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- PDB-2mjz: Capsid model of M13 bacteriophage virus from Magic-angle spinning... -

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Basic information

Entry
Database: PDB / ID: 2mjz
TitleCapsid model of M13 bacteriophage virus from Magic-angle spinning NMR and Rosetta modeling
ComponentsCapsid protein G8P
KeywordsVIRAL PROTEIN / molecular assembly
Function / homology
Function and homology information


helical viral capsid / host cell plasma membrane / membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #80 / Phage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage M13 (virus)
MethodSOLID-STATE NMR / Fold-and-dock
Model detailslowest energy, model1
AuthorsMorag, O. / Sgourakis, N.G. / Baker, D. / Goldbourt, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: The NMR-Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope.
Authors: Morag, O. / Sgourakis, N.G. / Baker, D. / Goldbourt, A.
History
DepositionJan 22, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 7, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references / Structure summary
Revision 1.2Jan 21, 2015Group: Other
Revision 1.3Feb 4, 2015Group: Database references
Revision 1.4Feb 11, 2015Group: Database references
Revision 1.5May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein G8P
B: Capsid protein G8P
C: Capsid protein G8P
D: Capsid protein G8P
E: Capsid protein G8P
F: Capsid protein G8P
G: Capsid protein G8P
H: Capsid protein G8P
I: Capsid protein G8P
J: Capsid protein G8P
K: Capsid protein G8P
L: Capsid protein G8P
M: Capsid protein G8P
N: Capsid protein G8P
O: Capsid protein G8P
P: Capsid protein G8P
Q: Capsid protein G8P
R: Capsid protein G8P
S: Capsid protein G8P
T: Capsid protein G8P
U: Capsid protein G8P
V: Capsid protein G8P
W: Capsid protein G8P
X: Capsid protein G8P
Y: Capsid protein G8P
Z: Capsid protein G8P
a: Capsid protein G8P
b: Capsid protein G8P
c: Capsid protein G8P
d: Capsid protein G8P
e: Capsid protein G8P
f: Capsid protein G8P
g: Capsid protein G8P
h: Capsid protein G8P
i: Capsid protein G8P


Theoretical massNumber of molelcules
Total (without water)183,50535
Polymers183,50535
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)3 / 5000target function
RepresentativeModel #1lowest energy
DetailsTHE ASSEMBLY REPRESENTED IN THIS ENTRY HAS A CLASS 1 SYMMETRY (C5S2). THERE IS A 5-FOLD CIRCULAR SYMMETRY AROUND THE VIRAL AXIS (Z COORDINATE) WITH THE FOLLOWING PARAMETERS: MODEL 1: ROTATION PER PENTAMER (TWIST) = 36.6 DEGREES RISE PER PENTAMER (HEIGHT) = 16.7 ANGSTROMS. MODEL 2: ROTATION PER PENTAMER (TWIST) = 36.1 DEGREES RISE PER PENTAMER (HEIGHT) = 16.7 ANGSTROMS. MODEL 3: ROTATION PER PENTAMER (TWIST) = 36.4 DEGREES RISE PER PENTAMER (HEIGHT) = 16.6 ANGSTROMS.

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Components

#1: Protein/peptide ...
Capsid protein G8P / Coat protein B / Gene 8 protein / G8P / M13 procoat / Major coat protein


Mass: 5243.014 Da / Num. of mol.: 35
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage M13 (virus) / Strain: M13KO7 / Gene: VIII / References: UniProt: P69541

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
Details: Solid-state NMR structure of an intact M13 bacteriophage capsid
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NCA
1212D NCO
1312D DARR
1422D CORD
1532D CORD
1612D RFDR
1713D NCOCX
1813D NCACX
1922D DARR
11032D DARR
NMR detailsText: IN THE PDB FILE THE 35 SUBUNITS MODELED ARE REPRESENTED AS CHAINS NUMBERED FROM A-Z, a-i. THE NOTATION WE USED IN THE PAPER FOR DESCRIBING THE CAPSID ARRANGEMENT IS BASED ON THE PENTAMER ...Text: IN THE PDB FILE THE 35 SUBUNITS MODELED ARE REPRESENTED AS CHAINS NUMBERED FROM A-Z, a-i. THE NOTATION WE USED IN THE PAPER FOR DESCRIBING THE CAPSID ARRANGEMENT IS BASED ON THE PENTAMER SYMMETRY; EACH SUBUNIT PNM IS GIVEN TWO INDICES, WHERE THE INDEX N INDICATES THE PENTAMER NUMBER (N BETWEEN 1-7 WHERE N=1 CORRESPONDS TO THE C-TERMINAL PART) AND M INDICATES THE IDENTITY OF THE SUBUNIT WITHIN EACH PENTAMER(M=1-5). THE TRANSFORMATION FROM THE PAPER'S NOTATION TO THE RESPECTIVE PDB CHAINS IS AS FOLLOWS: P11 J P12 K P13 L P14 M P15 N P21 O P22 P P23 Q P24 R P25 S P31 T P32 U P33 V P34 W P35 X P41 Y P42 Z P43 a P44 b P45 c P51 d P52 e P53 f P54 g P55 h P61 i P62 A P63 B P64 C P65 D P71 E P72 F P73 G P74 H P75 I

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Sample preparation

Details
Solution-IDContents
112 mg [U-99% 13C; U-99% 15N] M13 bacteriophage
28 mg [2-13C, 99%]- glycerol, [15N-U, 99%], [13C,99%] Sodium bicarbonate M13 bacteriophage
310 mg [1,3-13C2, 99%]- glycerol, [15N-U, 99%] M13 bacteriophage
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
12 mg/mLM13 bacteriophage-1[U-99% 13C; U-99% 15N]1
8 mg/mLM13 bacteriophage-2[2-13C, 99%]- glycerol, [15N-U, 99%], [13C,99%] Sodium bicarbonate2
10 mg/mLM13 bacteriophage-3[1,3-13C2, 99%]- glycerol, [15N-U, 99%]3
Sample conditionsIonic strength: 5 / pH: 8 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker Avance III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospinprocessing
TopSpin2.1Bruker Biospindata analysis
NMRPipe2012.090.12.09Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddarddata analysis
Sparky3.113Goddardpeak picking
RosettaShen, Vernon, Baker and Baxrefinement
RefinementMethod: Fold-and-dock / Software ordinal: 1
Details: magic angle spinning, backbone fragment-based Monte Carlo trials followed by combinatorial sidechain packing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 5000 / Conformers submitted total number: 3

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