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- PDB-2obe: Crystal Structure of Chimpanzee Adenovirus (Type 68/Simian 25) Ma... -

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Basic information

Entry
Database: PDB / ID: 2obe
TitleCrystal Structure of Chimpanzee Adenovirus (Type 68/Simian 25) Major Coat Protein Hexon
ComponentsHexon protein
KeywordsVIRAL PROTEIN / trimer / double-barrel subunit / viral jellyroll / base / hypervariable tower
Function / homology
Function and homology information


T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / host cell / symbiont entry into host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Hexon Major Viral Coat Protein; domain 3 / Hexon Major Viral Coat Protein, domain 3 / Hexon Major Viral Coat Protein; domain 2 / Hexon Major Viral Coat Protein, domain 2 / Adenovirus Type 2 Hexon; domain 1 / Adenovirus Type 2 Hexon, domain 1 / Adenovirus Type 2 Hexon, domain 4 / Adenovirus Type 2 Hexon; domain 4 / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal ...Hexon Major Viral Coat Protein; domain 3 / Hexon Major Viral Coat Protein, domain 3 / Hexon Major Viral Coat Protein; domain 2 / Hexon Major Viral Coat Protein, domain 2 / Adenovirus Type 2 Hexon; domain 1 / Adenovirus Type 2 Hexon, domain 1 / Adenovirus Type 2 Hexon, domain 4 / Adenovirus Type 2 Hexon; domain 4 / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, subdomain 2 / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Group II dsDNA virus coat/capsid protein / Beta Complex / Distorted Sandwich / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DIHYDROGENPHOSPHATE ION / Hexon protein
Similarity search - Component
Biological speciesSimian adenovirus 25
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXue, F. / Rux, J.J. / Burnett, R.M.
Citation
Journal: J.Virol. / Year: 2007
Title: Structure-based identification of a major neutralizing site in an adenovirus hexon
Authors: Pichla-Gollon, S.L. / Drinker, M. / Zhou, X. / Xue, F. / Rux, J.J. / Gao, G.-P. / Wilson, J.M. / Ertl, H.C.J. / Burnett, R.M. / Bergelson, J.M.
#1: Journal: J.Struct.Biol. / Year: 2006
Title: Capsid-like arrays in crystals of chimpanzee adenovirus hexon
Authors: Xue, F. / Burnett, R.M.
History
DepositionDec 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 2.0Feb 6, 2019Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_name_com / entity_src_nat / software / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_name_com.name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.strain / _software.classification / _software.version / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details
Revision 2.1Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE THE SEQUENCE DATABASE REFERENCE IS UNDEFINED AT THIS POSITION. THE AUTHORS STATE THAT ... SEQUENCE THE SEQUENCE DATABASE REFERENCE IS UNDEFINED AT THIS POSITION. THE AUTHORS STATE THAT THEY ASSIGNED THE SEQUENCE FOR THESE RESIDUES BY THE CLEAR HOMOLOGY TO OTHER ADENOVIRUS HEXONS AT THESE POSITIONS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hexon protein
B: Hexon protein
C: Hexon protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,64849
Polymers314,6783
Non-polymers4,97046
Water27,4011521
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61890 Å2
ΔGint-501 kcal/mol
Surface area85090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.800, 433.000, 159.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 5 / Auth seq-ID: 5 - 929 / Label seq-ID: 5 - 929

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
DetailsThe biological assembly is a trimer formed from the three chains with given coordinates

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Components

#1: Protein Hexon protein / CP-H / Protein II


Mass: 104892.617 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Simian adenovirus 25 / Genus: Mastadenovirus / Species: Human adenovirus E / References: UniProt: Q8UY79
#2: Chemical...
ChemComp-2HP / DIHYDROGENPHOSPHATE ION


Mass: 96.987 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: H2O4P
#3: Chemical...
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1521 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium cacodylate, 0.2 M ammonium phosphate, 45% 2-methyl-2,4-pentanediol (MPD), pH 5.0, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Nov 8, 2002
RadiationMonochromator: Si(111) channel-cut crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→99 Å / Num. obs: 177830 / % possible obs: 97.7 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.089 / Χ2: 1.11 / Net I/σ(I): 15.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 4.3 / Num. unique all: 15823 / Χ2: 0.684 / % possible all: 87.8

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.45 / Method translation: &STRIP%trans_method / Packing: 0.585

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RUX

1rux
PDB Unreleased entry


Resolution: 2.1→49.27 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.988 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2025 1.1 %RANDOM
Rwork0.169 ---
obs0.169 177795 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: 37.687 Å2
Baniso -1Baniso -2Baniso -3
1-2.49 Å20 Å20 Å2
2---3.11 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21511 0 302 1521 23334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02222353
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.95530490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14152717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62224.0641090
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.768153308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.69815125
X-RAY DIFFRACTIONr_chiral_restr0.1420.23229
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217448
X-RAY DIFFRACTIONr_nbd_refined0.2250.310493
X-RAY DIFFRACTIONr_nbtor_refined0.3220.515097
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.53098
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.353
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.522
X-RAY DIFFRACTIONr_mcbond_it1.457214016
X-RAY DIFFRACTIONr_mcangle_it2.135321930
X-RAY DIFFRACTIONr_scbond_it1.67729749
X-RAY DIFFRACTIONr_scangle_it2.26738560
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3616MEDIUM POSITIONAL0.20.5
2B3616MEDIUM POSITIONAL0.210.5
3C3616MEDIUM POSITIONAL0.220.5
1A3488LOOSE POSITIONAL0.365
2B3488LOOSE POSITIONAL0.365
3C3488LOOSE POSITIONAL0.425
1A3616MEDIUM THERMAL1.142
2B3616MEDIUM THERMAL1.262
3C3616MEDIUM THERMAL1.332
1A3488LOOSE THERMAL1.7910
2B3488LOOSE THERMAL1.8110
3C3488LOOSE THERMAL1.9510
LS refinement shellResolution: 2.1→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 162 -
Rwork0.192 11316 -
obs-11478 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.21440.16090.02831.22510.11610.23570.0724-0.00930.01940.277-0.09070.20940.0052-0.06010.0183-0.126-0.00910.0455-0.098-0.021-0.1498-89.458550.604137.8361
20.28570.0923-0.03271.10870.09430.19060.02670.0286-0.05470.0384-0.0278-0.2232-0.03420.01930.0011-0.21540.0002-0.0222-0.1170.0226-0.1344-60.502848.631324.419
30.19490.1406-0.00780.96420.08650.26690.0747-0.0733-0.0480.5486-0.0874-0.17060.05010.02840.01280.1432-0.063-0.102-0.07860.0242-0.1355-63.354848.719756.4115
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 1385 - 138
21AA143 - 194143 - 194
31AA198 - 413198 - 413
41AA417 - 929417 - 929
52BB5 - 1385 - 138
62BB144 - 194144 - 194
72BB201 - 236201 - 236
82BB241 - 413241 - 413
92BB418 - 929418 - 929
103CC5 - 1375 - 137
113CC144 - 194144 - 194
123CC201 - 413201 - 413
133CC418 - 929418 - 929

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