PDB-9ip6: The complex of rice immune receptor RGA5-HMA8 with rice blast eff...

ID or keywords:

Entry

Database: PDB / ID: 9ip6

Title

The complex of rice immune receptor RGA5-HMA8 with rice blast effector protein AVR1-CO39

Components

AVR1-CO39 protein
Disease resistance protein RGA5

Keywords

PLANT PROTEIN / NLR receptor / HMA domain / MAX effector

Function / homology

Function and homology information

innate immune response-activating signaling pathway / plant-type hypersensitive response / ADP binding / defense response to bacterium / ATP binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Oryza sativa (Asian cultivated rice)

Pyricularia grisea (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.63 Å

Authors

Zhang, X. / Liu, J.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: The complex of rice immune receptor RGA5-HMA8 with rice blast effector protein AVR1-CO39
Authors: Zhang, X. / Liu, J.

History

Deposition	Jul 10, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 16, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9ip6.cif.gz	147.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9ip6.ent.gz	116.4 KB	Display	PDB format
PDBx/mmJSON format	9ip6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9ip6_validation.pdf.gz	461.5 KB	Display	wwPDB validaton report
Full document	9ip6_full_validation.pdf.gz	464.8 KB	Display
Data in XML	9ip6_validation.xml.gz	16.3 KB	Display
Data in CIF	9ip6_validation.cif.gz	20.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ip/9ip6 ftp://data.pdbj.org/pub/pdb/validation_reports/ip/9ip6	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#177 - Sep 2014 Apoptosomes similarity (3)

Deposited unit

A: Disease resistance protein RGA5

C: AVR1-CO39 protein

B: Disease resistance protein RGA5

D: AVR1-CO39 protein

E: Disease resistance protein RGA5

44.2 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Disease resistance protein RGA5

C: AVR1-CO39 protein

defined by author
Evidence: gel filtration
17.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Disease resistance protein RGA5

D: AVR1-CO39 protein

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

3

E: Disease resistance protein RGA5

defined by author
9.21 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	40.600, 126.814, 47.231
Angle α, β, γ (deg.)	90.00, 110.74, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Disease resistance protein RGA5 / Os11gRGA5 / SasRGA5 Mass: 9213.937 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: RGA5 / Production host: Escherichia coli (E. coli) / References: UniProt: F7J0N2
#2: Protein	AVR1-CO39 protein Mass: 8295.212 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyricularia grisea (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8J180
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.57 Å³/Da / Density % sol: 52.22 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.5, 20% w/v Polyethylene glycol 3,000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.63→50 Å / Num. obs: 13262 / % possible obs: 99.8 % / Redundancy: 6 % / CC_1/2: 0.997 / Net I/σ(I): 13.83
Reflection shell	Resolution: 2.63→2.68 Å / Num. unique obs: 654 / CC_1/2: 0.892

-
Processing

Software

Name	Version	Classification
PHENIX	(1.18.2_3874: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.63→35.72 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2565	1302	9.94 %
R_work	0.185	-	-
obs	0.1921	13094	98.53 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.63→35.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2641	0	0	36	2677

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2670
X-RAY DIFFRACTION	f_angle_d	0.902	3607
X-RAY DIFFRACTION	f_dihedral_angle_d	24.637	1011
X-RAY DIFFRACTION	f_chiral_restr	0.057	437
X-RAY DIFFRACTION	f_plane_restr	0.005	457

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.63-2.74	0.3125	129	0.2297	1147	X-RAY DIFFRACTION	88
2.74-2.86	0.2863	143	0.2274	1329	X-RAY DIFFRACTION	100
2.86-3.01	0.3022	144	0.2111	1322	X-RAY DIFFRACTION	100
3.01-3.2	0.271	153	0.1935	1323	X-RAY DIFFRACTION	100
3.2-3.45	0.28	147	0.1874	1332	X-RAY DIFFRACTION	100
3.45-3.79	0.2672	143	0.1814	1335	X-RAY DIFFRACTION	100
3.79-4.34	0.2435	148	0.1744	1321	X-RAY DIFFRACTION	100
4.34-5.46	0.2105	146	0.1557	1340	X-RAY DIFFRACTION	100
5.47-35.72	0.2568	149	0.1906	1343	X-RAY DIFFRACTION	99

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	2.821	-0.1665	0.879	0.51	-0.5972	0.596	-0.4372	0.1387	-0.3109	-0.3367	-0.0086	0.0112	0.0284	-0.9541	0.0002	0.4022	0.08	-0.0458	0.3409	-0.0392	0.4085	16.403	23.832	-14.848
2	2.7036	1.1854	0.1304	3.2629	-0.626	0.6685	0.1268	-0.2178	0.5899	0.1327	0.0782	-0.2724	-0.1289	-0.1142	0	0.3345	-0.0319	-0.027	0.3759	-0.0574	0.3388	21.689	27.789	-14.295
3	2.0082	0.4677	0.9183	3.1827	-1.5867	0.8593	0.1981	-0.2691	-0.1091	0.2128	-0.1873	-0.4143	0.7635	-0.0784	-0.0001	0.4048	-0.0064	-0.0478	0.459	-0.0319	0.3089	25.087	22.15	-10.302
4	0.9706	-0.3122	0.5032	-0.4537	-0.2334	0.4823	-0.2922	0.6116	-3.2024	0.4278	-0.447	0.4217	1.8783	0.0327	-0.0486	0.3575	-0.0869	-0.0697	0.4799	0.1421	0.2244	17.188	18.203	-18.236
5	0.7825	1.1271	1.1305	1.0688	0.7669	3.5968	0.0301	-0.4973	-0.0545	0.1638	0.4531	0.0914	-0.4997	0.2859	0.0003	0.6511	-0.0534	0.1687	0.5166	0.0258	0.8842	16.147	-3.649	-24.192
6	1.909	-1.5443	-1.2388	2.8207	3.248	3.2046	-0.6664	0.0601	-2.3348	0.4283	0.6539	1.1643	-0.3285	-0.2715	-0.0033	0.5416	0.0215	0.0121	0.506	0.23	1.0905	18.953	-7.844	-26.628
7	0.0357	-0.1637	0.162	0.1718	-0.4365	0.3808	1.5178	-1.8925	0.7113	2.7409	-0.4533	0.1338	1.0497	-0.6779	0.0007	1.1596	-0.0403	0.2401	0.9352	0.1697	1.0853	16.045	-9.319	-15.575
8	1.1735	-0.6395	0.2118	1.8852	-1.7341	0.9163	0.1957	0.9012	1.0287	-0.4602	0.0681	-0.0945	-0.6825	-0.3062	0.0471	0.5989	-0.0658	0.0942	0.3506	-0.0366	0.9586	13.84	-11.344	-21.907
9	0.9596	1.7314	0.0485	1.7745	0.2251	1.8745	0.2535	1.072	-0.1563	-0.2206	-0.7312	0.0463	0.2309	0.7338	0.0011	0.3857	-0.0285	0.0107	0.4139	0.0078	0.4213	6.716	7.097	7.795
10	2.2106	2.1945	1.1595	1.9408	-2.1355	0.7161	-0.0424	-0.3062	-0.2622	-0.0518	0.0229	-0.1374	-0.0671	-0.0607	0.0001	0.3855	0.0155	0.0143	0.4733	0.0242	0.3128	11.995	12.569	7.678
11	1.5337	-1.2201	-1.4894	3.1897	0.6366	1.0681	0.1572	-0.0808	-1.2374	-0.1614	-0.0648	-0.0931	0.6252	-0.8233	0.021	0.3851	-0.0883	0.0966	0.5817	-0.0468	0.422	9.142	5.244	7.681
12	0.8624	0.4086	-0.0512	1.0707	0.347	0.0195	0.0429	-0.6034	-0.2094	0.2327	0.1782	0.0043	-0.5321	-0.2133	-0.0001	0.4055	-0.0625	-0.0152	0.3813	-0.081	0.3865	4.705	13.085	15.744
13	1.0263	1.5066	1.4828	1.5829	0.3145	1.9565	-0.0108	0.9055	-0.5357	0.3586	-0.4368	0.1204	-0.1311	-0.0148	-0.0009	0.3762	-0.0756	-0.0489	0.3328	0.1105	0.4743	5.533	1.734	12.467
14	2.2215	0.1587	0.5775	1.2099	-1.3841	0.3446	-0.0148	0.0338	-0.143	-0.0434	0.015	-0.158	-0.2923	-0.5724	0.0001	0.3297	-0.0196	-0.007	0.5355	-0.0696	0.3553	19.3	12.959	3.835
15	6.2076	0.5026	1.2592	1.1153	-0.721	3.8002	0.0925	0.1556	0.02	0.2434	-0.1776	-0.1761	-0.0915	0.0794	-0	0.3191	0.0233	-0.0007	0.3405	0.0486	0.3413	27.328	13.731	3.671
16	1.5386	-0.5817	0.8551	0.8363	1.3105	3.4888	-0.1564	-0.198	-0.3511	-0.5252	-0.0991	-0.8502	-0.3428	-0.0904	-0.0004	0.4603	-0.0169	0.0848	0.3814	-0.0038	0.504	3.805	32.25	-16.617
17	2.5556	-2.7321	0.3056	3.59	0.4226	1.6299	0.3408	-0.0722	-0.1287	0.0451	-0.2009	0.0512	0.3138	0.2934	0.0004	0.3811	-0.0103	-0.0159	0.3264	-0.0059	0.4163	8.211	26.013	-17.935
18	6.2787	-1.527	2.3903	4.8784	0.2782	0.6034	0.0374	0.1275	0.1453	-0.3454	0.0051	0.0674	0.1721	-0.2629	-0.0004	0.3633	0.0074	0.0335	0.2555	-0.0319	0.2989	3.363	31	-20.037
19	0.6885	-1.0126	-0.2051	1.6633	-1.2546	0.8263	-1.1001	0.8866	0.4458	-0.2887	0.8245	0.5177	-0.2323	-0.1553	-0.0032	0.4376	0.0814	-0.0922	0.3235	0.039	0.5104	1.636	37.979	-18.038

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN D AND RESID 22:34 )	D	22 - 34
2	X-RAY DIFFRACTION	2	( CHAIN D AND RESID 35:57 )	D	35 - 57
3	X-RAY DIFFRACTION	3	( CHAIN D AND RESID 58:72 )	D	58 - 72
4	X-RAY DIFFRACTION	4	( CHAIN D AND RESID 73:82 )	D	73 - 82
5	X-RAY DIFFRACTION	5	( CHAIN E AND RESID 996:1020 )	E	996 - 1020
6	X-RAY DIFFRACTION	6	( CHAIN E AND RESID 1021:1046 )	E	1021 - 1046
7	X-RAY DIFFRACTION	7	( CHAIN E AND RESID 1047:1055 )	E	1047 - 1055
8	X-RAY DIFFRACTION	8	( CHAIN E AND RESID 1056:1069 )	E	1056 - 1069
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 997:1008 )	A	997 - 1008
10	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 1009:1031 )	A	1009 - 1031
11	X-RAY DIFFRACTION	11	( CHAIN A AND RESID 1032:1046 )	A	1032 - 1046
12	X-RAY DIFFRACTION	12	( CHAIN A AND RESID 1047:1058 )	A	1047 - 1058
13	X-RAY DIFFRACTION	13	( CHAIN A AND RESID 1059:1069 )	A	1059 - 1069
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 22:42 )	C	22 - 42
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 43:82 )	C	43 - 82
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 996:1008 )	B	996 - 1008
17	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 1009:1031 )	B	1009 - 1031
18	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 1032:1058 )	B	1032 - 1058
19	X-RAY DIFFRACTION	19	( CHAIN B AND RESID 1059:1069 )	B	1059 - 1069

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi