832)173.37822, -45.56617, -168.1274
53generate(0.123456, 0.012649, 0.992269), (0.988151, -0.09345, -0.121753), (0.091188, 0.995544, -0.024036)152.72113, -171.10098, -17.36772
54generate(0.393779, 0.037265, 0.918449), (0.381085, 0.902646, -0.200011), (-0.836488, 0.428768, 0.341242)105.94844, -66.5853, 143.38593
55generate(0.439891, 0.301403, 0.845963), (-0.717816, 0.684078, 0.12953), (-0.539663, -0.664224, 0.517271)97.8179, 123.7296, 92.41959
56generate(-0.705773, 0.653927, 0.272514), (-0.469091, -0.719628, 0.511946), (0.530884, 0.233484, 0.814645)294.49768, 81.75175, -91.88463
57generate(-0.488463, 0.781353, 0.388448), (-0.822359, -0.263363, -0.504346), (-0.29177, -0.565798, 0.771196)257.21848, 140.61427, 50.07114
58generate(-0.428339, 0.651981, 0.625657), (-0.127153, 0.642013, -0.756077), (-0.894627, -0.403411, -0.192097)247.32935, 20.00494, 152.13536
59generate(-0.608073, 0.445325, 0.657216), (0.6601, 0.743528, 0.106932), (-0.441038, 0.498851, -0.746078)278.4523, -114.3088, 72.75543
60generate(-0.778929, 0.44601, 0.440845), (0.446131, -0.099932, 0.889371), (0.440723, 0.889432, -0.121139)307.55966, -75.7487, -78.31133

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Components

#1: Protein L2 PROTEIN III (PENTON BASE) / PENTON PROTEIN


Mass: 58050.332 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-542
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN ADENOVIRUS 3 / Strain: UNIDENTIFIED / Plasmid: BAC PAC6 / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q2Y0H9
#2: Protein/peptide FIBER PROTEIN / PIV


Mass: 2522.787 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN ADENOVIRUS 3 / Strain: UNIDENTIFIED / Plasmid: BAC PAC6 / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P03275
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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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: 3.61 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: HANGING DROP METHOD. RESERVOIR 10-15 % PEG 8000, 100 MM HEPES PH 6.5, 100 MM CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.033
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.8→30 Å / Num. obs: 249444 / % possible obs: 56.8 % / Observed criterion σ(I): 0 / Redundancy: 2.36 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 4.67
Reflection shellResolution: 3.8→3.9 Å / Redundancy: 1.29 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.29 / % possible all: 42.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0114refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AQQ

4aqq


Resolution: 3.8→258.2 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.862 / SU B: 0.001 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 1.245 / ESU R Free: 1.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. ONLY ONE SUBUNIT COMPOSED OF PROTEIN AND PEPTIDE IS GIVEN. THE OTHER SUBUNITS HAVE TO BE GENERATED USING ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. ONLY ONE SUBUNIT COMPOSED OF PROTEIN AND PEPTIDE IS GIVEN. THE OTHER SUBUNITS HAVE TO BE GENERATED USING MTRIX RECORDS IN ORDER TO OBTAIN THE 60 SUBUNITS OF THE VLP IN THE ASU.
RfactorNum. reflection% reflectionSelection details
Rfree0.27809 5040 2 %RANDOM
Rwork0.28048 ---
obs0.28043 244404 56.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.819 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--3.16 Å20 Å2
3----3.92 Å2
Refinement stepCycle: LAST / Resolution: 3.8→258.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3756 0 1 0 3757
LS refinement shellResolution: 3.8→3.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 266 -
Rwork0.454 13051 -
obs--41.53 %

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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

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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

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