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- PDB-5ldn: A viral capsid:antibody complex -

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Basic information

Entry
Database: PDB / ID: 5ldn
TitleA viral capsid:antibody complex
Components
  • (antibody) x 2
  • Hexon protein,hexon capsid
KeywordsVIRAL PROTEIN / TRIM21 / 9C12 / Adenovirus / neutralization
Function / homology
Function and homology information


T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral capsid / host cell / symbiont entry into host cell / host cell nucleus / structural molecule activity
Similarity search - Function
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman adenovirus C serotype 5
Human adenovirus 5
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsJames, L.
CitationJournal: Sci Rep / Year: 2016
Title: Antibody-antigen kinetics constrain intracellular humoral immunity.
Authors: Bottermann, M. / Lode, H.E. / Watkinson, R.E. / Foss, S. / Sandlie, I. / Andersen, J.T. / James, L.C.
History
DepositionJun 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hexon protein,hexon capsid
L: antibody
H: antibody


Theoretical massNumber of molelcules
Total (without water)152,2943
Polymers152,2943
Non-polymers00
Water8,701483
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-22 kcal/mol
Surface area67820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.999, 156.999, 144.891
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Hexon protein,hexon capsid / CP-H / Protein II


Mass: 105292.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus C serotype 5, (gene. exp.) Human adenovirus 5
Gene: L3 / Production host: Homo sapiens (human) / References: UniProt: P04133
#2: Antibody antibody


Mass: 23520.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody antibody


Mass: 23481.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, sodium chloride,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 0.987 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Dec 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.7→135.931 Å / Num. all: 55555 / Num. obs: 55555 / % possible obs: 100 % / Redundancy: 9.4 % / Rpim(I) all: 0.058 / Rrim(I) all: 0.176 / Rsym value: 0.167 / Net I/av σ(I): 3.575 / Net I/σ(I): 11.8 / Num. measured all: 520799
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.7-2.859.10.9640.71100
2.85-3.029.30.6211.11100
3.02-3.239.70.3841.91100
3.23-3.499.20.2253.21100
3.49-3.829.30.1484.91100
3.82-4.279.70.1086.31100
4.27-4.939.30.0897.41100
4.93-6.049.80.097.21100
6.04-8.549.20.0936.91100
8-109.20.064.4199.9

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.8.0151refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TG7

3tg7


Resolution: 2.7→78.5 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / SU B: 10.804 / SU ML: 0.215 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.544 / ESU R Free: 0.283
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 2821 5.1 %RANDOM
Rwork0.1644 ---
obs0.1673 52764 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 268.96 Å2 / Biso mean: 68.353 Å2 / Biso min: 2.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 2.7→78.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10672 0 0 483 11155
Biso mean---46.07 -
Num. residues----1358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01911067
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210084
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.9415076
X-RAY DIFFRACTIONr_angle_other_deg1.065323221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8951382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29324.175515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.451151743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2511559
X-RAY DIFFRACTIONr_chiral_restr0.1010.21633
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112771
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022670
X-RAY DIFFRACTIONr_mcbond_it5.2566.9835492
X-RAY DIFFRACTIONr_mcbond_other5.2466.9825491
X-RAY DIFFRACTIONr_mcangle_it8.45910.4446880
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 202 -
Rwork0.266 3879 -
all-4081 -
obs--99.9 %

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