PDB-8pfc: Crystal structure of binary complex between Aster yellows witches...

ID or keywords:

Entry

Database: PDB / ID: 8pfc

Title

Crystal structure of binary complex between Aster yellows witches'-broom phytoplasma effector SAP05 and the zinc finger domain of SPL5 from Arabidopsis thaliana

Components

Sequence-variable mosaic (SVM) signal sequence domain-containing protein
Squamosa promoter-binding-like protein 5

Keywords

PROTEIN BINDING / Targeted protein degradation / ubiquitin-independent / bacterial effector protein / 26S proteasome

Function / homology

Function and homology information

regulation of vegetative phase change / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Aster yellows witches'-broom phytoplasma AYWB (bacteria)

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.2 Å

Authors

Huang, W. / Liu, Q. / Maqbool, A. / Stevenson, C.E.M. / Lawson, D.M. / Kamoun, S. / Hogenhout, S.A.

Funding support

France,

United Kingdom, 4items

Organization	Grant number	Country
Human Frontier Science Program (HFSP)	RGP0024/2015	France
Engineering and Physical Sciences Research Council	EP/X024415/1	United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)	BBS/E/J/000PR9797	United Kingdom
John Innes Foundation	None	United Kingdom

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Bimodular architecture of bacterial effector SAP05 that drives ubiquitin-independent targeted protein degradation.
Authors: Liu, Q. / Maqbool, A. / Mirkin, F.G. / Singh, Y. / Stevenson, C.E.M. / Lawson, D.M. / Kamoun, S. / Huang, W. / Hogenhout, S.A.

History

Deposition	Jun 15, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 5, 2023	Provider: repository / Type: Initial release
Revision 1.1	Dec 13, 2023	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8pfc.cif.gz	558.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8pfc.ent.gz	458.7 KB	Display	PDB format
PDBx/mmJSON format	8pfc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8pfc_validation.pdf.gz	8.1 MB	Display	wwPDB validaton report
Full document	8pfc_full_validation.pdf.gz	8.1 MB	Display
Data in XML	8pfc_validation.xml.gz	49.1 KB	Display
Data in CIF	8pfc_validation.cif.gz	67.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pf/8pfc ftp://data.pdbj.org/pub/pdb/validation_reports/pf/8pfc	HTTPS FTP

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Related structure data

Related structure data	8pfdC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Sequence-variable mosaic (SVM) signal sequence domain-containing protein

B: Squamosa promoter-binding-like protein 5

C: Sequence-variable mosaic (SVM) signal sequence domain-containing protein

D: Squamosa promoter-binding-like protein 5

E: Sequence-variable mosaic (SVM) signal sequence domain-containing protein

F: Squamosa promoter-binding-like protein 5

G: Sequence-variable mosaic (SVM) signal sequence domain-containing protein

H: Squamosa promoter-binding-like protein 5

I: Sequence-variable mosaic (SVM) signal sequence domain-containing protein

J: Squamosa promoter-binding-like protein 5

K: Sequence-variable mosaic (SVM) signal sequence domain-containing protein

L: Squamosa promoter-binding-like protein 5

M: Sequence-variable mosaic (SVM) signal sequence domain-containing protein

N: Squamosa promoter-binding-like protein 5

O: Sequence-variable mosaic (SVM) signal sequence domain-containing protein

P: Squamosa promoter-binding-like protein 5

hetero molecules

166 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Sequence-variable mosaic (SVM) signal sequence domain-containing protein

B: Squamosa promoter-binding-like protein 5

hetero molecules

defined by author
20.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Sequence-variable mosaic (SVM) signal sequence domain-containing protein

D: Squamosa promoter-binding-like protein 5

hetero molecules

defined by author
20.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Sequence-variable mosaic (SVM) signal sequence domain-containing protein

F: Squamosa promoter-binding-like protein 5

hetero molecules

defined by author
20.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Sequence-variable mosaic (SVM) signal sequence domain-containing protein

H: Squamosa promoter-binding-like protein 5

hetero molecules

defined by author
20.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: Sequence-variable mosaic (SVM) signal sequence domain-containing protein

J: Squamosa promoter-binding-like protein 5

hetero molecules

defined by author
20.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

K: Sequence-variable mosaic (SVM) signal sequence domain-containing protein

L: Squamosa promoter-binding-like protein 5

hetero molecules

defined by author
20.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

M: Sequence-variable mosaic (SVM) signal sequence domain-containing protein

N: Squamosa promoter-binding-like protein 5

hetero molecules

defined by author
20.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

O: Sequence-variable mosaic (SVM) signal sequence domain-containing protein

P: Squamosa promoter-binding-like protein 5

hetero molecules

defined by author
20.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.686, 165.019, 80.862
Angle α, β, γ (deg.)	90.00, 109.65, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

#1: Protein	Sequence-variable mosaic (SVM) signal sequence domain-containing protein Mass: 12310.920 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: The crystallized sequence corresponds to residues 33-135 of the full 135-residue wild-type sequence, which is prepended by a GLY-PRO dipeptide left over from cleavage of the affinity tag. Source: (gene. exp.) Aster yellows witches'-broom phytoplasma AYWB (bacteria) Gene: AYWB_032 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2NK94
#2: Protein	Squamosa promoter-binding-like protein 5 Mass: 8228.453 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: The crystallised sequence corresponds to residues 60-127 of the full 181-residue wild-type sequence, which is prepended by a GLY-PRO dipeptide left over from cleavage of the affinity tag. Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SPL5, At3g15270, K7L4.7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9S758
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.01 Å³/Da / Density % sol: 59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: NULL

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 25, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.2→82.51 Å / Num. obs: 98262 / % possible obs: 100 % / Redundancy: 14.1 % / CC_1/2: 0.999 / R_merge(I) obs: 0.129 / R_pim(I) all: 0.035 / R_rim(I) all: 0.134 / Χ²: 0.94 / Net I/σ(I): 10.4 / Num. measured all: 1386043
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 14.3 % / R_merge(I) obs: 2.104 / Num. unique obs: 4890 / CC_1/2: 0.791 / R_pim(I) all: 0.577 / R_rim(I) all: 2.182 / Χ²: 0.89 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
Aimless		data scaling
DIALS		data reduction
CRANK2		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.2→74.21 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.932 / SU B: 18.5 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25069	4855	4.9 %	RANDOM
R_work	0.22301	-	-	-
obs	0.22438	93364	99.99 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 62.626 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.26 Å²	-0 Å²	2.34 Å²
2-	-	-4.47 Å²	-0 Å²
3-	-	-	-3.56 Å²

Refinement step

Cycle: 1 / Resolution: 2.2→74.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10736	0	20	317	11073

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	10953
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	10270
X-RAY DIFFRACTION	r_angle_refined_deg	1.509	1.651	14726
X-RAY DIFFRACTION	r_angle_other_deg	1.214	1.595	23494
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.13	5	1296
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.93	21.437	710
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.921	15	1949
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.425	15	106
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	1375
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	12515
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2857
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.981	3.743	5232
X-RAY DIFFRACTION	r_mcbond_other	3.981	3.742	5231
X-RAY DIFFRACTION	r_mcangle_it	5.225	5.614	6512
X-RAY DIFFRACTION	r_mcangle_other	5.225	5.614	6513
X-RAY DIFFRACTION	r_scbond_it	4.434	4.077	5721
X-RAY DIFFRACTION	r_scbond_other	4.434	4.077	5722
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	6.323	5.981	8214
X-RAY DIFFRACTION	r_long_range_B_refined	7.904	42.221	11724
X-RAY DIFFRACTION	r_long_range_B_other	7.907	42.124	11695
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

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	3120	0.07
1	2	C	3120	0.07
2	1	A	3224	0.05
2	2	E	3224	0.05
3	1	A	3192	0.05
3	2	G	3192	0.05
4	1	A	3110	0.07
4	2	I	3110	0.07
5	1	A	3201	0.06
5	2	K	3201	0.06
6	1	A	3148	0.08
6	2	M	3148	0.08
7	1	A	3155	0.07
7	2	O	3155	0.07
8	1	B	2002	0.08
8	2	D	2002	0.08
9	1	B	2041	0.04
9	2	F	2041	0.04
10	1	B	2020	0.05
10	2	H	2020	0.05
11	1	B	1963	0.06
11	2	J	1963	0.06
12	1	B	2022	0.05
12	2	L	2022	0.05
13	1	B	1954	0.06
13	2	N	1954	0.06
14	1	B	1932	0.07
14	2	P	1932	0.07
15	1	C	3118	0.07
15	2	E	3118	0.07
16	1	C	3095	0.07
16	2	G	3095	0.07
17	1	C	3128	0.06
17	2	I	3128	0.06
18	1	C	3127	0.06
18	2	K	3127	0.06
19	1	C	3177	0.04
19	2	M	3177	0.04
20	1	C	3172	0.06
20	2	O	3172	0.06
21	1	D	2009	0.07
21	2	F	2009	0.07
22	1	D	2009	0.06
22	2	H	2009	0.06
23	1	D	1991	0.06
23	2	J	1991	0.06
24	1	D	2007	0.06
24	2	L	2007	0.06
25	1	D	1973	0.07
25	2	N	1973	0.07
26	1	D	1969	0.07
26	2	P	1969	0.07
27	1	E	3185	0.05
27	2	G	3185	0.05
28	1	E	3105	0.07
28	2	I	3105	0.07
29	1	E	3204	0.05
29	2	K	3204	0.05
30	1	E	3150	0.07
30	2	M	3150	0.07
31	1	E	3148	0.07
31	2	O	3148	0.07
32	1	F	2029	0.04
32	2	H	2029	0.04
33	1	F	1972	0.04
33	2	J	1972	0.04
34	1	F	2032	0.04
34	2	L	2032	0.04
35	1	F	1957	0.05
35	2	N	1957	0.05
36	1	F	1946	0.06
36	2	P	1946	0.06
37	1	G	3090	0.07
37	2	I	3090	0.07
38	1	G	3182	0.05
38	2	K	3182	0.05
39	1	G	3119	0.08
39	2	M	3119	0.08
40	1	G	3114	0.08
40	2	O	3114	0.08
41	1	H	2001	0.05
41	2	J	2001	0.05
42	1	H	2087	0.04
42	2	L	2087	0.04
43	1	H	1983	0.05
43	2	N	1983	0.05
44	1	H	1969	0.06
44	2	P	1969	0.06
45	1	I	3107	0.07
45	2	K	3107	0.07
46	1	I	3161	0.05
46	2	M	3161	0.05
47	1	I	3176	0.06
47	2	O	3176	0.06
48	1	J	1998	0.05
48	2	L	1998	0.05
49	1	J	1957	0.07
49	2	N	1957	0.07
50	1	J	1984	0.06
50	2	P	1984	0.06
51	1	K	3156	0.07
51	2	M	3156	0.07
52	1	K	3152	0.08
52	2	O	3152	0.08
53	1	L	1981	0.06
53	2	N	1981	0.06
54	1	L	1967	0.06
54	2	P	1967	0.06
55	1	M	3208	0.04
55	2	O	3208	0.04
56	1	N	1933	0.07
56	2	P	1933	0.07

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.394	333	-
R_work	0.402	6917	-
obs	-	-	99.97 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	3.7948	0.3632	-2.5735	2.8069	0.3131	8.2444	0.0386	-0.1059	0.2515	-0.427	-0.0077	-0.2561	-0.324	0.6977	-0.0309	0.1639	0.002	0.0229	0.282	-0.0085	0.1974	-9.645	10.78	-11.697
2	3.0911	-0.4599	-1.2483	4.5472	-0.9914	6.1326	-0.1656	0.0293	-0.1456	-0.5757	0.0166	-0.1355	0.6552	0.1091	0.149	0.151	0.0089	-0.0237	0.1441	-0.0395	0.1394	-21.537	-0.045	3.821
3	4.4243	-0.5615	0.1784	6.3527	-1.4975	3.957	0.0161	-0.3898	-0.3679	0.8349	-0.0461	-0.4193	0.046	0.1538	0.03	0.2715	-0.0051	0.0025	0.1671	0.0649	0.3771	-6.756	-25.633	-14.848
4	5.6314	-2.1034	-2.3482	7.139	2.2852	5.572	-0.1264	0.3745	-0.0271	0.2764	-0.2654	0.6077	0.442	-0.6282	0.3918	0.0511	-0.05	-0.0138	0.2295	0.0114	0.3155	-22.549	-12.093	-23.348
5	3.7066	0.3626	-1.0595	2.4893	0.355	6.9064	-0.0415	0.1299	0.2069	-0.4757	-0.0021	-0.2864	-0.1911	0.3894	0.0436	0.3512	-0.0353	0.1012	0.1803	-0.0192	0.2289	30.459	11.351	-14.226
6	3.1953	0.3296	-2.2244	4.5494	-0.3912	4.2517	-0.059	-0.0707	-0.1403	-0.4203	0.052	-0.0729	0.1467	0.0744	0.0071	0.092	-0.0019	-0.0765	0.1519	-0.0189	0.1449	18.868	0.295	1.442
7	3.4082	0.0221	-1.2346	2.4307	-0.5397	7.0198	0.0269	0.2081	-0.2328	-0.113	-0.012	0.0408	0.1039	-0.0635	-0.0149	0.0697	0.0381	-0.0341	0.1208	0.0027	0.1615	3.741	-9.333	19.209
8	1.678	0.6817	-0.167	5.9587	-1.5823	5.9048	0.1632	-0.0443	0.1298	0.2938	-0.0057	0.0672	-0.6065	0.019	-0.1575	0.1624	0.0127	0.0722	0.1111	0.0152	0.1749	2.697	1.658	38.734
9	5.2158	-1.6296	-0.1096	7.4299	1.1028	4.8046	0.0132	-0.1779	-0.1177	0.2069	0.1139	1.1283	-0.4702	-0.3862	-0.1271	0.0992	0.0487	-0.0534	0.1726	-0.012	0.5722	5.127	28.037	16.424
10	4.1346	-1.8727	-0.7145	9.9703	1.0059	8.1219	-0.2125	-0.4851	-0.1063	0.6844	0.2921	0.0216	0.26	0.6556	-0.0797	0.0691	0.0446	-0.0541	0.2573	-0.0584	0.2149	22.336	13.396	17.906
11	3.9728	0.9207	-2.5582	3.8581	-1.0554	7.2811	-0.373	0.5054	-0.1945	-0.2361	0.2611	0.236	0.8956	-0.4841	0.1119	0.1756	-0.0755	-0.0649	0.2638	-0.0037	0.1569	42.081	-9.493	21.716
12	1.5579	0.391	-0.5288	4.7298	-0.8921	5.9595	0.0132	0.0528	0.045	0.1859	0.0003	0.0686	-0.2304	-0.113	-0.0135	0.071	0.043	0.0158	0.1514	0.0199	0.1686	41.517	1.266	41.4
13	4.2671	-1.1144	-0.0635	6.6281	-1.3741	4.6875	-0.005	-0.3876	-0.2327	0.6095	-0.0911	-0.4374	0.0063	0.2007	0.0961	0.0906	-0.0396	-0.1308	0.1657	0.0626	0.3271	32.7	-25.644	-17.15
14	5.1742	-1.0395	-2.5161	7.2092	-1.6093	5.4039	0.1404	0.2331	0.0719	0.513	0.0246	0.635	-0.2991	-0.6596	-0.1651	0.0596	0.0253	0.0008	0.2156	0.0421	0.2853	17.346	-12.004	-25.69
15	4.593	-1.249	-0.1023	7.3321	1.1636	4.6195	-0.0133	-0.0833	0.1405	0.0497	-0.0032	0.8655	-0.307	-0.4127	0.0165	0.0495	0.0378	-0.0728	0.1777	-0.053	0.4166	44.128	28.053	18.474
16	2.326	-0.2091	-1.5686	8.6699	1.2748	9.1546	-0.0349	-0.3029	-0.0198	0.7236	0.1621	-0.1887	0.4658	0.9259	-0.1271	0.1072	0.082	-0.0991	0.3034	-0.0838	0.2035	60.388	12.864	20.679

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	36 - 132
2	X-RAY DIFFRACTION	2	B	61 - 127
3	X-RAY DIFFRACTION	3	C	37 - 132
4	X-RAY DIFFRACTION	4	D	61 - 127
5	X-RAY DIFFRACTION	5	E	36 - 132
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