PDB-6o3u: Crystal structure of the Fab fragment of the human HIV-1 neutrali...

ID or keywords:

Entry

Database: PDB / ID: 6o3u

Title

Crystal structure of the Fab fragment of the human HIV-1 neutralizing antibody PGZL1.H4K3 in complex with 06:0 PA

Components

PGZL1.H4K3 heavy chain
PGZL1.H4K3 light chain

Keywords

IMMUNE SYSTEM / PGZL1.H4K3 ANTI HIV-1 / GP41 MPER /

MEMBRANE LIPIDS / BROADLY NEUTRALISING HIV-1 ANTIBODY

Function / homology

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta / (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.105 Å

Authors

Irimia, A. / Wilson, I.A.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2019
Title: An MPER antibody neutralizes HIV-1 using germline features shared among donors.
Authors: Lei Zhang / Adriana Irimia / Lingling He / Elise Landais / Kimmo Rantalainen / Daniel P Leaman / Thomas Vollbrecht / Armando Stano / Daniel I Sands / Arthur S Kim / / Pascal Poignard / ...
Abstract: The membrane-proximal external region (MPER) of HIV-1 envelope glycoprotein (Env) can be targeted by neutralizing antibodies of exceptional breadth. MPER antibodies usually have long, hydrophobic ...

History

Deposition	Feb 27, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 4, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 11, 2019	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Oct 11, 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6o3u.cif.gz	693.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6o3u.ent.gz	579.5 KB	Display	PDB format
PDBx/mmJSON format	6o3u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o3/6o3u ftp://data.pdbj.org/pub/pdb/validation_reports/o3/6o3u	HTTPS FTP

-
Related structure data

Related structure data	0620C 6o3dC 6o3gC 6o3jC 6o3kSC 6o3lC 6o41C 6o42C C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5d1z-2 4xbp-4 5ggu-1 5ibt-d 6lun-2 6x1s-4 4nzu-d 4wy7-d 4m6m-d 2ymx-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

6o3kSC

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

L: PGZL1.H4K3 light chain

H: PGZL1.H4K3 heavy chain

A: PGZL1.H4K3 light chain

B: PGZL1.H4K3 heavy chain

C: PGZL1.H4K3 light chain

D: PGZL1.H4K3 heavy chain

E: PGZL1.H4K3 light chain

F: PGZL1.H4K3 heavy chain

hetero molecules

195 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

L: PGZL1.H4K3 light chain

H: PGZL1.H4K3 heavy chain

hetero molecules

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

2

A: PGZL1.H4K3 light chain

B: PGZL1.H4K3 heavy chain

hetero molecules

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

3

C: PGZL1.H4K3 light chain

D: PGZL1.H4K3 heavy chain

hetero molecules

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

4

E: PGZL1.H4K3 light chain

F: PGZL1.H4K3 heavy chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	276.200, 276.200, 276.200
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	199
Space group name H-M	I2₁3

-
Antibody , 2 types, 8 molecules LACEHBDF

#1: Antibody	PGZL1.H4K3 light chain Mass: 23276.662 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi 293F / Production host: Homo sapiens (human)
#2: Antibody	PGZL1.H4K3 heavy chain Mass: 24220.318 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi 293F / Production host: Homo sapiens (human)

-
Non-polymers , 4 types, 66 molecules

#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-44E / (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate Mass: 368.360 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₅H₂₉O₈P / Comment: phospholipid*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.6 Å³/Da / Density % sol: 73 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.83 Details: 1.44 M ammonium sulfate, 0.01M cobalt chloride, 0.1 M MES pH 5.83

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 3.105→39.061 Å / Num. obs: 61847 / % possible obs: 98.2 % / Redundancy: 3.3 % / B_iso Wilson estimate: 90 Å² / CC_1/2: 0.995 / R_pim(I) all: 0.073 / R_sym value: 0.114 / Net I/σ(I): 9.8
Reflection shell	Resolution: 3.105→3.19 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4503 / CC_1/2: 0.425 / R_pim(I) all: 0.792 / R_sym value: 1.205 / % possible all: 97.8

-
Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS	20180319	data reduction
XSCALE	20180319	data scaling
PHASER	2.8.2	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6O3K

6o3k

Resolution: 3.105→39.061 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 23.86

	R_factor	Num. reflection	% reflection
R_free	0.2282	3111	5.03 %
R_work	0.186	-	-
obs	0.1881	61813	98.21 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 95 Å²

Refinement step

Cycle: LAST / Resolution: 3.105→39.061 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13182	0	252	34	13468

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	13821
X-RAY DIFFRACTION	f_angle_d	0.525	18802
X-RAY DIFFRACTION	f_dihedral_angle_d	15.32	8223
X-RAY DIFFRACTION	f_chiral_restr	0.042	2082
X-RAY DIFFRACTION	f_plane_restr	0.005	2381

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 (%)
3.1051-3.1536	0.3639	133	0.3342	2564	X-RAY DIFFRACTION	96
3.1536-3.2053	0.3507	145	0.2958	2719	X-RAY DIFFRACTION	100
3.2053-3.2606	0.3703	142	0.2967	2661	X-RAY DIFFRACTION	100
3.2606-3.3198	0.3179	143	0.2832	2722	X-RAY DIFFRACTION	100
3.3198-3.3836	0.322	143	0.2657	2630	X-RAY DIFFRACTION	99
3.3836-3.4527	0.2987	141	0.2656	2702	X-RAY DIFFRACTION	99
3.4527-3.5277	0.3052	140	0.2633	2677	X-RAY DIFFRACTION	99
3.5277-3.6097	0.2941	142	0.2133	2698	X-RAY DIFFRACTION	100
3.6097-3.6999	0.2602	144	0.2078	2692	X-RAY DIFFRACTION	99
3.6999-3.7999	0.2313	141	0.2041	2682	X-RAY DIFFRACTION	99
3.7999-3.9116	0.2831	133	0.1978	2630	X-RAY DIFFRACTION	97
3.9116-4.0377	0.2616	142	0.1947	2668	X-RAY DIFFRACTION	100
4.0377-4.1819	0.2063	145	0.1756	2692	X-RAY DIFFRACTION	100
4.1819-4.3491	0.188	145	0.1542	2715	X-RAY DIFFRACTION	99
4.3491-4.5467	0.1783	142	0.1341	2651	X-RAY DIFFRACTION	99
4.5467-4.786	0.1706	143	0.1302	2702	X-RAY DIFFRACTION	99
4.786-5.0853	0.1836	141	0.1333	2661	X-RAY DIFFRACTION	97
5.0853-5.477	0.1565	142	0.1395	2641	X-RAY DIFFRACTION	98
5.477-6.0264	0.2126	145	0.1628	2672	X-RAY DIFFRACTION	98
6.0264-6.8942	0.2195	140	0.1848	2662	X-RAY DIFFRACTION	97
6.8942-8.6703	0.2307	142	0.1804	2615	X-RAY DIFFRACTION	95
8.6703-39.0636	0.2207	137	0.188	2646	X-RAY DIFFRACTION	93

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	2.2005	0.5143	0.9001	4.879	-2.9108	3.4575	-0.0158	-1.1655	0.3448	0.7044	0.2882	0.9525	-1.1024	0.0645	-0.0995	0.7925	0.2829	0.1065	1.1324	0.1509	0.8615	-10.5204	38.5568	40.9433
2	4.9292	-2.2592	0.0354	8.0184	-4.1618	6.826	-0.0107	-0.5113	-0.3787	0.2962	0.605	0.756	-1.0144	-0.539	-0.264	0.6217	0.0852	0.034	0.8337	0.1362	0.6909	-10.9551	35.9776	31.1566
3	2.8067	-0.2073	-0.5116	4.9153	1.2096	3.5618	-0.5188	-0.8772	-0.844	0.1547	0.6405	1.434	-0.0743	-0.8299	-0.1977	0.529	0.0869	0.163	1.0443	0.1811	0.9968	-13.1401	28.5364	34.9747
4	6.3382	-0.0207	-3.7823	7.0419	-1.0195	2.5659	-0.1644	-0.4263	-0.248	0.2415	0.533	0.7312	0.2541	-0.6386	-0.372	0.5469	0.1157	0.0501	0.7325	0.1884	0.672	-7.8427	32.0655	35.9883
5	6.9836	1.116	0.2212	1.7083	0.5357	3.5906	0.3469	-0.5902	1.1142	0.3303	0.0169	0.0534	-1.1861	0.0984	-0.3289	1.1867	-0.0155	0.208	0.8401	-0.2857	0.8191	12.8849	42.0158	60.4829
6	7.5053	0.8279	1.0597	6.0089	-0.7295	3.6619	0.3665	-0.0928	-0.8552	0.3053	-0.187	-0.0774	0.4867	-0.3235	-0.1769	0.4855	0.0253	0.0908	0.4429	-0.0136	0.4652	10.133	20.0756	26.9397
7	7.1004	0.9634	0.9293	7.1777	0.8458	7.8785	0.0388	0.0089	0.3701	-0.0915	0.6323	0.0853	-0.5555	-0.0813	-0.1423	0.4388	-0.0642	0.0104	0.4483	0.0665	0.4989	4.7346	29.7739	22.7287
8	4.1236	1.2784	0.1239	5.9435	2.1775	2.7178	-0.2886	0.3003	-0.112	-0.5839	0.2797	0.2758	0.0212	0.191	-0.0761	0.6179	0.0322	0.0765	0.5356	0.0921	0.4576	12.1464	24.2143	22.1494
9	0.6105	-0.3798	-0.8053	1.5847	-0.6913	1.7566	0.0007	-0.1958	-0.1533	0.3567	0.1214	0.1496	0.1858	0.178	-0.0013	0.6116	-0.0187	0.1005	0.5074	0.0093	0.4956	10.5905	25.8483	42.6078
10	4.2703	1.0414	-1.4241	1.3024	-1.3613	3.4212	-0.0553	-1.0438	-0.0472	0.8147	0.2136	0.0637	0.2762	0.2816	-0.0793	1.0027	0.1005	0.0476	0.838	0.0063	0.4789	17.8628	26.3107	57.8129
11	3.2038	3.6845	-1.6701	9.4123	-3.0532	1.8312	-0.1779	-0.7981	0.5582	0.8644	0.2908	0.3505	-1.0693	-0.5156	-0.103	0.9136	0.0718	-0.1116	0.6989	-0.0611	0.787	-25.7664	49.288	6.3871
12	7.4257	2.1564	-0.9876	7.1953	0.0391	3.0706	0.0865	-0.155	0.3012	0.715	-0.4321	0.7408	-0.5378	-0.4689	0.1538	0.7463	-0.0137	0.0074	0.5885	0.0559	0.5459	-25.4145	39.3777	8.6912
13	5.938	-0.9324	0.9694	4.783	-0.241	3.416	0.1849	-0.7741	0.4698	0.8324	-0.0508	-0.11	-0.6474	0.0048	0.0962	1.0296	-0.0293	-0.0714	0.707	-0.0572	0.6226	-17.439	42.0762	10.4287
14	8.7527	3.7812	1.3382	2.7332	2.806	4.7941	0.0161	-0.2823	0.1757	0.8222	-0.2766	-1.305	-0.347	0.4828	0.0733	0.8543	-0.0014	-0.137	0.7049	0.0108	0.7595	-17.721	46.3101	6.2662
15	5.4996	3.5446	-0.6806	2.8614	-0.0988	4.6186	0.7088	-0.5014	0.212	0.042	-1.5311	0.3653	-0.5342	-0.4141	0.1863	0.5869	0.0755	-0.0067	0.7336	-0.0276	0.7054	-24.652	41.5892	1.553
16	1.1985	-0.8329	1.1235	5.4072	0.4908	5.4834	0.0085	0.0328	0.3593	0.2783	-0.0339	0.4419	-0.3212	0.1718	0.1432	0.6852	-0.0128	-0.0534	0.6426	0.0234	0.9044	-26.2827	62.9872	-20.7686
17	2.9286	0.2995	0.2973	2.8425	-0.1332	5.5485	0.0231	0.1729	0.4369	-0.3128	-0.1591	0.107	-0.4392	-0.1386	0.2399	0.8636	0.0704	-0.065	0.5339	0.0323	0.9103	-26.9521	65.4446	-21.9309
18	6.886	-1.0716	3.9465	2.5212	-1.7002	5.7395	0.1061	0.4845	0.1154	0.3274	-0.3941	-0.3521	0.6049	0.6331	0.3165	0.6616	0.1183	-0.0354	0.6782	0.1118	0.6402	-11.181	28.0878	-10.7818
19	5.3366	1.1385	-1.2999	7.8326	0.9606	6.0472	0.3126	-0.5467	0.422	0.1196	-0.4207	0.6879	-0.0119	-0.3268	0.2318	0.5028	-0.0045	-0.0392	0.4689	0.0556	0.3992	-19.4673	27.919	-4.0122
20	2.2488	1.0011	1.7826	5.8773	-0.041	6.8176	-0.6849	-0.5682	-0.2238	0.1636	0.1546	0.2918	0.8297	-0.466	0.1788	0.7774	0.026	-0.0059	0.5798	0.0749	0.5943	-17.5438	22.0992	-9.023
21	3.1345	-0.1468	2.0285	1.3928	1.781	5.6533	-0.0686	-0.2569	-0.0317	0.4163	-0.1409	-0.3408	0.054	0.0408	-0.0295	0.5492	0.0083	-0.0386	0.4638	0.0879	0.5275	-14.9053	31.5668	-3.1644
22	1.5796	1.056	-0.3067	3.298	0.3833	0.1965	0.1705	0.1681	0.4609	0.1013	-0.3112	-0.4475	-0.0327	0.3194	0.1108	0.6058	-0.0476	-0.0801	0.6846	0.1977	0.8009	-15.2045	55.3718	-24.5858
23	4.719	2.083	0.6238	3.1763	2.4815	2.4951	-0.144	0.353	0.4381	-0.5358	0.1258	-1.5336	-0.2248	0.4097	-0.075	0.6845	-0.0504	0.0314	0.8331	0.2034	0.8883	-8.0153	57.6775	-29.766
24	1.2689	-2.641	0.0891	5.8247	1.1238	5.6876	0.0668	0.5952	-1.4352	-0.6219	-0.1577	1.483	0.7915	-0.6759	0.1531	0.9575	-0.1109	-0.1692	0.595	0.0203	1.2136	-39.8351	-8.5628	-32.6571
25	5.256	-1.1563	-1.2046	5.137	2.6216	5.508	-0.111	0.8861	0.2154	0.1664	0.2584	0.4324	0.9842	-0.0762	0.0065	1.1388	-0.0305	0.0763	0.6314	0.1284	0.8271	-30.297	-10.7198	-29.9682
26	3.9307	-0.9979	0.3875	2.409	2.4255	5.5048	-0.245	-0.3338	-0.356	0.8405	-0.2264	1.3377	0.799	-0.2948	0.2064	1.0246	-0.0654	0.278	0.6549	0.0769	1.1137	-34.8511	-7.3621	-18.612
27	6.1793	-0.0304	0.2844	6.4265	0.7079	6.0791	-0.1093	-0.1539	-0.9863	-0.3313	0.0929	0.4473	1.2006	-0.1927	-0.0053	0.8337	-0.0309	0.0871	0.568	-0.0156	0.7249	-34.0854	-9.5739	-26.6128
28	4.0024	-3.5439	-1.1834	3.1916	0.7308	1.5886	-0.7149	0.6084	-2.0722	-0.0114	0.2476	1.3855	0.7038	-0.5483	0.4296	1.0296	-0.3142	-0.2191	0.9889	0.0622	1.1777	-49.6911	-0.9048	-32.8306
29	5.3682	1.9965	0.3136	7.7505	-0.2463	2.9154	-0.4918	0.7243	0.6896	-0.5281	0.2863	0.5859	0.2849	-0.6966	0.201	0.6923	-0.1957	-0.1643	1.16	0.1587	1.0789	-52.9059	20.391	-40.1193
30	2.5984	0.2989	-0.2164	4.5592	-1.4529	1.9864	-0.2183	0.5658	-0.2218	-0.6464	0.0811	0.4342	0.3234	-0.8016	0.1887	0.7029	-0.1504	-0.2053	1.0765	0.0057	0.8347	-53.2009	18.6106	-43.4995
31	4.7109	-1.8569	1.6496	6.3373	-2.6257	6.9257	-0.0068	-0.4846	-0.3365	0.7241	0.063	0.0329	-0.2703	0.4591	-0.0602	0.6486	0.1203	-0.0146	0.6053	0.0272	0.4722	-21.4153	11.3482	-17.8662
32	6.7403	2.6973	-0.1814	4.7889	2.9606	4.2975	-0.6293	0.1841	0.1894	-0.3091	-0.018	-0.1249	0.071	0.3381	0.7166	0.5718	0.1058	-0.01	0.4421	0.1282	0.4156	-19.8286	3.0917	-24.5453
33	6.0711	2.6602	-1.1195	7.5721	2.3371	1.9851	-0.0512	0.4183	-0.3427	-0.1951	0.4636	-0.9377	0.9075	0.6183	-0.3143	0.5922	0.1555	0.0604	0.6524	0.1191	0.7515	-14.4411	8.4463	-22.5062
34	2.2163	0.3818	0.1462	5.0854	-2.7516	3.4026	-0.2082	-0.1678	-0.4864	-0.1679	0.3309	-0.0224	0.8226	-0.1174	0.0827	0.666	0.0558	0.0375	0.5435	0.0289	0.6016	-24.3219	3.0922	-20.5876
35	3.8897	0.2853	0.7147	2.8084	-0.6843	0.2384	-0.1375	-0.2834	0.374	0.1882	0.1129	0.4624	0.0521	-0.4832	0.1117	0.4569	0.0006	-0.0008	0.8788	0.1266	0.687	-46.261	23.6644	-29.6368
36	7.5743	1.9506	0.4618	1.6365	0.3567	2.5456	-0.504	-0.7298	0.7113	0.6243	0.1079	1.1159	-0.3903	-1.114	0.0588	0.5755	0.1868	0.1098	1.1464	0.0268	1.1932	-51.9844	29.504	-23.8705
37	6.113	2.4144	0.9012	1.6977	1.754	6.1218	-0.2275	-0.172	1.197	-0.1562	-0.0948	1.1923	-0.9662	-1.1621	0.1265	1.0466	0.2396	0.0302	0.6984	0.0018	1.2014	-43.1488	20.3249	27.7924
38	4.1267	-0.6024	-1.9564	2.9809	1.185	5.5977	0.1388	0.2975	1.1479	-0.9515	-0.2013	0.6856	-1.7944	-0.2665	0.0751	1.0749	0.1173	-0.0087	0.5348	0.1734	1.0911	-34.5887	21.0011	21.7435
39	6.5286	-4.846	1.6857	8.8184	-3.3741	9.4468	-0.1859	0.7241	1.1416	0.348	0.0365	0.7244	-1.3214	-0.1552	-0.0351	0.9858	0.094	0.0122	0.7244	0.049	0.8723	-37.0648	16.5876	22.9914
40	3.9942	-0.653	-1.3662	4.7074	-0.8661	2.8452	-0.1154	-0.1983	0.2687	0.0012	-0.034	0.2352	-0.2416	-0.6913	0.1452	0.5204	0.1334	0.0174	1.1344	-0.1166	1.0794	-62.138	-2.6241	33.6003
41	3.8811	1.3169	-2.381	4.6973	-4.8418	8.7671	-0.0078	0.4845	0.2928	-0.3906	0.0672	-0.0121	0.3603	-0.0633	0.0108	0.6616	-0.062	0.1007	0.5697	0.0902	0.6424	-26.1268	-2.9972	16.5111
42	3.8076	-2.1847	2.8201	5.4973	1.3593	4.6042	-0.561	-0.0862	0.866	0.4602	0.1342	0.0785	-0.3016	0.1437	0.2048	0.5506	-0.0073	0.1407	0.4225	0.1679	0.5879	-24.3359	5.0246	23.4683
43	6.4563	-1.4317	-3.0031	8.5369	3.0625	2.3468	0.0716	-0.2161	-0.0883	0.1233	0.3009	-0.7898	-0.3111	0.7486	-0.1706	0.4735	-0.0882	-0.0344	0.7672	0.1121	0.741	-19.7523	-1.2249	22.4309
44	1.0603	-0.2961	-1.4376	2.8077	-0.9341	2.4778	0.064	0.6281	0.1369	-0.0819	0.0778	0.0202	-0.6019	-0.0357	-0.0295	0.5236	-0.0649	-0.0373	0.5461	0.153	0.5129	-27.9018	5.7555	18.7825
45	2.261	0.8821	-0.0458	1.422	0.1505	0.7543	-0.0791	0.5279	0.1992	-0.3108	-0.1463	0.6009	0.4227	-0.9293	0.1048	0.4904	0.0199	-0.0766	1.0258	-0.0212	0.9167	-54.5643	-10.7231	23.6791
46	5.6469	-0.1669	-1.7176	3.3956	-0.912	0.7935	0.6017	0.1365	-1.4838	-0.3186	0.2814	0.9297	0.2743	-1.4024	-0.188	0.5601	0.2065	-0.1463	1.4224	-0.1302	1.0125	-62.0065	-6.7304	21.2416
47	1.6679	-0.3611	0.1761	2.3436	-0.3075	3.5808	-0.2187	1.0038	-0.7571	-0.7508	0.2671	0.9666	-0.0149	-0.9219	0.2318	0.5987	-0.1073	-0.1144	1.2897	0.0031	1.3265	-59.2703	-15.8895	17.0114

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 1 through 18 )
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 19 through 38 )
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 39 through 75 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 76 through 102 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 103 through 213 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 1 through 32 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 33 through 66 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 67 through 87 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 88 through 164 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 165 through 228 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 1 through 18 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 19 through 38 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 39 through 75 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 76 through 92 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 93 through 106 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 107 through 163 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 164 through 213 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 1 through 32 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 33 through 59 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 60 through 82 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 82A through 111 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 112 through 197 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 198 through 229 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 1 through 18 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 19 through 38 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 39 through 61 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 62 through 98 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 99 through 113 )
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 114 through 150 )
30	X-RAY DIFFRACTION	30	chain 'C' and (resid 151 through 212 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 1 through 32 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 33 through 59 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 60 through 82 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 82A through 111 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 112 through 194 )
36	X-RAY DIFFRACTION	36	chain 'D' and (resid 496 through 524 )
37	X-RAY DIFFRACTION	37	chain 'E' and (resid 1 through 18 )
38	X-RAY DIFFRACTION	38	chain 'E' and (resid 19 through 75 )
39	X-RAY DIFFRACTION	39	chain 'E' and (resid 76 through 102 )
40	X-RAY DIFFRACTION	40	chain 'E' and (resid 103 through 213 )
41	X-RAY DIFFRACTION	41	chain 'F' and (resid 1 through 32 )
42	X-RAY DIFFRACTION	42	chain 'F' and (resid 33 through 59 )
43	X-RAY DIFFRACTION	43	chain 'F' and (resid 60 through 82 )
44	X-RAY DIFFRACTION	44	chain 'F' and (resid 82A through 111 )
45	X-RAY DIFFRACTION	45	chain 'F' and (resid 112 through 184 )
46	X-RAY DIFFRACTION	46	chain 'F' and (resid 185 through 197 )
47	X-RAY DIFFRACTION	47	chain 'F' and (resid 198 through 229 )

-
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

-
Antibody , 2 types, 8 molecules LACEHBDF

-
Non-polymers , 4 types, 66 molecules

-
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

-Antibody , 2 types, 8 molecules LACEHBDF

-Non-polymers , 4 types, 66 molecules

-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

-
Antibody , 2 types, 8 molecules LACEHBDF

-
Non-polymers , 4 types, 66 molecules

-
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