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- PDB-2c6s: human adenovirus penton base 2 12 chimera -

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Basic information

Entry
Database: PDB / ID: 2c6s
Titlehuman adenovirus penton base 2 12 chimera
ComponentsADENOVIRUS 2,12 PENTON BASE CHIMERA
KeywordsVIRUS/VIRAL PROTEIN / ADENOVIRUS / CAPSID / PENTON / DODECAHEDRA / FIBER / VIRAL PROTEIN / VIRUS-VIRAL PROTEIN complex
Function / homology
Function and homology information


T=25 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / host cell nucleus / 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
Biological speciesHUMAN ADENOVIRUS C
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsZubieta, C. / Blanchoin, L. / Cusack, S.
CitationJournal: FEBS J. / Year: 2006
Title: Structural and Biochemical Characterization of a Human Adenovirus 2/12 Penton Base Chimera.
Authors: Zubieta, C. / Blanchoin, L. / Cusack, S.
History
DepositionNov 11, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 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 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADENOVIRUS 2,12 PENTON BASE CHIMERA
B: ADENOVIRUS 2,12 PENTON BASE CHIMERA
C: ADENOVIRUS 2,12 PENTON BASE CHIMERA
D: ADENOVIRUS 2,12 PENTON BASE CHIMERA
E: ADENOVIRUS 2,12 PENTON BASE CHIMERA
F: ADENOVIRUS 2,12 PENTON BASE CHIMERA
G: ADENOVIRUS 2,12 PENTON BASE CHIMERA
H: ADENOVIRUS 2,12 PENTON BASE CHIMERA
I: ADENOVIRUS 2,12 PENTON BASE CHIMERA
J: ADENOVIRUS 2,12 PENTON BASE CHIMERA
K: ADENOVIRUS 2,12 PENTON BASE CHIMERA
L: ADENOVIRUS 2,12 PENTON BASE CHIMERA
M: ADENOVIRUS 2,12 PENTON BASE CHIMERA
N: ADENOVIRUS 2,12 PENTON BASE CHIMERA
O: ADENOVIRUS 2,12 PENTON BASE CHIMERA


Theoretical massNumber of molelcules
Total (without water)873,04015
Polymers873,04015
Non-polymers00
Water00
1
A: ADENOVIRUS 2,12 PENTON BASE CHIMERA
B: ADENOVIRUS 2,12 PENTON BASE CHIMERA
C: ADENOVIRUS 2,12 PENTON BASE CHIMERA
D: ADENOVIRUS 2,12 PENTON BASE CHIMERA
E: ADENOVIRUS 2,12 PENTON BASE CHIMERA
F: ADENOVIRUS 2,12 PENTON BASE CHIMERA
G: ADENOVIRUS 2,12 PENTON BASE CHIMERA
H: ADENOVIRUS 2,12 PENTON BASE CHIMERA
I: ADENOVIRUS 2,12 PENTON BASE CHIMERA
J: ADENOVIRUS 2,12 PENTON BASE CHIMERA
K: ADENOVIRUS 2,12 PENTON BASE CHIMERA
L: ADENOVIRUS 2,12 PENTON BASE CHIMERA
M: ADENOVIRUS 2,12 PENTON BASE CHIMERA
N: ADENOVIRUS 2,12 PENTON BASE CHIMERA
O: ADENOVIRUS 2,12 PENTON BASE CHIMERA

A: ADENOVIRUS 2,12 PENTON BASE CHIMERA
B: ADENOVIRUS 2,12 PENTON BASE CHIMERA
C: ADENOVIRUS 2,12 PENTON BASE CHIMERA
D: ADENOVIRUS 2,12 PENTON BASE CHIMERA
E: ADENOVIRUS 2,12 PENTON BASE CHIMERA
F: ADENOVIRUS 2,12 PENTON BASE CHIMERA
G: ADENOVIRUS 2,12 PENTON BASE CHIMERA
H: ADENOVIRUS 2,12 PENTON BASE CHIMERA
I: ADENOVIRUS 2,12 PENTON BASE CHIMERA
J: ADENOVIRUS 2,12 PENTON BASE CHIMERA
K: ADENOVIRUS 2,12 PENTON BASE CHIMERA
L: ADENOVIRUS 2,12 PENTON BASE CHIMERA
M: ADENOVIRUS 2,12 PENTON BASE CHIMERA
N: ADENOVIRUS 2,12 PENTON BASE CHIMERA
O: ADENOVIRUS 2,12 PENTON BASE CHIMERA

A: ADENOVIRUS 2,12 PENTON BASE CHIMERA
B: ADENOVIRUS 2,12 PENTON BASE CHIMERA
C: ADENOVIRUS 2,12 PENTON BASE CHIMERA
D: ADENOVIRUS 2,12 PENTON BASE CHIMERA
E: ADENOVIRUS 2,12 PENTON BASE CHIMERA
F: ADENOVIRUS 2,12 PENTON BASE CHIMERA
G: ADENOVIRUS 2,12 PENTON BASE CHIMERA
H: ADENOVIRUS 2,12 PENTON BASE CHIMERA
I: ADENOVIRUS 2,12 PENTON BASE CHIMERA
J: ADENOVIRUS 2,12 PENTON BASE CHIMERA
K: ADENOVIRUS 2,12 PENTON BASE CHIMERA
L: ADENOVIRUS 2,12 PENTON BASE CHIMERA
M: ADENOVIRUS 2,12 PENTON BASE CHIMERA
N: ADENOVIRUS 2,12 PENTON BASE CHIMERA
O: ADENOVIRUS 2,12 PENTON BASE CHIMERA

A: ADENOVIRUS 2,12 PENTON BASE CHIMERA
B: ADENOVIRUS 2,12 PENTON BASE CHIMERA
C: ADENOVIRUS 2,12 PENTON BASE CHIMERA
D: ADENOVIRUS 2,12 PENTON BASE CHIMERA
E: ADENOVIRUS 2,12 PENTON BASE CHIMERA
F: ADENOVIRUS 2,12 PENTON BASE CHIMERA
G: ADENOVIRUS 2,12 PENTON BASE CHIMERA
H: ADENOVIRUS 2,12 PENTON BASE CHIMERA
I: ADENOVIRUS 2,12 PENTON BASE CHIMERA
J: ADENOVIRUS 2,12 PENTON BASE CHIMERA
K: ADENOVIRUS 2,12 PENTON BASE CHIMERA
L: ADENOVIRUS 2,12 PENTON BASE CHIMERA
M: ADENOVIRUS 2,12 PENTON BASE CHIMERA
N: ADENOVIRUS 2,12 PENTON BASE CHIMERA
O: ADENOVIRUS 2,12 PENTON BASE CHIMERA


Theoretical massNumber of molelcules
Total (without water)3,492,16060
Polymers3,492,16060
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation3_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)266.500, 292.900, 307.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRALAALAAA49 - 2941 - 246
21THRTHRALAALABB49 - 2941 - 246
31THRTHRALAALACC49 - 2941 - 246
41THRTHRALAALADD49 - 2941 - 246
51THRTHRALAALAEE49 - 2941 - 246
61THRTHRALAALAFF49 - 2941 - 246
71THRTHRALAALAGG49 - 2941 - 246
81THRTHRALAALAHH49 - 2941 - 246
91THRTHRALAALAII49 - 2941 - 246
101THRTHRALAALAJJ49 - 2941 - 246
111THRTHRALAALAKK49 - 2941 - 246
121THRTHRALAALALL49 - 2941 - 246
131THRTHRALAALAMM49 - 2941 - 246
141THRTHRALAALANN49 - 2941 - 246
151THRTHRALAALAOO49 - 2941 - 246
12LEULEUARGARGAA312 - 506327 - 521
22LEULEUARGARGBB312 - 506327 - 521
32LEULEUARGARGCC312 - 506327 - 521
42LEULEUARGARGDD312 - 506327 - 521
52LEULEUARGARGEE312 - 506327 - 521
62LEULEUARGARGFF312 - 506327 - 521
72LEULEUARGARGGG312 - 506327 - 521
82LEULEUARGARGHH312 - 506327 - 521
92LEULEUARGARGII312 - 506327 - 521
102LEULEUARGARGJJ312 - 506327 - 521
112LEULEUARGARGKK312 - 506327 - 521
122LEULEUARGARGLL312 - 506327 - 521
132LEULEUARGARGMM312 - 506327 - 521
142LEULEUARGARGNN312 - 506327 - 521
152LEULEUARGARGOO312 - 506327 - 521

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.30949, -0.80989, 0.49828), (0.81002, 0.49902, 0.30797), (-0.49808, 0.3083, 0.81047)-0.22123, 0.15986, -0.03825
3given(-0.80882, -0.50073, 0.30835), (0.50083, -0.31174, 0.80746), (-0.30819, 0.80752, 0.50292)-0.05122, 0.34306, -0.12568
4given(-0.80945, 0.50032, -0.30736), (-0.49934, -0.3111, 0.80863), (0.30895, 0.80802, 0.50165)0.10193, 0.23468, -0.11255
5given(0.30749, 0.80996, -0.49942), (-0.80987, 0.4983, 0.30951), (0.49955, 0.3093, 0.80919)0.18921, 0.05852, 0.0109
6given(0.50178, -0.30733, -0.80856), (-0.30986, 0.80885, -0.49974), (0.80759, 0.5013, 0.31063)0.12704, 0.09259, -0.02233
7given(0.80968, -0.49969, 0.30779), (0.49912, 0.31046, -0.80901), (0.3087, 0.80866, 0.50078)0.02585, 0.19129, 0.07743
8given(0.00172, -0.00362, 0.99999), (1, -0.00074, -0.00172), (0.00075, 0.99999, 0.00361)-0.10181, 0.31042, -0.18599
9given(-0.80886, 0.49929, 0.31057), (0.50002, 0.30615, 0.81009), (0.3094, 0.81054, -0.49729)0.00831, 0.24655, -0.22377
10given(-0.50051, 0.31061, -0.80809), (-0.31055, 0.80688, 0.5025), (0.80811, 0.50246, -0.3074)0.19736, 0.11068, -0.11444
11given(-0.30622, 0.80903, -0.50169), (-0.80989, -0.49838, -0.30936), (-0.50031, 0.31158, 0.80784)-0.02013, -0.0555, 0.13133
12given(0.31104, 0.81003, 0.4971), (-0.80799, 0.50078, -0.31045), (-0.50041, -0.30509, 0.81025)-0.11438, -0.20198, -0.02076
13given(0.49959, -0.30797, 0.80967), (-0.30661, 0.8113, 0.49777), (-0.81019, -0.49694, 0.31089)-0.11174, -0.21964, -0.07744
14given(-0.00284, -0.99999, 0.00212), (0.00121, 0.00212, 1), (-1, 0.00285, 0.0012)-0.10198, -0.15664, -0.11728
15given(-0.5022, -0.30775, -0.80814), (-0.30988, -0.80843, 0.50042), (-0.80733, 0.50174, 0.31062)-0.10794, 0.00159, -0.13176
DetailsA COMPLETE DODECAHEDRAL PARTICLE CAN BE GENERATED BYUSING THE TRANSFORMATIONS IN REMARK 350.

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Components

#1: Protein
ADENOVIRUS 2,12 PENTON BASE CHIMERA / PENTON PROTEIN


Mass: 58202.660 Da / Num. of mol.: 15 / Fragment: RESIDUES 49-571
Source method: isolated from a genetically manipulated source
Details: HYPERVARIABLE LOOP OF HUMAN ADENOVIRUS 2 PENTON BASE REPLACED WITH HYPERVARIABLE LOOP OF HUMAN ADENOVIRUS 12
Source: (gene. exp.) HUMAN ADENOVIRUS C / Strain: SEROTYPE 2 / Plasmid: HTB / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P03276

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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: 3.5 Å3/Da / Density % sol: 64 %
Crystal growpH: 7.5
Details: 50% MPD, 0.1 M TRIS 7.5, 0.2 M AMMONIUM PHOSPHATE, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.976
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 124622 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.12
Reflection shellResolution: 3.6→3.7 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.33 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X9P

1x9p


Resolution: 3.6→15 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.877 / SU B: 63.703 / SU ML: 0.865 / Cross valid method: THROUGHOUT / ESU R Free: 0.824 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 297-311 WERE DISORDERED AND NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.34 3041 2.5 %RANDOM
Rwork0.275 ---
obs0.276 118747 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 136.36 Å2
Baniso -1Baniso -2Baniso -3
1-18.34 Å20 Å20 Å2
2---7 Å20 Å2
3----11.34 Å2
Refinement stepCycle: LAST / Resolution: 3.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53010 0 0 0 53010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02254255
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1381.95573890
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99256615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.38123.7932610
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.194158880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.22915405
X-RAY DIFFRACTIONr_chiral_restr0.1570.28310
X-RAY DIFFRACTIONr_gen_planes_refined0.0590.0241745
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1740.325345
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.534821
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.52558
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.3139
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.527
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.162234325
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.067354270
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.262223100
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.415319620
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1764tight positional0.010.05
2B1764tight positional0.010.05
3C1764tight positional0.010.05
4D1764tight positional0.010.05
5E1764tight positional0.010.05
6F1764tight positional0.010.05
7G1764tight positional0.010.05
8H1764tight positional0.010.05
9I1764tight positional0.010.05
10J1764tight positional0.010.05
11K1764tight positional0.010.05
12L1764tight positional0.010.05
13M1764tight positional0.010.05
14N1764tight positional0.010.05
15O1764tight positional0.010.05
1A1756loose positional0.485
2B1756loose positional0.515
3C1756loose positional0.515
4D1756loose positional0.545
5E1756loose positional0.545
6F1756loose positional0.535
7G1756loose positional0.515
8H1756loose positional0.515
9I1756loose positional0.515
10J1756loose positional0.525
11K1756loose positional0.485
12L1756loose positional0.55
13M1756loose positional0.535
14N1756loose positional0.555
15O1756loose positional0.525
1A1764tight thermal0.010.5
2B1764tight thermal0.010.5
3C1764tight thermal0.010.5
4D1764tight thermal0.010.5
5E1764tight thermal0.010.5
6F1764tight thermal0.010.5
7G1764tight thermal0.010.5
8H1764tight thermal0.010.5
9I1764tight thermal0.010.5
10J1764tight thermal0.010.5
11K1764tight thermal0.010.5
12L1764tight thermal0.010.5
13M1764tight thermal0.010.5
14N1764tight thermal0.010.5
15O1764tight thermal0.010.5
1A1756loose thermal0.4210
2B1756loose thermal0.4310
3C1756loose thermal0.4810
4D1756loose thermal0.4710
5E1756loose thermal0.4410
6F1756loose thermal0.4210
7G1756loose thermal0.4410
8H1756loose thermal0.4310
9I1756loose thermal0.4610
10J1756loose thermal0.4310
11K1756loose thermal0.4510
12L1756loose thermal0.4510
13M1756loose thermal0.4510
14N1756loose thermal0.4510
15O1756loose thermal0.5210
LS refinement shellResolution: 3.6→3.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.528 202
Rwork0.487 8132

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