PDB-3mnv: Crystal structure of the non-neutralizing HIV antibody 13H11 Fab ...

ID or keywords:

Entry

Database: PDB / ID: 3mnv

Title

Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment

Components

(ANTI-HIV-1 ANTIBODY 13H11 ...) x 2

Keywords

IMMUNE SYSTEM /

HIV-1 /

HIV /

gp41 / MPER / 13H11 / 2F5 / Z13 / 4E10 / Fab antibody

Function / homology

Function and homology information

immunoglobulin complex / extracellular region /

plasma membrane
Similarity search - Function

Biological species

Mus musculus (house mouse)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Nicely, N.I. / Dennison, S.M. / Kelsoe, G. / Liao, H.-X. / Alam, S.M. / Haynes, B.F.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Crystal structure of a non-neutralizing antibody to the HIV-1 gp41 membrane-proximal external region.
Authors: Nicely, N.I. / Dennison, S.M. / Spicer, L. / Scearce, R.M. / Kelsoe, G. / Ueda, Y. / Chen, H. / Liao, H.X. / Alam, S.M. / Haynes, B.F.

History

Deposition	Apr 22, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 17, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Aug 16, 2017	Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3mnv.cif.gz	359.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3mnv.ent.gz	294.9 KB	Display	PDB format
PDBx/mmJSON format	3mnv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mn/3mnv ftp://data.pdbj.org/pub/pdb/validation_reports/mn/3mnv	HTTPS FTP

-
Related structure data

Related structure data	1mhhS 1tjgS 3mnw 3mnz 3mo1 3moa 3mob 3mod S: Starting model for refinement
Similar structure data	4c83-2 3mck-2 6vbp-1 4iml-1 3pp3-1 4nrz-2 2c1o-2 5ywf-2 6jc2-d 5dd3-d 6a0x-1 4jdv-1 2aab-d 6vl9-1 4xce-3 4q0x-d 1b4j-d 6cw3-2 2dqu-d 3cmo-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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

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 (2) #163 - Jul 2013 HIV Capsid similarity (2) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN

B: ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN

C: ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN

D: ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN

hetero molecules

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

1

A: ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN

B: ANTI-HIV-1 ANTIBODY 13H11 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

C: ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN

D: ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN

hetero molecules

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

Unit cell

Length a, b, c (Å)	158.378, 158.378, 92.975
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

-
Antibody , 2 types, 4 molecules ACBD

#1: Antibody	ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN Mass: 24719.545 Da / Num. of mol.: 2 / Fragment: FUSION PROTEIN between mouse Fv and a human Fc Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Cell line (production host): HEK293T CELL / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: UniProt: Q8TCD0
#2: Antibody	ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN Mass: 23521.475 Da / Num. of mol.: 2 / Fragment: FUSION PROTEIN between mouse Fv and a human Fc Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Cell line (production host): HEK293T CELL / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: UniProt: Q6N089

#1: Antibody

ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN

Mass: 24719.545 Da / Num. of mol.: 2 / Fragment: FUSION PROTEIN between mouse Fv and a human Fc
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse), (gene. exp.)

Homo sapiens (human)
Cell line (production host): HEK293T CELL / Organ (production host): KIDNEY / Production host:

Homo sapiens (human) / References: UniProt: Q8TCD0

#2: Antibody

ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN

Mass: 23521.475 Da / Num. of mol.: 2 / Fragment: FUSION PROTEIN between mouse Fv and a human Fc
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse), (gene. exp.)

Homo sapiens (human)
Cell line (production host): HEK293T CELL / Organ (production host): KIDNEY / Production host:

Homo sapiens (human) / References: UniProt: Q6N089

-
Non-polymers , 5 types, 429 molecules

#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-NO3 / NITRATE ION / Nitrate Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO₃
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 417 / 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: 3.49 Å³/Da / Density % sol: 64.75 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion Details: Qiagen AmSO4 suite, reservoir: 2.2 M ammonium sulfate, 0.2 M lithium nitrate. Drop: 0.5 uL protein + 0.5 uL reservoir., VAPOR DIFFUSION, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 10, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.4→45.278 Å / Num. all: 51941 / Num. obs: 51525 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / R_merge(I) obs: 0.058 / Net I/σ(I): 11.4

-
Processing

Software

Name	Version	Classification
PHENIX		model building
PHENIX	(phenix.refine: dev_271)	refinement
d*TREK		data reduction
d*TREK		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1MHH, 1TJG

1mhh

1tjg

Resolution: 2.4→45.278 Å / SU ML: 0.35 / σ(F): 0.06 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2278	1983	3.87 %
R_work	0.1808	-	-
obs	0.1826	51189	98.49 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 49.154 Å² / k_sol: 0.406 e/Å³

Refinement step

Cycle: LAST / Resolution: 2.4→45.278 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6595	0	51	417	7063

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6839
X-RAY DIFFRACTION	f_angle_d	1.075	9288
X-RAY DIFFRACTION	f_dihedral_angle_d	15.407	2411
X-RAY DIFFRACTION	f_chiral_restr	0.072	1039
X-RAY DIFFRACTION	f_plane_restr	0.005	1176

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 (%)
2.4-2.4602	0.2269	136	0.1937	3439	X-RAY DIFFRACTION	98
2.4602-2.5267	0.2685	141	0.1908	3514	X-RAY DIFFRACTION	98
2.5267-2.601	0.2716	143	0.2084	3505	X-RAY DIFFRACTION	99
2.601-2.685	0.2541	141	0.1982	3518	X-RAY DIFFRACTION	99
2.685-2.7809	0.2947	141	0.1957	3511	X-RAY DIFFRACTION	99
2.7809-2.8923	0.2763	142	0.1951	3498	X-RAY DIFFRACTION	99
2.8923-3.0239	0.2418	143	0.1887	3519	X-RAY DIFFRACTION	99
3.0239-3.1833	0.2517	144	0.1814	3536	X-RAY DIFFRACTION	99
3.1833-3.3826	0.217	141	0.173	3506	X-RAY DIFFRACTION	99
3.3826-3.6437	0.1997	142	0.1574	3527	X-RAY DIFFRACTION	99
3.6437-4.0102	0.2134	141	0.15	3530	X-RAY DIFFRACTION	99
4.0102-4.59	0.173	143	0.1293	3532	X-RAY DIFFRACTION	99
4.59-5.781	0.1785	141	0.138	3528	X-RAY DIFFRACTION	98
5.781-45.2865	0.2228	144	0.2046	3543	X-RAY DIFFRACTION	97

Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

ID	Method	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	refined	0.8388	-0.5141	-0.9292	1.3162	1.0958	1.3235	-0.2734	0.7247	0.1355	0.1322	-0.3045	0.2973	0.5908	-0.1556	0.1088	0.5013	-0.0877	0.031	0.3366	0.1415	0.2805	106.3835	-27.192	141.6919
2		0.4253	-0.4552	0.1771	1.2536	0.3756	0.2007	-0.2449	-0.0125	0.2118	0.4769	0.0622	-0.1861	-0.5505	-0.1422	0.1245	0.5263	-0.0378	0.0007	0.1774	0.0217	0.2618
3		4.5281	-3.8323	1.8436	3.4291	-2.3503	3.7795	-0.1677	0.0036	0.7717	0.231	-0.0425	-0.2861	-1.2149	0.0707	0.2408	0.557	0.0719	-0.0117	0.2914	0.0015	0.3298
4		1.5438	-1.5624	1.294	3.7647	-0.796	2.2085	0.594	-0.5512	0.5076	-0.4485	0.0374	1.955	-0.1867	-1.1553	-0.0801	0.3976	0.1943	0.0357	0.713	-0.0533	0.7935
5		3.0151	0.1004	1.4848	2.3909	0.3528	2.838	0.2451	-0.2646	-0.2382	0.4918	-0.0426	0.0355	0.5194	-0.3011	-0.151	0.3944	-0.0052	0.0298	0.1698	0.0372	0.1201
6		1.721	-0.0667	1.9046	0.6243	1.1479	1.7946	0.0584	0.0249	0.079	0.1328	0.0043	-0.0883	-0.15	0.0435	-0.0144	0.4416	-0.0079	0.0217	0.1745	0.0041	0.1961
7		5.4355	-1.3042	-1.0306	1.6768	-0.3594	2.3518	-0.0856	0.2031	0.6291	0.1927	-0.0379	-0.9609	-0.4571	0.2615	-0.1968	0.373	-0.1207	0.0611	0.1832	0.059	0.2749
8		4.3299	0.5431	2.2541	0.976	1.3663	3.2241	-0.437	0.7181	1.6696	-1.7875	-0.1225	-0.2143	-1.4285	-0.0356	0.0166	0.7923	-0.2597	0.1795	0.5187	0.2865	0.9066
9		1.8797	-1.4289	-0.8878	1.4787	-0.0328	2.9127	0.0731	-0.0274	0.1556	-0.1315	-0.2033	-0.2448	-0.2706	-0.1632	0.0192	0.4207	-0.0823	0.0199	0.2454	0.0493	0.2808
10		3.8499	-1.2323	-2.1416	0.6064	-0.4481	3.8561	0.2268	-0.1844	1.3319	-0.4096	0.1903	-0.821	-0.8454	0.6401	-0.3185	0.4843	-0.2829	0.1515	0.5007	0.0565	0.67
11		0.9182	-0.7967	1.239	4.1965	-2.8526	3.3049	0.4955	0.0188	-0.4524	-0.4838	0.3194	0.5827	-0.0137	-0.1983	-0.539	0.4446	0	0.1185	0.3503	0.0812	0.5697
12		1.4125	-0.4505	1.43	1.5678	-0.3855	1.5336	0.1889	-0.0963	-0.3727	-0.5073	-0.0225	0.1327	0.3114	-0.0771	-0.1658	0.3987	0.0038	-0.0624	0.1731	0.0525	0.2321
13		5.9241	-0.8242	0.0524	2.1641	-0.1584	0.2821	-0.0145	-0.1639	0.7467	-0.3247	0.156	0.0004	-0.0923	0.1074	0.0195	0.3464	-0.0053	0.0174	0.1709	-0.0044	0.1595
14		2.3955	-0.9192	-1.1115	0.8565	-0.3498	1.9361	0.3751	0.6258	0.9359	-0.4198	0.071	0.4679	-0.1671	-0.5628	-0.2535	0.3897	0.0155	-0.0285	0.2808	0.1066	0.169
15		2.3469	-0.5448	-1.1864	2.0904	-0.4296	1.4556	0.6986	0.5273	0.1388	0.0944	-0.0397	-0.0591	-0.1499	-0.6581	-0.479	0.4503	0.0562	-0.0818	0.2796	0.0243	0.1115
16		6.6075	3.7017	0.9427	5.9193	1.14	0.2803	0.3735	0.9958	0.0499	-0.77	-0.0945	0.4472	0.2495	-0.2421	-0.2171	0.4131	-0.0052	-0.1235	0.2525	0.0192	0.2194
17		1.8821	-1.3841	-1.4591	4.2762	-0.4344	5.0848	0.5964	0.3419	0.6728	-0.2491	-0.717	0.2934	0.0524	-0.3855	-0.1511	0.4616	-0.0151	0.0725	0.1859	0.0798	0.1973
18		2.0763	-0.2452	-1.3359	0.8463	-0.2045	1.0683	-0.0256	-0.2087	0.102	-0.0167	-0.0439	0.0097	0.0832	0.1654	0.0267	0.3709	0.0075	0.0152	0.1988	-0.0376	0.1522
19		1.6563	-0.4937	-0.6018	1.773	-1.0374	2.1798	0.1243	0.1074	0.071	-0.2763	-0.1016	-0.1117	-0.094	-0.035	-0.0643	0.2493	0.0018	0.0944	0.1357	0.0075	0.1591
20		6.0234	2.8666	-0.5117	1.5837	0.2663	3.3619	-0.2442	-0.3126	-0.9149	-0.9412	0.1275	-0.1345	-0.0081	0.4366	0.1304	0.4467	0.1183	0.1221	0.2269	-0.0105	0.4131
21		3.685	-0.5096	-5.0394	6.9935	3.5418	8.0612	0.443	0.6705	0.3497	1.2351	0.3285	-0.662	1.3485	-0.5553	-0.1646	0.524	-0.319	-0.1026	0.6377	0.402	0.6514
22		1.5789	-1.8355	1.0259	2.6742	-0.3199	1.6016	0.6939	0.1495	-1.0733	-0.5631	0.0873	0.9371	0.6492	-0.0602	-0.4837	0.5634	-0.0431	-0.2035	0.21	-0.0703	0.4691
23		1.6527	-0.4002	0.764	0.204	-0.121	0.6174	0.1421	0.2856	-1.2828	-0.0819	0.199	0.9065	0.6161	0.0153	-0.3624	0.7082	-0.1787	-0.2551	0.2716	0.0916	0.8666
24		9.3339	3.2097	5.3253	3.7702	1.1511	3.2084	0.1606	-1.0385	0.1673	-0.8183	-0.0709	1.6116	0.1309	-0.2416	0.0067	0.4883	-0.125	-0.2677	0.4787	0.0662	0.8014
25		2.1559	-1.0189	0.7925	3.6581	0.2045	1.4558	0.2895	0.0326	-0.3478	-0.3886	-0.0269	0.2341	0.3352	0.0707	-0.2705	0.3743	-0.0432	-0.0945	0.1738	0.0061	0.3025
26		3.0901	0.5009	1.4736	0.506	-0.3139	1.2524	-0.1227	-0.8851	-0.8527	-0.3623	0.4302	0.7655	0.5111	-0.191	-0.3345	0.3012	-0.0966	-0.0951	0.2335	0.1602	0.5154
27		0.8299	-1.3095	0.1674	2.864	0.2783	0.936	-0.239	-0.0192	-0.2459	0.1682	0.2104	-0.1448	0.0585	0.1675	0.0207	0.3261	0.021	0.0682	0.1831	-0.0302	0.2054
28		1.892	-2.7414	-1.1261	6.2203	3.9277	3.4533	-0.6708	-0.126	-0.6753	1.0232	0.9116	1.2223	1.1339	-0.1392	0.1101	0.6559	-0.1099	0.1949	0.3632	0.051	0.5804
29		0.4138	0.598	-0.1637	0.7788	-0.6196	5.9408	-0.2407	-0.1388	-0.3046	-0.0689	-0.148	0.1678	1.1881	-0.1967	0.2874	0.5481	0.1799	0.1351	0.185	0.0438	0.2792
30		3.4136	-0.5957	-0.4009	0.3371	0.3738	6.745	-0.2586	-0.4246	-0.5559	0.6905	0.1957	0.1884	1.9589	0.4319	0.1222	0.6573	0.2202	0.1291	0.2274	0.0261	0.2651
31		1.5871	0.2318	-3.2289	0.5594	-0.9062	6.8478	0.0973	0.5668	-1.4391	0.6137	-0.3159	-0.7075	-1.1041	0.5599	-0.0243	0.462	-0.0906	0.1008	0.3702	-0.1152	0.2721
32		0.5423	-0.6988	1.2708	0.8179	-1.8438	5.5202	-0.0988	-0.1249	-0.0573	0.0188	0.2744	0.2773	-0.5069	-0.1098	-0.2283	0.4507	-0.0117	0.118	0.2785	0.0664	0.3612
33		2.8693	-0.9768	2.041	0.3438	-0.3182	7.0005	0.7899	0.1931	-0.3613	-0.2144	-0.4129	0.3488	0.3905	0.0649	-0.4113	0.3023	-0.0596	0.0025	0.3222	0.1187	0.3516
34		2.0804	-2.0906	1.177	2.0203	-1.0648	6.2739	-0.1152	-0.2763	0.1169	0.479	0.6058	0.2781	-0.9273	-0.8032	-0.5492	0.3247	0.1254	0.1908	0.3722	0.1731	0.3365
35		0.6474	0.1635	-0.338	1.3637	0.3719	3.4886	0.0125	-0.2737	-0.1786	0.4318	-0.1498	0.1778	0.5589	-1.9502	-0.2146	0.4949	0.0503	0.1662	0.6094	0.2361	0.4692
36		1.2179	0.1466	0.9676	1.5463	-0.9476	2.6786	0.0925	-0.136	-0.0514	-0.1396	0.2935	0.2074	-0.3971	0.1463	-0.2734	0.1949	-0.0246	0.0638	0.1452	0.0397	0.1582
37		3.6974	-1.281	-0.1288	5.91	1.7336	0.9538	-0.0624	-0.1703	-0.5502	0.5549	0.1644	0.3001	0.096	0.2827	-0.1415	0.2343	0.0427	-0.0858	0.141	-0.0133	0.1186
38		1.1012	-0.7595	0.1291	1.3993	0.1678	1.0783	0.0723	0.1565	-0.0852	-0.0112	0.0461	0.0037	0.2165	0.05	-0.0613	0.2608	-0.0207	0.0209	0.1855	-0.014	0.1705
39		1.7818	0.3715	-2.0112	1.5165	0.0549	3.8751	0.3352	-0.4098	0.352	0.0962	0.0396	-0.2034	-0.42	0.4863	-0.3783	0.2395	0.029	0.0065	0.1778	-0.0395	0.1374
40		1.5261	-1.7223	-0.5742	7.8975	-1.549	2.1509	0.3719	0.1521	0.2991	-0.2101	-1.1015	-0.7278	0.5123	1.1257	0.4955	0.369	0.1338	-0.1101	0.476	0.0478	0.2681

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid -2:3)	A	-2 - 3
2	X-RAY DIFFRACTION	2	(chain A and resid 4:21)	A	4 - 21
3	X-RAY DIFFRACTION	3	(chain A and resid 22:29)	A	22 - 29
4	X-RAY DIFFRACTION	4	(chain A and resid 30:30F)	A	30
5	X-RAY DIFFRACTION	5	(chain A and resid 31:69)	A	31 - 69
6	X-RAY DIFFRACTION	6	(chain A and resid 70:109)	A	70 - 109
7	X-RAY DIFFRACTION	7	(chain A and resid 110:146)	A	110 - 146
8	X-RAY DIFFRACTION	8	(chain A and resid 147:158)	A	147 - 158
9	X-RAY DIFFRACTION	9	(chain A and resid 159:184)	A	159 - 184
10	X-RAY DIFFRACTION	10	(chain A and resid 185:213)	A	185 - 213
11	X-RAY DIFFRACTION	11	(chain B and resid 0:4)	B	0 - 4
12	X-RAY DIFFRACTION	12	(chain B and resid 5:30)	B	5 - 30
13	X-RAY DIFFRACTION	13	(chain B and resid 31:49)	B	31 - 49
14	X-RAY DIFFRACTION	14	(chain B and resid 50:64)	B	50 - 64
15	X-RAY DIFFRACTION	15	(chain B and resid 65:72)	B	65 - 72
16	X-RAY DIFFRACTION	16	(chain B and resid 73:82A)	B	73 - 82
17	X-RAY DIFFRACTION	17	(chain B and resid 82B:85)	B	82
18	X-RAY DIFFRACTION	18	(chain B and resid 86:114)	B	86 - 114
19	X-RAY DIFFRACTION	19	(chain B and resid 115:215)	B	115 - 215
20	X-RAY DIFFRACTION	20	(chain B and resid 216:226)	B	216 - 226
21	X-RAY DIFFRACTION	21	(chain C and resid -1:3)	C	-1 - 3
22	X-RAY DIFFRACTION	22	(chain C and resid 4:21)	C	4 - 21
23	X-RAY DIFFRACTION	23	(chain C and resid 22:30)	C	22 - 30
24	X-RAY DIFFRACTION	24	(chain C and resid 30A:30E)	C	30
25	X-RAY DIFFRACTION	25	(chain C and resid 30F:93)	C	30
26	X-RAY DIFFRACTION	26	(chain C and resid 94:105)	C	94 - 105
27	X-RAY DIFFRACTION	27	(chain C and resid 106:141)	C	106 - 141
28	X-RAY DIFFRACTION	28	(chain C and resid 142:147)	C	142 - 147
29	X-RAY DIFFRACTION	29	(chain C and resid 148:195)	C	148 - 195
30	X-RAY DIFFRACTION	30	(chain C and resid 196:212)	C	196 - 212
31	X-RAY DIFFRACTION	31	(chain D and resid 1:5)	D	1 - 5
32	X-RAY DIFFRACTION	32	(chain D and resid 6:40)	D	6 - 40
33	X-RAY DIFFRACTION	33	(chain D and resid 41:53)	D	41 - 53
34	X-RAY DIFFRACTION	34	(chain D and resid 54:80)	D	54 - 80
35	X-RAY DIFFRACTION	35	(chain D and resid 81:85)	D	81 - 85
36	X-RAY DIFFRACTION	36	(chain D and resid 86:116)	D	86 - 116
37	X-RAY DIFFRACTION	37	(chain D and resid 117:127)	D	117 - 127
38	X-RAY DIFFRACTION	38	(chain D and resid 136:194)	D	136 - 194
39	X-RAY DIFFRACTION	39	(chain D and resid 195:221)	D	195 - 221
40	X-RAY DIFFRACTION	40	(chain D and resid 222:226)	D	222 - 226

-
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, 4 molecules ACBD

-
Non-polymers , 5 types, 429 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, 4 molecules ACBD

-Non-polymers , 5 types, 429 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, 4 molecules ACBD

-
Non-polymers , 5 types, 429 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