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

Basic information

• Entry: Database: PDB / ID: 4qff
• Title: Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, quadruple mutant, P212121 form
• Components: Non-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera
• Keywords: OXIDOREDUCTASE / VIRAL PROTEIN / protein design / bionanotechnology / protein assembly / symmetry / biomaterials

Function / homology

Function:

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

Domain/homology:

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

Component:

Matrix protein 1 / Non-haem bromoperoxidase BPO-A2

• Biological species: Streptomyces aureofaciens (bacteria); Influenza A virus
• Method: X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 7.811 Å
• Authors: Lai, Y.-T. / Yeates, T.O.
• Citation: Journal: 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

Deposition	May 20, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 20, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jul 26, 2017	Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Refinement description Category: 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 / _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

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

D: Non-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera

E: Non-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera

F: Non-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera

G: Non-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera

H: Non-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera

I: Non-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera

J: Non-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera

K: Non-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera

L: Non-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera

Summary:

• 602 kDa, 12 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	602,271	12
Polymers	602,271	12
Non-polymers	0	0
Water	0	0

1

Summary:

• Idetical with deposited unit
• defined by author&software

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	32320 Å2
ΔGint	-86 kcal/mol
Surface area	190580 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	155.500, 156.520, 325.030
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P212121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	G
1	7	A
2	7	H
1	8	A
2	8	I
1	9	A
2	9	J
1	10	A
2	10	K
1	11	A
2	11	L
1	12	B
2	12	C
1	13	B
2	13	D
1	14	B
2	14	E
1	15	B
2	15	F
1	16	B
2	16	G
1	17	B
2	17	H
1	18	B
2	18	I
1	19	B
2	19	J
1	20	B
2	20	K
1	21	B
2	21	L
1	22	C
2	22	D
1	23	C
2	23	E
1	24	C
2	24	F
1	25	C
2	25	G
1	26	C
2	26	H
1	27	C
2	27	I
1	28	C
2	28	J
1	29	C
2	29	K
1	30	C
2	30	L
1	31	D
2	31	E
1	32	D
2	32	F
1	33	D
2	33	G
1	34	D
2	34	H
1	35	D
2	35	I
1	36	D
2	36	J
1	37	D
2	37	K
1	38	D
2	38	L
1	39	E
2	39	F
1	40	E
2	40	G
1	41	E
2	41	H
1	42	E
2	42	I
1	43	E
2	43	J
1	44	E
2	44	K
1	45	E
2	45	L
1	46	F
2	46	G
1	47	F
2	47	H
1	48	F
2	48	I
1	49	F
2	49	J
1	50	F
2	50	K
1	51	F
2	51	L
1	52	G
2	52	H
1	53	G
2	53	I
1	54	G
2	54	J
1	55	G
2	55	K
1	56	G
2	56	L
1	57	H
2	57	I
1	58	H
2	58	J
1	59	H
2	59	K
1	60	H
2	60	L
1	61	I
2	61	J
1	62	I
2	62	K
1	63	I
2	63	L
1	64	J
2	64	K
1	65	J
2	65	L
1	66	K
2	66	L

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-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	A	A
2	4	E	E
1	5	A	A
2	5	F	F
1	6	A	A
2	6	G	G
1	7	A	A
2	7	H	H
1	8	A	A
2	8	I	I
1	9	A	A
2	9	J	J
1	10	A	A
2	10	K	K
1	11	A	A
2	11	L	L
1	12	B	B
2	12	C	C
1	13	B	B
2	13	D	D
1	14	B	B
2	14	E	E
1	15	B	B
2	15	F	F
1	16	B	B
2	16	G	G
1	17	B	B
2	17	H	H
1	18	B	B
2	18	I	I
1	19	B	B
2	19	J	J
1	20	B	B
2	20	K	K
1	21	B	B
2	21	L	L
1	22	C	C
2	22	D	D
1	23	C	C
2	23	E	E
1	24	C	C
2	24	F	F
1	25	C	C
2	25	G	G
1	26	C	C
2	26	H	H
1	27	C	C
2	27	I	I
1	28	C	C
2	28	J	J
1	29	C	C
2	29	K	K
1	30	C	C
2	30	L	L
1	31	D	D
2	31	E	E
1	32	D	D
2	32	F	F
1	33	D	D
2	33	G	G
1	34	D	D
2	34	H	H
1	35	D	D
2	35	I	I
1	36	D	D
2	36	J	J
1	37	D	D
2	37	K	K
1	38	D	D
2	38	L	L
1	39	E	E
2	39	F	F
1	40	E	E
2	40	G	G
1	41	E	E
2	41	H	H
1	42	E	E
2	42	I	I
1	43	E	E
2	43	J	J
1	44	E	E
2	44	K	K
1	45	E	E
2	45	L	L
1	46	F	F
2	46	G	G
1	47	F	F
2	47	H	H
1	48	F	F
2	48	I	I
1	49	F	F
2	49	J	J
1	50	F	F
2	50	K	K
1	51	F	F
2	51	L	L
1	52	G	G
2	52	H	H
1	53	G	G
2	53	I	I
1	54	G	G
2	54	J	J
1	55	G	G
2	55	K	K
1	56	G	G
2	56	L	L
1	57	H	H
2	57	I	I
1	58	H	H
2	58	J	J
1	59	H	H
2	59	K	K
1	60	H	H
2	60	L	L
1	61	I	I
2	61	J	J
1	62	I	I
2	62	K	K
1	63	I	I
2	63	L	L
1	64	J	J
2	64	K	K
1	65	J	J
2	65	L	L
1	66	K	K
2	66	L	L

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66

Components

#1: Protein

A B C D E F G H I J K L
Non-haem bromoperoxidase BPO-A2, Matrix protein 1 chimera / Designed 16nm tetrahedral protein cage / BPO2 / Bromide peroxidase / M1

Details:

Mass: 50189.266 Da / Num. of mol.: 12 / 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 details: THE DESIGNED PROTEIN CONSTRUCT IS A CHIMERA COMPRISING BPO2 (UNP P29715) AND RESIDUES 2-164 (UNP P03485) OF M1, SEPARATED BY A LINKER.

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 3.28 ų/Da / Density % sol: 62.54 %
• Crystal grow: Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 ; Details: 0.1 M sodium/potassium phosphate, pH 5.8, 10% PEG8000, 0.2 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
• Detector: Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 27, 2014
• Radiation: Monochromator: VARIMAX HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.542 Å / Relative weight: 1
• Reflection: Resolution: 7.81→91.273 Å / Num. obs: 8723 / % possible obs: 92.1 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 127.481 Ų / R_merge(I) obs: 0.142 / Χ²: 0.89 / Net I/σ(I): 10.67

Reflection shell

Resolution (Å)	Rmerge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	Diffraction-ID	% possible all
7.81-8.01	0.597	2.35	1724	516	1	77.4
8.01-8.23	0.418	3.98	2643	650	1	95.9
8.23-8.47	0.33	5.11	2597	617	1	96.9
8.47-8.73	0.261	6.1	2486	605	1	95.9
8.73-9.02	0.213	7.31	2518	603	1	96.8
9.02-9.34	0.188	8.5	2339	564	1	95.4
9.34-9.69	0.147	9.92	2265	560	1	96.2
9.69-10.08	0.145	10.41	2196	518	1	95.2
10.08-10.53	0.128	11.72	2125	519	1	94.5
10.53-11.05	0.129	11.64	1989	483	1	96
11.05-11.64	0.102	14.21	1972	473	1	95
11.64-12.35	0.09	15.21	1749	424	1	93.2
12.35-13.2	0.08	16.14	1691	410	1	93.8
13.2-14.26	0.093	14.07	1546	382	1	93.4
14.26-15.62	0.072	16.22	1497	371	1	93.2
15.62-17.47	0.05	22.27	1235	312	1	92.9
17.47-20.17	0.058	20.47	1084	287	1	91.7
20.17-24.7	0.057	18.5	560	224	1	83
24.7-34.93	0.026	21.3	217	113	1	53.6
34.93-91.273	0.735	0.01	282	92	1	68.1

Phasing

• Phasing: Method: molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	7.81 Å	91.27 Å
Translation	7.81 Å	91.27 Å

Processing

Software

Name	Version	Classification	NB
XSCALE		data scaling
PHASER	2.5.6	phasing
REFMAC	5.8.0071	refinement
PDB_EXTRACT	3.14	data extraction

Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 7.811→91.27 Å / Cor.coef. F_o:F_c: 0.704 / Cor.coef. F_o:F_c free: 0.602 / WR_factor R_free: 0.3508 / WR_factor R_work: 0.2847 / FOM work R set: 0.7872 / SU B: 560.278 / SU ML: 4.205 / SU R_free: 6.1184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 6.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.3388	437	5 %	RANDOM
Rwork	0.2876	-	-	-
obs	0.2901	8723	92.13 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 500 Ų / B_iso mean: 241.153 Ų / B_iso min: 90.49 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-13.46 Å2	-0 Å2	-0 Å2
2-	-	-9.11 Å2	0 Å2
3-	-	-	22.57 Å2

Refinement step

Cycle: LAST / Resolution: 7.811→91.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	40512	0	0	0	40512

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	41436
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	38664
X-RAY DIFFRACTION	r_angle_refined_deg	1.437	1.953	56448
X-RAY DIFFRACTION	r_angle_other_deg	1.421	3	88596
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.143	5	5280
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.023	23.742	1860
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.718	15	6300
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.39	15	264
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	6420
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	47784
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	9744
X-RAY DIFFRACTION	r_mcbond_it	5.873	24.36	21156
X-RAY DIFFRACTION	r_mcbond_other	5.873	24.36	21155
X-RAY DIFFRACTION	r_mcangle_it	10.827	36.532	26424

Refine LS restraints NCS

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

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	25960	0.09
1	2	B	25960	0.09
2	1	A	25974	0.09
2	2	C	25974	0.09
3	1	A	27329	0.05
3	2	D	27329	0.05
4	1	A	27435	0.02
4	2	E	27435	0.02
5	1	A	27414	0.02
5	2	F	27414	0.02
6	1	A	27339	0.03
6	2	G	27339	0.03
7	1	A	26024	0.09
7	2	H	26024	0.09
8	1	A	25959	0.09
8	2	I	25959	0.09
9	1	A	27387	0.02
9	2	J	27387	0.02
10	1	A	25710	0.11
10	2	K	25710	0.11
11	1	A	25937	0.09
11	2	L	25937	0.09
12	1	B	27274	0.03
12	2	C	27274	0.03
13	1	B	25838	0.1
13	2	D	25838	0.1
14	1	B	25943	0.09
14	2	E	25943	0.09
15	1	B	25936	0.09
15	2	F	25936	0.09
16	1	B	25914	0.09
16	2	G	25914	0.09
17	1	B	27306	0.04
17	2	H	27306	0.04
18	1	B	27332	0.03
18	2	I	27332	0.03
19	1	B	25906	0.09
19	2	J	25906	0.09
20	1	B	27051	0.06
20	2	K	27051	0.06
21	1	B	27196	0.04
21	2	L	27196	0.04
22	1	C	25896	0.09
22	2	D	25896	0.09
23	1	C	25983	0.09
23	2	E	25983	0.09
24	1	C	25958	0.09
24	2	F	25958	0.09
25	1	C	25852	0.09
25	2	G	25852	0.09
26	1	C	27346	0.02
26	2	H	27346	0.02
27	1	C	27286	0.03
27	2	I	27286	0.03
28	1	C	25937	0.09
28	2	J	25937	0.09
29	1	C	27056	0.06
29	2	K	27056	0.06
30	1	C	27259	0.03
30	2	L	27259	0.03
31	1	D	27332	0.04
31	2	E	27332	0.04
32	1	D	27294	0.04
32	2	F	27294	0.04
33	1	D	27207	0.05
33	2	G	27207	0.05
34	1	D	25915	0.09
34	2	H	25915	0.09
35	1	D	25847	0.1
35	2	I	25847	0.1
36	1	D	27294	0.04
36	2	J	27294	0.04
37	1	D	25624	0.11
37	2	K	25624	0.11
38	1	D	25861	0.1
38	2	L	25861	0.1
39	1	E	27416	0.02
39	2	F	27416	0.02
40	1	E	27316	0.03
40	2	G	27316	0.03
41	1	E	26009	0.09
41	2	H	26009	0.09
42	1	E	25942	0.09
42	2	I	25942	0.09
43	1	E	27386	0.02
43	2	J	27386	0.02
44	1	E	25696	0.11
44	2	K	25696	0.11
45	1	E	25938	0.09
45	2	L	25938	0.09
46	1	F	27323	0.03
46	2	G	27323	0.03
47	1	F	25986	0.09
47	2	H	25986	0.09
48	1	F	25943	0.09
48	2	I	25943	0.09
49	1	F	27346	0.03
49	2	J	27346	0.03
50	1	F	25718	0.11
50	2	K	25718	0.11
51	1	F	25924	0.09
51	2	L	25924	0.09
52	1	G	25890	0.09
52	2	H	25890	0.09
53	1	G	25916	0.09
53	2	I	25916	0.09
54	1	G	27276	0.03
54	2	J	27276	0.03
55	1	G	25654	0.11
55	2	K	25654	0.11
56	1	G	25820	0.1
56	2	L	25820	0.1
57	1	H	27330	0.03
57	2	I	27330	0.03
58	1	H	25956	0.09
58	2	J	25956	0.09
59	1	H	27078	0.06
59	2	K	27078	0.06
60	1	H	27269	0.04
60	2	L	27269	0.04
61	1	I	25920	0.09
61	2	J	25920	0.09
62	1	I	27050	0.06
62	2	K	27050	0.06
63	1	I	27205	0.04
63	2	L	27205	0.04
64	1	J	25670	0.11
64	2	K	25670	0.11
65	1	J	25888	0.09
65	2	L	25888	0.09
66	1	K	26980	0.06
66	2	L	26980	0.06

LS refinement shell

Resolution: 7.811→8.013 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.31	26	-
Rwork	0.323	484	-
all	-	510	-
obs	-	-	77.04 %