PDB-5xli: Structure of anti-Angiotensin II type2 receptor antibody (D5711-4A03)

ID or keywords:

Entry

Database: PDB / ID: 5xli

Title

Structure of anti-Angiotensin II type2 receptor antibody (D5711-4A03)

Components

FabH
FabL

Keywords

IMMUNE SYSTEM / antigbody / IgG / Fab

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.696 Å

Authors

Asada, H. / Horita, S. / Iwata, S. / Hirata, K.

Funding support

Japan, 3items

Organization	Grant number	Country
Japan Agency for Medical Research and Development	A19170600003	Japan
Japan Society for the Promotion of Science	15J04343	Japan
Japan Society for the Promotion of Science	22590270	Japan

Citation

Journal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Crystal structure of the human angiotensin II type 2 receptor bound to an angiotensin II analog.
Authors: Asada, H. / Horita, S. / Hirata, K. / Shiroishi, M. / Shiimura, Y. / Iwanari, H. / Hamakubo, T. / Shimamura, T. / Nomura, N. / Kusano-Arai, O. / Uemura, T. / Suno, C. / Kobayashi, T. / Iwata, S.

History

Deposition	May 10, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 11, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jul 25, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Nov 22, 2023	Group: 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5xli.cif.gz	358.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5xli.ent.gz	293.2 KB	Display	PDB format
PDBx/mmJSON format	5xli.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xl/5xli ftp://data.pdbj.org/pub/pdb/validation_reports/xl/5xli	HTTPS FTP

-
Related structure data

Related structure data	5xjmC 1bafS 1mreS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1cbv-d 3ifn-d 2ojz-1 1xf2-2 4evn-5 6ev2-1 1bog-d 6al4-1 6vl8-4 1i8m-2 6uoe-d 1jfq-d 1dfb-d 4uim-1 3ifp-3 35c8-d 3kym-8 4uil-d 1cfq-d 2a1w-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

5xjmC

1bafS

1mreS

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

a: FabL

b: FabL

c: FabH

d: FabH

93.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

a: FabL

c: FabH

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

2

b: FabL

d: FabH

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

Unit cell

Length a, b, c (Å)	41.654, 150.498, 75.322
Angle α, β, γ (deg.)	90.000, 93.100, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	FabL Mass: 23365.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody	FabH Mass: 23371.201 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 822 / 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: 2.52 Å³/Da / Density % sol: 51.23 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 50mM KH2PO4, 20% PEG 8000, 10% Glycerol

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-1A / Wavelength: 1.1 Å

Detector

Type: DECTRIS EIGER X 4M / Detector: CCD / Date: Feb 22, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.1 Å / Relative weight: 1

Reflection

Resolution: 1.7→19.771 Å / Num. obs: 101148 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.801 % / B_iso Wilson estimate: 25.67 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.131 / R_rim(I) all: 0.142 / Χ²: 1.002 / Net I/σ(I): 9.02 / Num. measured all: 687903

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.7-1.8	6.865	1.203	1.49	107222	16477	15619	0.633	1.301	94.8
1.8-1.92	6.948	0.773	2.63	107201	15431	15428	0.822	0.836	100
1.92-2.08	6.905	0.459	4.75	99561	14425	14418	0.938	0.497	100
2.08-2.27	6.737	0.297	7.35	89179	13241	13237	0.968	0.323	100
2.27-2.54	6.356	0.216	9.77	76129	11991	11977	0.98	0.236	99.9
2.54-2.93	6.6	0.147	14.01	69943	10600	10598	0.989	0.16	100
2.93-3.59	7.157	0.101	19.13	64303	8986	8985	0.994	0.11	100
3.59-5.06	6.988	0.086	22.43	48648	6961	6962	0.993	0.093	100
5.06-19.771	6.554	0.085	22.84	25717	3936	3924	0.992	0.092	99.7

-
Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
XSCALE		data scaling
PDB_EXTRACT	3.22	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1MRE, 1BAF

1mre

1baf

Resolution: 1.696→19.771 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2159	5135	5.08 %
R_work	0.1795	95903	-
obs	0.1814	101038	99.12 %

Solvent computation

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

Displacement parameters

B_iso max: 130.86 Å² / B_iso mean: 37.5325 Å² / B_iso min: 14.56 Å²

Refinement step

Cycle: final / Resolution: 1.696→19.771 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6550	0	0	822	7372
B_iso mean	-	-	-	42.43	-
Num. residues	-	-	-	-	866

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6804
X-RAY DIFFRACTION	f_angle_d	0.883	9315
X-RAY DIFFRACTION	f_chiral_restr	0.058	1054
X-RAY DIFFRACTION	f_plane_restr	0.005	1175
X-RAY DIFFRACTION	f_dihedral_angle_d	9.817	4083

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6964-1.7157	0.3355	119	0.2876	2425	2544	75
1.7157-1.7359	0.2874	189	0.2681	3251	3440	100
1.7359-1.757	0.2845	179	0.2583	3173	3352	100
1.757-1.7793	0.299	181	0.2474	3172	3353	100
1.7793-1.8027	0.2852	209	0.2336	3211	3420	100
1.8027-1.8273	0.2666	191	0.234	3205	3396	100
1.8273-1.8534	0.246	167	0.2199	3175	3342	100
1.8534-1.8811	0.2524	195	0.2241	3253	3448	100
1.8811-1.9104	0.2844	162	0.2304	3205	3367	100
1.9104-1.9417	0.278	156	0.2137	3191	3347	100
1.9417-1.9752	0.2367	161	0.2052	3295	3456	100
1.9752-2.0111	0.2132	165	0.1926	3179	3344	100
2.0111-2.0497	0.2371	163	0.1922	3253	3416	100
2.0497-2.0915	0.2119	176	0.2011	3246	3422	100
2.0915-2.1369	0.2777	152	0.2001	3164	3316	100
2.1369-2.1866	0.2385	174	0.193	3273	3447	100
2.1866-2.2412	0.2372	143	0.1901	3201	3344	100
2.2412-2.3017	0.2545	147	0.1944	3295	3442	100
2.3017-2.3693	0.2392	172	0.1905	3181	3353	100
2.3693-2.4457	0.2478	167	0.1971	3274	3441	100
2.4457-2.5329	0.2264	188	0.1855	3155	3343	100
2.5329-2.6341	0.2348	161	0.1899	3251	3412	100
2.6341-2.7537	0.2188	153	0.1858	3266	3419	100
2.7537-2.8984	0.2139	183	0.1817	3189	3372	100
2.8984-3.0794	0.2428	148	0.1875	3235	3383	100
3.0794-3.3161	0.209	187	0.1819	3234	3421	100
3.3161-3.648	0.209	191	0.1663	3219	3410	100
3.648-4.1715	0.1898	200	0.1581	3238	3438	100
4.1715-5.2395	0.1509	181	0.1336	3230	3411	100
5.2395-19.7725	0.1897	175	0.149	3264	3439	100

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	1.0234	0.7563	-0.0387	3.7014	0.5264	3.5388	-0.0348	-0.008	0.0305	0.8686	0.271	-0.9676	0.2278	0.4558	-0.1414	0.4518	0.103	-0.1942	0.3009	-0.0734	0.3686	24.6316	-13.8699	44.1854
2	1.8555	-0.1815	-0.5896	1.9671	-0.2102	3.3782	0.1762	-0.1226	0.1982	-0.0079	0.0082	-0.0635	-0.324	0.1903	-0.1595	0.1309	-0.0333	0.033	0.1858	-0.0387	0.259	13.7814	26.1754	-13.1741
3	-0.6212	-0.4462	0.0679	4.2799	0.7481	0.1571	0.0349	-0.0591	-0.1502	-0.4727	0.0042	-0.3945	-0.1511	-0.0204	-0.0069	0.2725	-0.0052	0.0167	0.247	-0.0236	0.2934	6.9058	50.7273	0.863
4	2.8991	-0.303	-1.2943	6.9039	1.7073	4.9435	-0.15	-0.1594	-0.04	-0.0114	0.1648	-0.6056	0.2253	0.2302	0.02	0.3227	-0.0021	-0.0305	0.1787	0.041	0.2315	6.0547	59.3688	4.6144
5	3.4496	-4.1183	-3.08	7.3422	1.2554	5.6484	-0.4288	0.1849	-0.2451	-0.2322	0.0544	0.4749	0.4525	-0.365	0.3618	0.3535	-0.0784	-0.0001	0.2166	-0.084	0.3359	15.6678	4.9246	15.9239
6	4.4586	0.3788	-1.4681	2.3379	0.6581	2.9553	-0.0531	-0.0256	0.1376	-0.0891	-0.0482	0.0405	0.1968	-0.0966	0.0905	0.2808	0.0098	-0.0253	0.1768	-0.0075	0.1754	21.5227	13.783	17.3333
7	4.3745	-1.7256	-1.9527	8.3126	1.5935	4.4451	-0.331	-0.176	-0.0506	0.145	0.0976	-0.2407	0.4597	0.1374	0.2575	0.2671	-0.0151	-0.0348	0.2359	0.0031	0.1755	22.7285	8.089	19.3572
8	0.1918	-0.4981	0.3642	6.1312	-0.5072	0.7085	0.0456	-0.0992	0.035	0.0635	-0.0769	-0.0503	0.1359	-0.0651	-0.0128	0.2001	-0.0263	0.005	0.2688	-0.003	0.216	16.9228	-7.5334	31.3663
9	3.1299	0.6948	-2.1862	6.4427	-1.672	5.3883	-0.0316	-0.1067	-0.1031	0.1077	0.0694	0.6901	0.0174	-0.253	-0.0656	0.2278	0.014	0.0005	0.2177	0.0067	0.2323	12.6787	-22.206	33.7949
10	1.4601	-0.4103	-0.6894	3.4489	1.099	2.9379	0.0327	0.0269	-0.024	0.0564	0.0385	-0.0002	-0.0007	-0.0268	-0.0676	0.0867	-0.0142	-0.0121	0.1731	0.0026	0.1912	-5.153	17.3802	-0.2906
11	6.7028	0.792	0.2772	3.0103	4.7589	8.4848	0.174	0.784	-0.4549	0.0646	0.047	-0.567	0.4427	-0.2068	-0.1419	0.21	-0.0425	0.0144	0.193	0.0138	0.3031	0.8729	16.4263	-9.403
12	0.5388	-0.5911	-0.2679	4.136	1.0057	1.2811	-0.0391	0.0345	0.0773	0.0617	-0.1099	0.1471	-0.3572	-0.0328	0.1401	0.2462	-0.0174	-0.0728	0.2138	0.0277	0.1973	-6.5535	48.0398	1.2146
13	2.9278	0.1312	-0.5773	1.273	1.4061	1.7358	-0.0219	0.4825	0.0082	-0.9371	0.0734	0.1516	0.5497	-0.3398	-0.1045	0.7481	-0.1458	-0.1432	0.3463	0.0098	0.3485	-7.9508	50.7774	-5.5768
14	4.7971	0.0695	-0.3114	5.262	-2.8503	5.4465	-0.5371	0.1563	0.2714	-0.8506	0.579	0.7763	0.0198	-0.8123	-0.0307	0.5421	-0.1015	-0.2014	0.3698	0.0128	0.3362	-10.0979	54.7687	-0.5303
15	2.2586	0.5861	-1.5741	3.9822	-0.0745	3.8273	-0.1107	-0.073	0.0624	-0.1323	0.112	-0.1912	0.0024	0.3576	0.0009	0.1662	-0.0054	-0.0475	0.2413	-0.0487	0.1688	17.8829	19.4975	39.7164
16	7.8484	-2.4014	2.7021	8.0049	4.6186	6.4795	-0.6611	0.2275	1.234	-0.8947	-0.1815	-0.8048	-1.7358	0.9141	0.6246	0.5138	-0.1381	-0.1115	0.4914	-0.0412	0.4181	25.6726	21.4064	28.8402
17	1.5936	-0.1652	-0.5772	4.9298	-0.3889	1.0832	-0.1425	-0.0088	-0.3567	0.6448	0.1385	0.1603	0.5009	-0.0091	-0.0075	0.5339	0.0446	-0.1059	0.2775	-0.0392	0.1856	18.3811	-13.0962	45.7904

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 142 through 220 )	d	142 - 220
2	X-RAY DIFFRACTION	2	chain 'a' and (resid 1 through 90 )	a	1 - 90
3	X-RAY DIFFRACTION	3	chain 'a' and (resid 91 through 154 )	a	91 - 154
4	X-RAY DIFFRACTION	4	chain 'a' and (resid 155 through 213 )	a	155 - 213
5	X-RAY DIFFRACTION	5	chain 'b' and (resid 1 through 18 )	b	1 - 18
6	X-RAY DIFFRACTION	6	chain 'b' and (resid 19 through 74 )	b	19 - 74
7	X-RAY DIFFRACTION	7	chain 'b' and (resid 75 through 90 )	b	75 - 90
8	X-RAY DIFFRACTION	8	chain 'b' and (resid 91 through 127 )	b	91 - 127
9	X-RAY DIFFRACTION	9	chain 'b' and (resid 128 through 213 )	b	128 - 213
10	X-RAY DIFFRACTION	10	chain 'c' and (resid 1 through 91 )	c	1 - 91
11	X-RAY DIFFRACTION	11	chain 'c' and (resid 92 through 107 )	c	92 - 107
12	X-RAY DIFFRACTION	12	chain 'c' and (resid 108 through 152 )	c	108 - 152
13	X-RAY DIFFRACTION	13	chain 'c' and (resid 153 through 173 )	c	153 - 173
14	X-RAY DIFFRACTION	14	chain 'c' and (resid 174 through 220 )	c	174 - 220
15	X-RAY DIFFRACTION	15	chain 'd' and (resid 1 through 98 )	d	1 - 98
16	X-RAY DIFFRACTION	16	chain 'd' and (resid 99 through 113 )	d	99 - 113
17	X-RAY DIFFRACTION	17	chain 'd' and (resid 114 through 141 )	d	114 - 141

-
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