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- PDB-3vdx: Structure of a 16 nm protein cage designed by fusing symmetric ol... -

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Basic information

Entry
Database: PDB / ID: 3vdx
TitleStructure of a 16 nm protein cage designed by fusing symmetric oligomeric domains
ComponentsDesigned 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1
KeywordsDE NOVO PROTEIN / protein design / bionanotechnology / protein assembly / symmetry / 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 / peroxidase activity / viral budding from plasma membrane / structural constituent of virion / host cell nucleus / virion membrane / RNA binding / extracellular region / plasma membrane
Similarity search - Function
Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix protein M1, N-terminal subdomain 2 / Influenza Virus Matrix Protein; Chain A, domain 1 / 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 M1, N-terminal subdomain 1 / Influenza matrix protein M1, N-terminal subdomain 2 / Influenza Virus Matrix Protein; Chain A, domain 1 / 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, catalytic domain / Alpha/Beta hydrolase fold / Arc Repressor Mutant, subunit A / Up-down Bundle / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
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: 3.002 Å
AuthorsLai, Y.-T. / Cascio, D. / Yeates, T.O.
CitationJournal: Science / Year: 2012
Title: Structure of a 16-nm cage designed by using protein oligomers.
Authors: Lai, Y.T. / Cascio, D. / Yeates, T.O.
History
DepositionJan 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Sep 13, 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: Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1
B: Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1
C: Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)150,7933
Polymers150,7933
Non-polymers00
Water0
1
A: Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1
B: Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1
C: Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1

A: Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1
B: Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1
C: Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1

A: Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1
B: Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1
C: Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1

A: Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1
B: Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1
C: Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)603,17312
Polymers603,17312
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 area40820 Å2
ΔGint-100 kcal/mol
Surface area184730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.590, 127.710, 204.220
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 Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1 / BPO2 / Bromide peroxidase / M1


Mass: 50264.414 Da / Num. of mol.: 3
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, M, M1 Matrix / 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: 2.65 Å3/Da / Density % sol: 53.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.3
Details: 1.2M NaH2PO4, 0.8M K2HPO4, 0.1M CAPS, pH 10.3, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 25, 2011
RadiationMonochromator: VARIMAX HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→19.73 Å / Num. obs: 22135 / % possible obs: 68.3 % / Observed criterion σ(I): -3 / Redundancy: 4.95 % / Biso Wilson estimate: 38.558 Å2 / Rmerge(I) obs: 0.206 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
3-3.080.6692.912724478120.4
3.08-3.160.583.154646826135.8
3.16-3.260.5992.9358551035146.3
3.26-3.360.5393.2468751231156.2
3.36-3.470.4863.32582576127
3.47-3.590.4623.6270701386168.4
3.59-3.720.4143.443197768138.7
3.72-3.880.3324.5275021597183.6
3.88-4.050.3734.724476991154.5
4.05-4.250.236.8987041765199.3
4.25-4.480.1838.3681641658199.7
4.48-4.750.1958.277431574199.6
4.75-5.070.1728.9773331483199.7
5.07-5.480.1898.0868991398199.8
5.48-60.2137.3163121281199.8
6-6.710.1878.0757701178199.7
6.71-7.750.12411.3850231033199.9
7.75-9.490.05621.634285898199.7
9.49-13.430.0429.823217706199.6
13.43-19.730.04428.331146273165.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å19.63 Å
Translation4 Å19.63 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1BRO, 1AA7

1bro

1aa7


Resolution: 3.002→19.728 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7889 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 27.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2813 1133 5.12 %
Rwork0.2285 --
obs0.2312 22131 68.63 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0.001 Å2 / ksol: 0.284 e/Å3
Displacement parametersBiso max: 150.45 Å2 / Biso mean: 54.1428 Å2 / Biso min: 17.38 Å2
Baniso -1Baniso -2Baniso -3
1--7.6483 Å2-0 Å2-0 Å2
2---7.6447 Å2-0 Å2
3----5.1296 Å2
Refinement stepCycle: LAST / Resolution: 3.002→19.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10149 0 0 0 10149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210380
X-RAY DIFFRACTIONf_angle_d0.55514127
X-RAY DIFFRACTIONf_chiral_restr0.041599
X-RAY DIFFRACTIONf_plane_restr0.0031836
X-RAY DIFFRACTIONf_dihedral_angle_d11.6923684
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.002-3.13850.3658590.2753966102526
3.1385-3.30330.3217870.28781797188447
3.3033-3.50910.3196900.29521525161541
3.5091-3.77830.32731260.27262300242661
3.7783-4.15540.31881460.24322775292173
4.1554-4.74930.27292180.191738094027100
4.7493-5.95620.26192030.219538434046100
5.9562-19.72870.2372040.209639834187100

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