[English] 日本語
Yorodumi
- PDB-4aqq: Dodecahedron formed of penton base protein from adenovirus Ad3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4aqq
TitleDodecahedron formed of penton base protein from adenovirus Ad3
ComponentsL2 PROTEIN III (PENTON BASE)
KeywordsVIRAL PROTEIN / CAPSID PROTEIN / DSDNA VIRUS / VIRUS-LIKE PARTICLE / STRAND SWAPPING
Function / homologyAdenovirus penton base protein / Adenovirus penton base protein / T=25 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / metal ion binding / Penton protein
Function and homology information
Biological speciesHUMAN ADENOVIRUS 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.75 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 19, 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 / struct_conn / struct_site
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 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: L2 PROTEIN III (PENTON BASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0902
Polymers58,0501
Non-polymers401
Water00
1
A: L2 PROTEIN III (PENTON BASE)
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)3,485,425120
Polymers3,483,02060
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)
hetero molecules
x 5


  • icosahedral pentamer
  • 290 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)290,45210
Polymers290,2525
Non-polymers2005
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: L2 PROTEIN III (PENTON BASE)
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 349 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)348,54212
Polymers348,3026
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)342.701, 342.701, 342.701
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.941, -0.33799, 0.01655), (0.10206, 0.33009, 0.93842), (-0.32264, -0.88137, 0.34511)2.70386, 160.69077, -112.14434
3generate(0.84483, -0.44495, -0.29712), (-0.17269, -0.75238, 0.6357), (-0.5064, -0.48575, -0.71247)-51.05784, 108.80674, -293.12048
4generate(0.8441, -0.16809, -0.50916), (-0.44404, -0.7514, -0.48808), (-0.30054, 0.63808, -0.70889)-87.28722, -83.52425, -292.1412
5generate(0.94102, 0.10444, -0.32182), (-0.33804, 0.33039, -0.88123), (0.01429, 0.93805, 0.34621)-55.18031, -150.78491, -111.69801
6generate(0.67434, 0.48708, -0.555), (0.70383, -0.19663, 0.68261), (0.22335, -0.85094, -0.47542)-95.18713, 117.36673, -252.58156
7generate(0.8652, 0.41782, 0.27723), (0.41801, -0.90636, 0.06144), (0.27695, 0.06273, -0.95884)47.10107, 11.41701, -335.12631
8generate(0.76906, -0.39622, 0.50155), (0.28303, -0.49246, -0.82303), (0.5731, 0.77491, -0.26659)85.37015, -140.14326, -216.21837
9generate(0.52011, -0.83314, -0.18803), (0.48072, 0.46753, -0.74184), (0.70597, 0.29545, 0.64368)-32.51867, -126.19143, -60.52098
10generate(0.46107, -0.29176, -0.83803), (0.74158, 0.64533, 0.18333), (0.48732, -0.70599, 0.5139)-143.57373, 31.91926, -82.89653
11generate(0.63655, 0.71151, -0.29759), (-0.19196, 0.51988, 0.83239), (0.74696, -0.47273, 0.46751)-51.36223, 143.02258, -90.43436
12generate(0.77047, 0.28286, 0.57128), (-0.39185, -0.49671, 0.77442), (0.50282, -0.82053, -0.27186)97.08134, 132.61191, -216.81081
13generate(0.56306, -0.67462, 0.47734), (-0.67203, -0.70994, -0.21064), (0.48098, -0.20218, -0.8531)81.32407, -35.70772, -316.56448
14generate(0.30725, -0.83199, -0.46194), (-0.63789, 0.18015, -0.74876), (0.70618, 0.52472, -0.47537)-79.54729, -127.68522, -251.89003
15generate(0.35392, 0.03398, -0.93466), (-0.34502, 0.9336, -0.0967), (0.86931, 0.3567, 0.34215)-160.55394, -15.58765, -111.76771
16generate(0.0458, 0.9638, 0.26268), (0.40895, -0.258, 0.87533), (0.91141, 0.06733, -0.40596)44.24019, 150.43338, -239.48529
17generate(-0.27797, 0.56735, -0.77515), (0.48638, 0.77899, 0.39575), (0.82836, -0.26701, -0.49247)-133.3548, 68.49478, -254.32678
18generate(-0.47188, -0.57015, -0.6725), (0.20074, 0.67325, -0.71164), (0.85851, -0.47081, -0.20324)-115.38923, -121.05467, -204.65771
19generate(-0.25574, -0.8827, 0.39425), (-0.04089, -0.39758, -0.91666), (0.96588, -0.25055, 0.06559)66.28629, -157.21521, -159.07819
20generate(0.05045, 0.05668, 0.99712), (0.07854, -0.99552, 0.05261), (0.99563, 0.07566, -0.05467)170.47577, 9.34358, -179.38301
21generate(-1), (-1), (1)-171.35, -171.35
22generate(0.32264, 0.88137, -0.34511), (-0.941, 0.33799, -0.01655), (0.10206, 0.33009, 0.93842)-59.20566, -2.70386, -10.65923
23generate(0.5064, 0.48575, 0.71247), (-0.84483, 0.44495, 0.29712), (-0.17269, -0.75238, 0.6357)121.77048, 51.05784, -62.54326
24generate(0.30054, -0.63808, 0.70889), (-0.8441, 0.16809, 0.50916), (-0.44404, -0.7514, -0.48808)120.7912, 87.28722, -254.87425
25generate(-0.01429, -0.93805, -0.34621), (-0.94102, -0.10444, 0.32182), (-0.33804, 0.33039, -0.88123)-59.65199, 55.18031, -322.13491
26generate(-0.22335, 0.85094, 0.47542), (-0.67434, -0.48708, 0.555), (0.70383, -0.19663, 0.68261)81.23156, 95.18713, -53.98327
27generate(-0.27695, -0.06273, 0.95884), (-0.8652, -0.41782, -0.27723), (0.41801, -0.90636, 0.06144)163.77631, -47.10107, -159.93299
28generate(-0.5731, -0.77491, 0.26659), (-0.76906, 0.39622, -0.50155), (0.28303, -0.49246, -0.82303)44.86837, -85.37015, -311.49326
29generate(-0.70597, -0.29545, -0.64368), (-0.52011, 0.83314, 0.18803), (0.48072, 0.46753, -0.74184)-110.82902, 32.51867, -297.54143
30generate(-0.48732, 0.70599, -0.5139), (-0.46107, 0.29176, 0.83803), (0.74158, 0.64533, 0.18333)-88.45347, 143.57373, -139.43074
31generate(-0.74696, 0.47273, -0.46751), (-0.63655, -0.71151, 0.29759), (-0.19196, 0.51988, 0.83239)-80.91564, 51.36223, -28.32742
32generate(-0.50282, 0.82053, 0.27186), (-0.77047, -0.28286, -0.57128), (-0.39185, -0.49671, 0.77442)45.46081, -97.08134, -38.73809
33generate(-0.48098, 0.20218, 0.8531), (-0.56306, 0.67462, -0.47734), (-0.67203, -0.70994, -0.21064)145.21448, -81.32407, -207.05772
34generate(-0.70618, -0.52472, 0.47537), (-0.30725, 0.83199, 0.46194), (-0.63789, 0.18015, -0.74876)80.54003, 79.54729, -299.03522
35generate(-0.86931, -0.3567, -0.34215), (-0.35392, -0.03398, 0.93466), (-0.34502, 0.9336, -0.0967)-59.58229, 160.55394, -186.93765
36generate(-0.91141, -0.06733, 0.40596), (-0.0458, -0.9638, -0.26268), (0.40895, -0.258, 0.87533)68.13529, -44.24019, -20.91662
37generate(-0.82836, 0.26701, 0.49247), (0.27797, -0.56735, 0.77515), (0.48638, 0.77899, 0.39575)82.97678, 133.3548, -102.85522
38generate(-0.85851, 0.47081, 0.20324), (0.47188, 0.57015, 0.6725), (0.20074, 0.67325, -0.71164)33.30771, 115.38923, -292.40467
39generate(-0.96588, 0.25055, -0.06559), (0.25574, 0.8827, -0.39425), (-0.04089, -0.39758, -0.91666)-12.27181, -66.28629, -328.56521
40generate(-0.99563, -0.07566, 0.05467), (-0.05045, -0.05668, -0.99712), (0.07854, -0.99552, 0.05261)8.03301, -170.47577, -162.00642
41generate(-1), (1), (-1)171.35, -171.35
42generate(-0.10206, -0.33009, -0.93842), (-0.32264, -0.88137, 0.34511), (-0.941, 0.33799, -0.01655)-160.69077, 59.20566, -174.05386
43generate(0.17269, 0.75238, -0.6357), (-0.5064, -0.48575, -0.71247), (-0.84483, 0.44495, 0.29712)-108.80674, -121.77048, -120.29216
44generate(0.44404, 0.7514, 0.48808), (-0.30054, 0.63808, -0.70889), (-0.8441, 0.16809, 0.50916)83.52425, -120.7912, -84.06278
45generate(0.33804, -0.33039, 0.88123), (0.01429, 0.93805, 0.34621), (-0.94102, -0.10444, 0.32182)150.78491, 59.65199, -116.16969
46generate(-0.70383, 0.19663, -0.68261), (0.22335, -0.85094, -0.47542), (-0.67434, -0.48708, 0.555)-117.36673, -81.23156, -76.16287
47generate(-0.41801, 0.90636, -0.06144), (0.27695, 0.06273, -0.95884), (-0.8652, -0.41782, -0.27723)-11.41701, -163.77631, -218.45107
48generate(-0.28303, 0.49246, 0.82303), (0.5731, 0.77491, -0.26659), (-0.76906, 0.39622, -0.50155)140.14326, -44.86837, -256.72015
49generate(-0.48072, -0.46753, 0.74184), (0.70597, 0.29545, 0.64368), (-0.52011, 0.83314, 0.18803)126.19143, 110.82902, -138.83133
50generate(-0.74158, -0.64533, -0.18333), (0.48732, -0.70599, 0.5139), (-0.46107, 0.29176, 0.83803)-31.91926, 88.45347, -27.77627
51generate(0.19196, -0.51988, -0.83239), (0.74696, -0.47273, 0.46751), (-0.63655, -0.71151, 0.29759)-143.02258, 80.91564, -119.98777
52generate(0.39185, 0.49671, -0.77442), (0.50282, -0.82053, -0.27186), (-0.77047, -0.28286, -0.57128)-132.61191, -45.46081, -268.43134
53generate(0.67203, 0.70994, 0.21064), (0.48098, -0.20218, -0.8531), (-0.56306, 0.67462, -0.47734)35.70772, -145.21448, -252.67407
54generate(0.63789, -0.18015, 0.74876), (0.70618, 0.52472, -0.47537), (-0.30725, 0.83199, 0.46194)127.68522, -80.54003, -91.80271
55generate(0.34502, -0.9336, 0.0967), (0.86931, 0.3567, 0.34215), (-0.35392, -0.03398, 0.93466)15.58765, 59.58229, -10.79606
56generate(-0.40895, 0.258, -0.87533), (0.91141, 0.06733, -0.40596), (-0.0458, -0.9638, -0.26268)-150.43338, -68.13529, -215.59019
57generate(-0.48638, -0.77899, -0.39575), (0.82836, -0.26701, -0.49247), (0.27797, -0.56735, 0.77515)-68.49478, -82.97678, -37.9952
58generate(-0.20074, -0.67325, 0.71164), (0.85851, -0.47081, -0.20324), (0.47188, 0.57015, 0.6725)121.05467, -33.30771, -55.96077
59generate(0.04089, 0.39758, 0.91666), (0.96588, -0.25055, 0.06559), (0.25574, 0.8827, -0.39425)157.21521, 12.27181, -237.63629
60generate(-0.07854, 0.99552, -0.05261), (0.99563, 0.07566, -0.05467), (-0.05045, -0.05668, -0.99712)-9.34358, -8.03301, -341.82577

-
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: Chemical ChemComp-CA / CALCIUM ION


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: HANGING DROP METHOD WITH 2UL:2UL DROPS. RESERVOIR 12 % PEG 8000, 100 MM HEPES PH 6.5, 100 MM CACL2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933
DetectorType: MARRESEARCH MAR133 / Detector: CCD / Date: Jul 4, 1998
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 4.75→69.3 Å / Num. obs: 67599 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.212 / Net I/σ(I): 3.3
Reflection shellResolution: 4.75→5.01 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 1.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C9G

2c9g


Resolution: 4.75→242.33 Å / Cor.coef. Fo:Fc: 0.83 / Cor.coef. Fo:Fc free: 0.817 / SU B: 0.001 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 1.517 / ESU R Free: 1.513 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: REFINEMENT PROTOCOL USED CNS_SOLVE 1.1 REFINEMENT FOR POSITIONAL AND B-FACTOR REFINEMENT IMPOSING STRICT 60-FOLD NCS FOLLOWED BY A RIGID BODY CYCLE (USING AN EXPANDED MODEL IN REFMAC (REPORTED ABOVE).
RfactorNum. reflection% reflectionSelection details
Rfree0.29029 3418 5.1 %RANDOM
Rwork0.29108 ---
obs0.29104 64099 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.381 Å2
Refinement stepCycle: LAST / Resolution: 4.75→242.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3724 0 1 0 3725
LS refinement shellResolution: 4.75→4.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 267 -
Rwork0.328 4489 -
obs--99.46 %

+
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