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- PDB-4iq4: Structure of a 16 nm protein cage designed by fusing symmetric ol... -

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Basic information

Entry
Database: PDB / ID: 4iq4
TitleStructure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, triple mutant, P21212 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 / Viral mRNA Translation / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / 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
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.495 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 10, 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
D: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
E: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
F: Non-haem bromoperoxidase BPO-A2, Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)301,6886
Polymers301,6886
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
D: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
E: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
F: 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
D: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
E: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
F: 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_555-x,-y,z1
Buried area34910 Å2
ΔGint-81 kcal/mol
Surface area186480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.710, 137.870, 171.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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.: 6 / 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 fusion, 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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1M Na Citrate pH 4.4, 10% PEG 3,000, 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: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.495→93.3 Å / Num. all: 37857 / Num. obs: 37857 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 71.073 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 9.74
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
3.5-3.590.6062.42114642618192.8
3.59-3.680.4853.11120182708198.8
3.68-3.790.383.78109282610196.9
3.79-3.910.3244.65117762570198.2
3.91-4.040.2825.34118502503199.6
4.04-4.180.2196.64114662448199.5
4.18-4.340.1817.79109682346199.2
4.34-4.510.1558.76104152259199
4.51-4.710.1449.4998852162198.2
4.71-4.940.12710.2887782027196.4
4.94-5.210.12110.5686401932196.5
5.21-5.530.12210.9890091897199.1
5.53-5.910.12910.2882261756198.8
5.91-6.380.11711.1475821630198.1
6.38-6.990.09912.5867491506197
6.99-7.820.06716.6556261327194.1
7.82-9.030.04225.757501230198.2
9.03-11.050.03530.8447151049198
11.05-15.630.03731.423318799192.7
15.63-93.30.03732.762045480195

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.6 Å93.29 Å
Translation3.6 Å93.29 Å

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Processing

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

1bro

1aa7


Resolution: 3.495→93.294 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8435 / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 22.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 1893 5 %RANDOM
Rwork0.1995 ---
obs0.2011 37833 97.51 %-
all-37857 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 318.09 Å2 / Biso mean: 103.9704 Å2 / Biso min: 39.87 Å2
Refinement stepCycle: LAST / Resolution: 3.495→93.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20388 0 0 0 20388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00320850
X-RAY DIFFRACTIONf_angle_d0.72328374
X-RAY DIFFRACTIONf_chiral_restr0.0593204
X-RAY DIFFRACTIONf_plane_restr0.0033696
X-RAY DIFFRACTIONf_dihedral_angle_d15.1877404
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4954-3.58290.31541260.25862390251693
3.5829-3.67970.27641350.23862577271299
3.6797-3.7880.25251320.21882507263997
3.788-3.91030.24311340.20672552268698
3.9103-4.050.23281360.207825822718100
4.05-4.21220.22821360.19512586272299
4.2122-4.40390.23191360.18122583271999
4.4039-4.63610.2171360.18792583271999
4.6361-4.92650.24591340.1762548268297
4.9265-5.30690.21031350.19162551268697
5.3069-5.84090.25991370.20462605274299
5.8409-6.68580.26041380.21882621275998
6.6858-8.42260.2181350.20362563269896
8.4226-93.3270.18491430.18162692283595
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)
11.32630.33960.09642.4359-0.5483.3280.0919-0.11540.47450.3945-0.0917-0.0348-0.40770.09540.02310.5538-0.00370.02150.4636-0.06850.715538.797145.8201202.6478
21.132.0648-1.29313.7673-2.34971.46470.5897-0.6849-0.22260.6455-0.2247-0.4896-0.05880.3185-0.32921.4414-0.2323-0.32860.9537-0.00011.426849.159530.8972221.6766
34.4549-0.32012.78224.8266-0.14524.1545-0.23450.18240.21830.3061-0.0439-0.2383-0.4740.33220.27280.9692-0.12310.00490.7051-0.02080.664845.96789.9118224.3894
41.9279-0.05340.04872.98211.05372.6789-0.0342-0.02480.2903-0.3274-0.1450.7206-0.3704-0.87930.21610.45130.0927-0.06940.7199-0.0220.775714.741539.4986174.5345
53.2107-1.1803-3.35811.31750.54634.64810.60920.72520.48010.0586-0.38340.0415-0.3269-0.9828-0.20751.10070.44510.25891.72470.23581.1778-3.819255.4872184.1686
66.5211-1.3327-2.61183.8244-1.99665.63170.19221.98180.6814-0.31010.24851.5957-0.521-1.2153-0.39741.0394-0.0152-0.04251.75360.10281.6348-20.410761.8982194.3592
76.9058-1.7877-1.27264.7905-1.07575.0609-0.8252-1.5201-0.38610.47610.0543-1.05071.04511.61130.81641.49550.51530.27031.76460.2060.9734-13.49854.802209.4729
87.1804-1.6098-3.83257.3912-1.00518.7124-1.1285-1.4655-1.2038-0.1407-0.15070.6972.78042.07481.28781.83740.64620.58111.70610.07541.6113-12.90848.4022200.7364
91.96860.3796-0.26043.01130.21414.14280.09340.0549-0.17530.0565-0.03750.03070.54690.1975-0.04930.44010.03350.01050.42130.00620.597240.648813.933182.9218
105.17912.0594-2.57732.993-0.84393.9477-0.0367-0.09040.38340.26810.09220.27070.2013-0.4952-0.04371.41080.0096-0.08230.911-0.09841.270326.4123-5.6489172.6894
114.50491.8266-2.14467.58610.52625.94031.1770.2061.72570.7608-0.59340.8079-2.0058-1.456-0.54961.76940.15940.59961.12020.00941.48539.2299-17.2186171.1644
121.04130.09550.07980.10010.20180.421.2377-0.2851.63670.6431-0.98590.6279-0.7037-0.8178-0.25813.6149-0.26341.90983.0246-0.76793.06123.2467-11.3221187.1248
136.64412.48430.57164.40740.56915.97121.2458-1.76291.41571.1543-0.6941.4075-0.9606-0.0206-0.47662.6636-0.5311.01491.6042-0.34891.893513.2147-13.6285187.1715
142.02920.2572-0.05863.33680.23442.44250.0682-0.17020.0086-0.2767-0.03330.19630.1762-0.166-0.03160.5530.0057-0.03650.5367-0.03530.6452-40.91614.7526247.044
155.9057-4.6126-1.99766.95691.95270.7205-0.2273-0.6434-0.5303-0.29480.1222-0.80220.48031.0160.10151.21520.3972-0.11521.20940.14271.4295-28.2151-5.9754257.0403
167.6495-0.1656-2.95776.67750.73686.59711.2762-1.380.7466-0.9514-0.4766-1.5665-1.81980.5056-0.87411.5575-0.00120.53941.3654-0.22442.0011-11.1394-15.0529259.1197
170.52370.1111-0.75080.0071-0.16691.1380.89251.09380.7393-1.3804-1.8342-1.0427-0.31830.58410.83274.13051.3551.52443.27641.23762.9818-4.5412-9.1007243.1697
184.7011-0.73770.95014.3745-0.67375.15312.02331.91440.9317-2.4214-0.6376-1.0799-2.01760.1419-1.32063.32860.94020.92021.91110.23132.1104-13.9903-12.5372242.6851
191.28860.29470.16741.24280.69261.92470.04630.09830.4168-0.44760.0970.0134-0.6156-0.0594-0.12360.93360.04180.03340.517-0.01790.7007-34.409546.3015227.6304
200.3288-0.0425-0.1351.49971.29061.58290.40480.1982-0.2345-0.3714-0.1006-0.3876-0.6932-0.3558-0.27671.72750.0445-0.37590.78940.07911.3366-45.876932.7007208.101
214.1727-1.18663.62814.803-0.77644.1366-0.2115-0.01780.1961-0.04910.00360.1205-0.5902-0.11210.25821.01380.01890.11370.64270.00850.7266-44.402611.2512205.2651
222.35590.1251-0.35622.8083-0.35012.92790.2445-0.31230.33980.3568-0.0648-0.3216-0.68690.4662-0.18890.6977-0.1490.10980.6735-0.10590.6005-12.475537.1641256.6588
231.98370.475-0.82831.3914-1.20411.1320.11990.398-0.19220.0697-0.3676-0.3385-0.38280.33030.25490.9663-0.3188-0.10641.8989-0.12671.44376.153550.5225243.7748
245.55223.1772-2.19654.3035-0.99694.87270.15680.36630.2690.0175-0.22220.654-0.2661-0.9155-0.03150.7587-0.00980.17711.0755-0.12650.941612.294649.0443223.1726
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 1:276A1 - 276
2X-RAY DIFFRACTION2chain A and resid 277:285A277 - 285
3X-RAY DIFFRACTION3chain A and resid 286:440A286 - 440
4X-RAY DIFFRACTION4chain B and resid 1:276B1 - 276
5X-RAY DIFFRACTION5chain B and resid 277:285B277 - 285
6X-RAY DIFFRACTION6chain B and resid 286:352B286 - 352
7X-RAY DIFFRACTION7chain B and resid 353:388B353 - 388
8X-RAY DIFFRACTION8chain B and resid 389:440B389 - 440
9X-RAY DIFFRACTION9chain C and resid 1:276C1 - 276
10X-RAY DIFFRACTION10chain C and resid 277:285C277 - 285
11X-RAY DIFFRACTION11chain C and resid 286:352C286 - 352
12X-RAY DIFFRACTION12chain C and resid 353:388C353 - 388
13X-RAY DIFFRACTION13chain C and resid 389:440C389 - 440
14X-RAY DIFFRACTION14chain D and resid 1:276D1 - 276
15X-RAY DIFFRACTION15chain D and resid 277:285D277 - 285
16X-RAY DIFFRACTION16chain D and resid 286:352D286 - 352
17X-RAY DIFFRACTION17chain D and resid 353:388D353 - 388
18X-RAY DIFFRACTION18chain D and resid 389:440D389 - 440
19X-RAY DIFFRACTION19chain E and resid 1:276E1 - 276
20X-RAY DIFFRACTION20chain E and resid 277:285E277 - 285
21X-RAY DIFFRACTION21chain E and resid 286:440E286 - 440
22X-RAY DIFFRACTION22chain F and resid 1:276F1 - 276
23X-RAY DIFFRACTION23chain F and resid 277:285F277 - 285
24X-RAY DIFFRACTION24chain F and resid 286:440F286 - 440

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