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- PDB-4v4u: The quasi-atomic model of Human Adenovirus type 5 capsid -

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Basic information

Entry
Database: PDB / ID: 4v4u
TitleThe quasi-atomic model of Human Adenovirus type 5 capsid
Components
  • HEXON PROTEIN
  • N-TERMINAL PEPTIDE OF FIBER PROTEIN
  • PENTON PROTEIN
KeywordsVIRUS / ADENOVIRUS / MINOR CAPSID PROTEIN / QUASI ATOMIC
Function / homology
Function and homology information


T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral capsid / clathrin-dependent endocytosis of virus by host cell / symbiont entry into host cell / host cell nucleus / structural molecule activity / virion attachment to host cell
Similarity search - Function
Adenovirus Pll, hexon, subdomain 2 / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Adenovirus penton base protein / Adenovirus penton base protein / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
Penton protein / Hexon protein
Similarity search - Component
Biological speciesHUMAN ADENOVIRUS 2
HUMAN ADENOVIRUS TYPE 5
HUMAN ADENOVIRUS TYPE 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10 Å
AuthorsFabry, C.M.S. / Rosa-Calatrava, M. / Conway, J.F. / Zubieta, C. / Cusack, S. / Ruigrok, R.W.H. / Schoehn, G.
CitationJournal: EMBO J / Year: 2005
Title: A quasi-atomic model of human adenovirus type 5 capsid.
Authors: Céline M S Fabry / Manuel Rosa-Calatrava / James F Conway / Chloé Zubieta / Stephen Cusack / Rob W H Ruigrok / Guy Schoehn /
Abstract: Adenoviruses infect a wide range of vertebrates including humans. Their icosahedral capsids are composed of three major proteins: the trimeric hexon forms the facets and the penton, a noncovalent ...Adenoviruses infect a wide range of vertebrates including humans. Their icosahedral capsids are composed of three major proteins: the trimeric hexon forms the facets and the penton, a noncovalent complex of the pentameric penton base and trimeric fibre proteins, is located at the 12 capsid vertices. Several proteins (IIIa, VI, VIII and IX) stabilise the capsid. We have obtained a 10 A resolution map of the human adenovirus 5 by image analysis from cryo-electron micrographs (cryoEMs). This map, in combination with the X-ray structures of the penton base and hexon, was used to build a quasi-atomic model of the arrangement of the two major capsid components and to analyse the hexon-hexon and hexon-penton interactions. The secondary proteins, notably VIII, were located by comparing cryoEM maps of native and pIX deletion mutant virions. Minor proteins IX and IIIa are located on the outside of the capsid, whereas protein VIII is organised with a T=2 lattice on the inner face of the capsid. The capsid organisation is compared with the known X-ray structure of bacteriophage PRD1.
History
DepositionMar 3, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 2BLD, 2BVI
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Jul 26, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.3Oct 23, 2019Group: Data collection / Other / Category: atom_sites / cell / pdbx_database_status
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _pdbx_database_status.process_site

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Structure visualization

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Assembly

Deposited unit
A: PENTON PROTEIN
B: PENTON PROTEIN
C: PENTON PROTEIN
D: PENTON PROTEIN
E: PENTON PROTEIN
S: N-TERMINAL PEPTIDE OF FIBER PROTEIN
T: N-TERMINAL PEPTIDE OF FIBER PROTEIN
U: N-TERMINAL PEPTIDE OF FIBER PROTEIN
V: N-TERMINAL PEPTIDE OF FIBER PROTEIN
W: N-TERMINAL PEPTIDE OF FIBER PROTEIN
F: HEXON PROTEIN
G: HEXON PROTEIN
H: HEXON PROTEIN
I: HEXON PROTEIN
J: HEXON PROTEIN
K: HEXON PROTEIN
L: HEXON PROTEIN
M: HEXON PROTEIN
N: HEXON PROTEIN
O: HEXON PROTEIN
P: HEXON PROTEIN
Q: HEXON PROTEIN


Theoretical massNumber of molelcules
Total (without water)1,592,89222
Polymers1,592,89222
Non-polymers00
Water0
1
A: PENTON PROTEIN
B: PENTON PROTEIN
C: PENTON PROTEIN
D: PENTON PROTEIN
E: PENTON PROTEIN
S: N-TERMINAL PEPTIDE OF FIBER PROTEIN
T: N-TERMINAL PEPTIDE OF FIBER PROTEIN
U: N-TERMINAL PEPTIDE OF FIBER PROTEIN
V: N-TERMINAL PEPTIDE OF FIBER PROTEIN
W: N-TERMINAL PEPTIDE OF FIBER PROTEIN
x 12
F: HEXON PROTEIN
G: HEXON PROTEIN
H: HEXON PROTEIN
I: HEXON PROTEIN
J: HEXON PROTEIN
K: HEXON PROTEIN
L: HEXON PROTEIN
M: HEXON PROTEIN
N: HEXON PROTEIN
O: HEXON PROTEIN
P: HEXON PROTEIN
Q: HEXON PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)81,309,123840
Polymers81,309,123840
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation72
2


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
PENTON PROTEIN /


Mass: 58218.684 Da / Num. of mol.: 5 / Fragment: RESIDUES 49-571
Source method: isolated from a genetically manipulated source
Details: VIRION COMPONENT III, PENTON BASE PROTEIN / Source: (gene. exp.) HUMAN ADENOVIRUS 2 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P03276
#2: Protein/peptide
N-TERMINAL PEPTIDE OF FIBER PROTEIN


Mass: 1216.295 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: VIRION COMPONENT IV, FIBER PROTEIN / Source: (synth.) HUMAN ADENOVIRUS TYPE 2
#3: Protein
HEXON PROTEIN /


Mass: 107976.422 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: VIRION COMPONENT II, HEXON PROTEIN / Source: (gene. exp.) HUMAN ADENOVIRUS TYPE 5 / Cell line (production host): HELA S3 / Production host: HOMO SAPIENS (human) / References: UniProt: P04133

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HUMAN ADENOVIRUS TYPE 5 / Type: VIRUS
Buffer solutionName: TRIS / pH: 7.5 / Details: TRIS
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: ZEISS PLUNGE FREEZER CRYOBOX / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200T / Date: Oct 1, 2003
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 27500 X / Calibrated magnification: 28600 X / Nominal defocus max: 250 nm / Nominal defocus min: 100 nm / Cs: 2 mm
Specimen holderTemperature: 95 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 21
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1CTFMIXCTF correction
2Situsmodel fitting
3UROmodel fitting
4X3Dparticle selection
5EM3DR3D reconstruction
6PFT23D reconstruction
7SPIDER3D reconstruction
CTF correctionDetails: AMPLITUDE, PHASE TMV AND COMPARISON WITH X-RAY DATA
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: POLAR FOURIER TRANSFORM, FOURIER BESSELS RECONSTRUCTION
Resolution: 10 Å / Num. of particles: 4100 / Nominal pixel size: 2.55 Å / Actual pixel size: 2.45 Å
Details: THE NUMBER OF ATOMS IN THIS STRUCTURE EXCEEDS THE MAXIMUM ALLOWED BY THE PDB FORMAT. IT HAS THEREFORE BEEN SPLIT ACROSS TWO PDB ENTRIES: 2BLD CONTAINS THE PENTON BASE, 2BVI CONTAINS THE FOUR ...Details: THE NUMBER OF ATOMS IN THIS STRUCTURE EXCEEDS THE MAXIMUM ALLOWED BY THE PDB FORMAT. IT HAS THEREFORE BEEN SPLIT ACROSS TWO PDB ENTRIES: 2BLD CONTAINS THE PENTON BASE, 2BVI CONTAINS THE FOUR UNIQUE COPIES OF THE HEXON. THE COMPLETE CAPSID CAN BE GENERATED BY APPLYING ICOSAHEDRAL SYMMETRY OPERATORS TO THE COORDINATES IN THE TWO ENTRIES AND THEN COMBINING THE RESULTING CAPSID FRAGMENTS. THE PENTON BASE COMPRISES CHAINS A,B,C,D,E,S,T,U,V AND W AND MUST BE TRANSFORMED BY 12 SPECIFIC MATRICES DEFINED IN REMARK 350. THE HEXONS COMPRISE CHAINS F,G,H,I,J,K,L M,N,O,P AND Q AND MUST BE TRANSFORMED BY ALL ICOSAHEDRAL OPERATORS.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: R-FACTOR, CORRELATION COEFFICIENT / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
RefinementHighest resolution: 10 Å
Refinement stepCycle: LAST / Highest resolution: 10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18025 0 0 0 18025

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