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- PDB-4ivj: Structure of a 16 nm protein cage designed by fusing symmetric ol... -

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Basic information

Entry
Database: PDB / ID: 4ivj
TitleStructure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, triple mutant, I222 form
ComponentsNon-haem bromoperoxidase BPO-A2, Matrix protein 1
KeywordsOXIDOREDUCTASE / protein design / bionanotechnology / protein assembly / symmetric oligomeric domains / biomaterials
Function / homology
Function and homology information


Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery ...Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / Viral mRNA Translation / antibiotic biosynthetic process / viral budding from plasma membrane / peroxidase activity / structural constituent of virion / host cell nucleus / virion membrane / RNA binding / extracellular region / plasma membrane
Similarity search - Function
Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain / : ...Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain / : / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Matrix protein 1 / Non-haem bromoperoxidase BPO-A2
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
Influenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 7.351 Å
AuthorsLai, Y.-T. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Structure and flexibility of nanoscale protein cages designed by symmetric self-assembly.
Authors: Lai, Y.T. / Tsai, K.L. / Sawaya, M.R. / Asturias, F.J. / Yeates, T.O.
History
DepositionJan 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
B: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
C: Non-haem bromoperoxidase BPO-A2, Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)150,8443
Polymers150,8443
Non-polymers00
Water00
1
A: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
B: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
C: Non-haem bromoperoxidase BPO-A2, Matrix protein 1

A: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
B: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
C: Non-haem bromoperoxidase BPO-A2, Matrix protein 1

A: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
B: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
C: Non-haem bromoperoxidase BPO-A2, Matrix protein 1

A: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
B: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
C: Non-haem bromoperoxidase BPO-A2, Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)603,37612
Polymers603,37612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area34510 Å2
ΔGint-112 kcal/mol
Surface area188550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.670, 160.980, 167.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Non-haem bromoperoxidase BPO-A2, Matrix protein 1 / BPO2 / Bromide peroxidase / M1


Mass: 50281.359 Da / Num. of mol.: 3 / Mutation: K118A, L279Q, Q24T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aureofaciens (bacteria), (gene. exp.) Influenza A virus
Strain: A/Puerto Rico/8/1934 H1N1 / Gene: bpoA2, BROMOPEROXIDASE A2 and M1 Matrix, M / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P29715, UniProt: P03485, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases

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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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1M Na Citrate pH 4.4, 10% PEG 3000, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Aug 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 7.35→29.283 Å / Num. all: 2438 / Num. obs: 2438 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 383.646 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 13.24
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
7.35-7.540.7781.44558177196.7
7.54-7.750.4682.69658180198.9
7.75-7.970.3374.036721671100
7.97-8.220.3843.71664165197.1
8.22-8.490.1936.54656161198.8
8.49-8.790.148.98659160197.6
8.79-9.120.1111.06605152199.3
9.12-9.490.10412.65598148196.7
9.49-9.910.07714.63547136197.1
9.91-10.40.07317.01550136197.8
10.4-10.960.05718.34520130196.3
10.96-11.620.04919.24467120197.6
11.62-12.420.04322.93470117196.7
12.42-13.420.04423.08429109195.6
13.42-14.70.04522.838799197.1
14.7-16.440.04226.0836493196.9
16.44-18.980.03828.0132686198.9
18.98-23.240.0429.7624268195.8
23.24-32.870.04326.349834154.8
1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.35 Å29.28 Å
Translation7.35 Å29.28 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.1phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BRO and 1AA7

1bro

1aa7


Resolution: 7.351→28.419 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.735 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 31.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2876 121 4.98 %random
Rwork0.2764 ---
obs0.2771 2431 97.05 %-
all-2431 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 509.25 Å2 / Biso mean: 318.4546 Å2 / Biso min: 160.94 Å2
Refinement stepCycle: LAST / Resolution: 7.351→28.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10194 0 0 0 10194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01510425
X-RAY DIFFRACTIONf_angle_d2.3914187
X-RAY DIFFRACTIONf_chiral_restr0.1141602
X-RAY DIFFRACTIONf_plane_restr0.0081848
X-RAY DIFFRACTIONf_dihedral_angle_d15.8963702
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)
1-0.1127-1.0663-0.80592.6937-0.15021.77751.24491.22030.4773-3.2035-0.7876-0.29340.2291-0.20240.99413.04820.9584-0.1523.26160.18381.5458-21.4924-9.9458-46.5575
20.1544-0.3267-1.2571.45810.06354.5457-0.71260.89720.91980.02371.17250.72491.7696-3.0428-1.4012.0737-0.1233-0.2612.72660.44051.6132-18.456410.4953-9.5139
30.36550.48090.91070.32940.9791.47320.40680.6485-0.9438-4.32193.08162.72553.3496-4.49644.98314.9966-1.4471-3.3653.40230.38355.7894-43.2757-41.3402-45.6845
42.5681-0.94392.15413.3008-1.28482.65421.1276-0.7317-2.14720.20362.30213.047-0.5486-1.61891.36164.3621-1.0683-0.94453.17730.20815.1499-70.731-12.6252-59.423
53.1097-1.08532.74882.4024-1.23475.59590.77531.1553-1.7417-0.13461.73662.03561.121.48088.12791.61150.46620.33242.1174-1.27291.1633-20.4393-33.5752-16.6105
62.610.39531.50092.34152.98564.04011.9225-1.3373-1.14891.31020.7601-0.85810.07061.19853.40622.38910.11851.50783.06020.50152.8469-53.172-43.76738.3307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 1:287A1 - 287
2X-RAY DIFFRACTION2chain A and resid 288:440A288 - 440
3X-RAY DIFFRACTION3chain B and resid 1:287B1 - 287
4X-RAY DIFFRACTION4chain B and resid 288:440B288 - 440
5X-RAY DIFFRACTION5chain C and resid 1:287C1 - 287
6X-RAY DIFFRACTION6chain C and resid 288:440C288 - 440

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