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

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Basic information

Entry
Database: PDB / ID: 4qes
TitleStructure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, quadruple mutant, I222 form
ComponentsNon-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera
KeywordsOXIDOREDUCTASE / VIRAL 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 / Viral mRNA Translation / antibiotic biosynthetic process / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / 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 / Epoxide hydrolase-like ...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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.193 Å
AuthorsLai, Y.-T. / Yeates, T.O.
CitationJournal: To be Published
Title: Structural transition of a protein nanocage as a function of pH and salt concentration.
Authors: Lai, Y.-T. / Yeates, T.O.
History
DepositionMay 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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 chimera
B: Non-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera
C: Non-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera


Theoretical massNumber of molelcules
Total (without water)150,5683
Polymers150,5683
Non-polymers00
Water00
1
A: Non-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera
B: Non-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera
C: Non-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera

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

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

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


Theoretical massNumber of molelcules
Total (without water)602,27112
Polymers602,27112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area34160 Å2
ΔGint-102 kcal/mol
Surface area186590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.510, 165.520, 167.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 1 - 441 / Label seq-ID: 2 - 442

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Non-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera / Designed 16nm tetrahedral protein cage / BPO2 / Bromide peroxidase / M1


Mass: 50189.266 Da / Num. of mol.: 3 / Fragment: SEE REMARK 999 / Mutation: K118A, L279Q, Q24T, Y51A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aureofaciens (bacteria), (gene. exp.) Influenza A virus
Gene: bpoA2, 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
Sequence detailsTHE DESIGNED PROTEIN CONSTRUCT IS A CHIMERA COMPRISING BPO2 (UNP P29715) AND RESIDUES 2-164 (UNP ...THE DESIGNED PROTEIN CONSTRUCT IS A CHIMERA COMPRISING BPO2 (UNP P29715) AND RESIDUES 2-164 (UNP P03485) OF M1, SEPARATED BY A LINKER.

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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: 2.85 Å3/Da / Density % sol: 56.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1 M sodium citrate, pH 4.4, 11% PEG3000, 200 mM sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 28, 2014
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 4.19→83.835 Å / Num. obs: 12914 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 161.223 Å2 / Rmerge(I) obs: 0.127 / Χ2: 0.824 / Net I/σ(I): 14.16
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
4.19-4.30.8853.3211554911196.4
4.3-4.420.7364.37126429291100
4.42-4.550.6365118398761100
4.55-4.690.5835.44115228631100
4.69-4.840.4436.88109568371100
4.84-5.010.3937.6910572825199.9
5.01-5.20.3887.7398547921100
5.2-5.410.3278.6586427581100
5.41-5.650.27110.9393887241100
5.65-5.930.26711.2895237081100
5.93-6.250.22413.1890306701100
6.25-6.630.18915.5787286411100
6.63-7.090.15118.679565921100
7.09-7.660.11122.7372705641100
7.66-8.390.07628.225982508199.2
8.39-9.380.05837.9964764741100
9.38-10.830.05841.6456274201100
10.83-13.260.05841.5845833611100
13.26-18.750.06539.23220291199.3
18.75-83.8350.07541.561838170198.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.19 Å83.83 Å
Translation4.19 Å83.83 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.6phasing
REFMAC5.8.0071refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.193→83.83 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2867 / WRfactor Rwork: 0.2438 / FOM work R set: 0.737 / SU B: 76.252 / SU ML: 0.981 / SU Rfree: 1.1442 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2948 646 5 %RANDOM
Rwork0.2513 ---
obs0.2535 12914 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 500 Å2 / Biso mean: 198.022 Å2 / Biso min: 87.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å20 Å2
2---3.72 Å2-0 Å2
3---2.84 Å2
Refinement stepCycle: LAST / Resolution: 4.193→83.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10128 0 0 0 10128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910359
X-RAY DIFFRACTIONr_bond_other_d0.0040.029666
X-RAY DIFFRACTIONr_angle_refined_deg1.441.95314112
X-RAY DIFFRACTIONr_angle_other_deg0.949322149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.27151320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45323.742465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.472151575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2861566
X-RAY DIFFRACTIONr_chiral_restr0.0750.21605
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111946
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022436
X-RAY DIFFRACTIONr_mcbond_it17.36719.6755289
X-RAY DIFFRACTIONr_mcbond_other17.36819.6745288
X-RAY DIFFRACTIONr_mcangle_it28.12429.4766606
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A272290.05
12B272290.05
21A271710.06
22C271710.06
31B272280.05
32C272280.05
LS refinement shellResolution: 4.193→4.302 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 45 -
Rwork0.325 865 -
all-910 -
obs--96.4 %

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