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

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Basic information

Entry
Database: PDB / ID: 4itv
TitleStructure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, triple mutant, P212121 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: 3.598 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 18, 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
G: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
H: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
I: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
J: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
K: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
L: Non-haem bromoperoxidase BPO-A2, Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)603,37612
Polymers603,37612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35620 Å2
ΔGint-97 kcal/mol
Surface area187760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.620, 156.610, 321.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 12 / 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: 2.74 Å3/Da / Density % sol: 55.16 %
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: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / 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: 3.598→160.575 Å / Num. all: 76475 / Num. obs: 76475 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 102.21 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.61
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
3.6-3.690.6192.5247395452195.7
3.69-3.790.4553.4251445470199.1
3.79-3.90.3494.37240725315198.7
3.9-4.020.2835.43227725155198.2
4.02-4.160.2166.63198574852195.7
4.16-4.30.1738.7234174900199.7
4.3-4.460.12811.31228084759199.7
4.46-4.650.11212.71217244576199.7
4.65-4.850.09414.91205514358199.6
4.85-5.090.08316.26197004204199.4
5.09-5.360.07916.86182953992199.3
5.36-5.690.07218.35169303783199
5.69-6.080.06917.9139103388195.1
6.08-6.570.05921.73152123324198.6
6.57-7.20.04328.33145233063199.4
7.2-8.050.03138.38128642779199.1
8.05-9.290.02252.23112882486199
9.29-11.380.0257.2587522068196.6
11.38-16.090.01960.1968631591194.5
16.09-160.5750.0262.514152960196.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.6 Å96.14 Å
Translation3.6 Å96.14 Å

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Processing

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

1bro

1aa7


Resolution: 3.598→96.14 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8376 / SU ML: 0.39 / σ(F): 1.99 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 3821 5 %random
Rwork0.2061 ---
all0.2078 76445 --
obs0.2078 76445 98.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 423.59 Å2 / Biso mean: 151.8637 Å2 / Biso min: 53.78 Å2
Refinement stepCycle: LAST / Resolution: 3.598→96.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40776 0 0 0 40776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00341700
X-RAY DIFFRACTIONf_angle_d0.60956748
X-RAY DIFFRACTIONf_chiral_restr0.0426408
X-RAY DIFFRACTIONf_plane_restr0.0047392
X-RAY DIFFRACTIONf_dihedral_angle_d13.19214808
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5984-3.64390.3171320.30072508264092
3.6439-3.69190.28431400.28512672281299
3.6919-3.74250.34561410.27032676281799
3.7425-3.79590.25571410.25962672281399
3.7959-3.85260.2971400.24952655279599
3.8526-3.91280.27121400.24212668280899
3.9128-3.9770.28961410.23832676281798
3.977-4.04550.27041380.24452629276798
4.0455-4.11910.24831370.22422590272795
4.1191-4.19830.24251380.22092635277398
4.1983-4.2840.24431420.204527152857100
4.284-4.37720.22481430.19727202863100
4.3772-4.4790.2491420.19626952837100
4.479-4.5910.25281420.199726992841100
4.591-4.71510.21921450.200327402885100
4.7151-4.85390.24291410.18726932834100
4.8539-5.01050.22191440.182327212865100
5.0105-5.18960.22711420.1882699284199
5.1896-5.39740.24711430.19442721286499
5.3974-5.6430.21521420.18772700284299
5.643-5.94050.26811400.21632662280297
5.9405-6.31260.26911390.22562635277495
6.3126-6.79990.2651450.218427622907100
6.7999-7.48390.22191450.19682746289199
7.4839-8.56630.21121450.17962759290499
8.5663-10.79030.18581460.14972770291698
10.7903-96.1740.23721470.22572806295395
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)
12.17710.22960.90683.0007-1.01124.29350.065-0.0024-0.10970.34220.03820.2248-0.1449-0.2475-0.10150.47040.01740.09850.6516-0.14120.530416.657447.4243342.8757
29.6883-3.44784.37677.2286-2.14276.90350.264-0.43470.23590.0561-0.5666-0.22280.16710.3730.29950.7864-0.01110.03031.0670.11720.4977-13.529739.8594371.1818
33.26550.52320.63223.82130.88862.896-0.26030.62810.4601-0.8909-0.01660.202-0.7725-0.04520.26940.99350.0191-0.09760.78360.02390.58214.728567.675311.3918
48.46754.9857-4.34625.7022-3.68928.2636-0.17190.01810.1989-0.2130.0025-0.0665-0.55290.20170.11421.08620.1717-0.12820.6077-0.08560.57821.387588.8284346.7508
53.0607-0.73121.28443.2909-0.04734.41020.06570.0836-0.2959-0.2435-0.13530.96710.1328-0.81420.06060.5009-0.0106-0.06880.9934-0.18231.015-9.831840.1002317.4054
69.7289-4.6225-0.17862.7352-0.23997.53780.10610.17431.29480.1158-0.1491-0.9076-1.75720.26570.05961.2248-0.1065-0.0340.9882-0.01721.7462-38.920166.5276304.3239
73.1089-0.1242-0.63663.6498-0.12242.71170.0122-0.19510.7969-1.0602-0.16440.1721-0.606-0.4290.11311.30550.2179-0.2820.8139-0.28340.939414.7307111.5375372.5944
84.33723.3062-0.76632.1299-1.81696.10020.1487-0.0020.6622-0.61740.35471.34940.067-0.9529-0.65921.72470.4509-0.39321.5004-0.02661.8437-19.2818118.429350.517
92.6372-0.1882-0.31163.42810.86232.2745-0.1032-1.18840.26430.6257-0.14970.31180.0294-0.40620.23160.95860.0207-0.01631.3873-0.29640.657110.300991.2894403.7505
109.6872-4.91462.60348.6757-0.62439.4059-0.1303-0.0251-0.05-0.1151-0.0725-0.01280.05390.29970.20630.7204-0.08490.01770.5939-0.0610.552719.915369.5511369.6195
111.7184-0.1551-0.84792.20280.17283.2453-0.2363-0.82451.0655-0.0087-0.32150.9411-0.7582-1.51980.43861.06760.5981-0.39142.2517-0.93651.7951-13.4942119.112395.919
122.23798.57855.9248.85925.24813.3616-1.18090.4711-1.6168-1.8680.6099-0.42970.4739-0.89170.71052.2138-0.4030.18692.1948-0.32192.3624-44.370692.1873406.7296
133.17690.989-0.78690.7870.05273.4280.0140.06160.6168-0.61550.2494-0.4566-0.69170.6588-0.26361.3797-0.09870.53460.8064-0.01151.7778-42.0911116.9717320.8955
145.9084-5.5679-0.18048.9762-0.72962.19-0.0697-0.1109-1.92540.71730.19892.34941.04390.8312-0.06521.79970.20110.05771.52760.10322.2332-12.270488.6354311.7
154.63781.1601-0.52041.51710.34674.17460.02710.10560.6852-0.01190.0434-0.2027-0.4407-0.0912-0.09591.01350.04410.12060.5470.01430.9659-71.174110.6979343.4952
164.9177-2.87953.90547.7299-0.42345.1642-0.40910.67560.32673.3830.0084-1.70650.65781.66720.48192.91030.2053-0.34413.22560.21951.7077-44.4635117.1763376.3639
173.6889-0.99760.13093.70730.60922.4593-0.34130.5957-0.3487-1.0070.1345-0.65460.4911-0.12260.20241.8567-0.13550.49470.784-0.03221.0343-64.650587.644314.6246
188.84315.75862.60768.00172.82277.6822-0.19720.2142-0.1426-0.3540.1429-0.55630.3045-0.29640.05810.96010.05760.20840.55140.08580.8074-75.871668.9726349.8814
192.78670.20331.5265.37610.63924.2390.0663-0.6939-0.65290.0830.2252-0.73650.2649-0.323-0.2270.68850.07980.02010.90250.2321.0281-73.238548.8048378.4184
206.28864.77044.00715.86691.5928.66410.2086-0.60170.5637-0.1182-0.73710.5722-0.068-0.650.51450.71650.1995-0.08980.8033-0.12330.7568-38.478841.4866355.9113
211.3947-0.36080.65184.6397-0.22273.5631-0.3296-1.24390.20872.30410.1982-0.606-0.7719-0.57720.09532.00880.2664-0.26981.4956-0.05940.9549-72.131771.8556407.9764
229.4993-6.1516-1.13266.30440.49519.3972-0.1913-0.69780.09390.43810.3698-0.1725-0.5344-0.5784-0.22450.8889-0.07950.02660.7591-0.10630.7402-77.827290.2238371.0915
232.09570.32710.89582.0351-0.25372.69850.0285-0.6933-0.60521.39020.0871-2.13110.1280.3049-0.09141.61970.1642-0.98541.47530.31332.7177-47.573143.6277405.1817
241.87431.7995-0.42672.79970.52010.35960.0063-1.14291.8253-1.15670.3268-0.5665-1.15522.333-0.36522.6837-0.44790.31843.39080.0213.5728-18.210371.2114418.2901
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 277:440A277 - 440
3X-RAY DIFFRACTION3chain B and resid 1:276B1 - 276
4X-RAY DIFFRACTION4chain B and resid 277:440B277 - 440
5X-RAY DIFFRACTION5chain C and resid 1:276C1 - 276
6X-RAY DIFFRACTION6chain C and resid 277:440C277 - 440
7X-RAY DIFFRACTION7chain D and resid 1:276D1 - 276
8X-RAY DIFFRACTION8chain D and resid 277:440D277 - 440
9X-RAY DIFFRACTION9chain E and resid 1:276E1 - 276
10X-RAY DIFFRACTION10chain E and resid 277:440E277 - 440
11X-RAY DIFFRACTION11chain F and resid 1:276F1 - 276
12X-RAY DIFFRACTION12chain F and resid 277:440F277 - 440
13X-RAY DIFFRACTION13chain G and resid 1:276G1 - 276
14X-RAY DIFFRACTION14chain G and resid 277:440G277 - 440
15X-RAY DIFFRACTION15chain H and resid 1:276H1 - 276
16X-RAY DIFFRACTION16chain H and resid 277:440H277 - 440
17X-RAY DIFFRACTION17chain I and resid 1:276I1 - 276
18X-RAY DIFFRACTION18chain I and resid 277:440I277 - 440
19X-RAY DIFFRACTION19chain J and resid 1:276J1 - 276
20X-RAY DIFFRACTION20chain J and resid 277:440J277 - 440
21X-RAY DIFFRACTION21chain K and resid 1:276K1 - 276
22X-RAY DIFFRACTION22chain K and resid 277:440K277 - 440
23X-RAY DIFFRACTION23chain L and resid 1:276L1 - 276
24X-RAY DIFFRACTION24chain L and resid 277:440L277 - 440

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