PDB-4u0b: Hexamer HIV-1 CA in complex with CPSF6 peptide, P212121 crystal form

ID or keywords:

Entry

Database: PDB / ID: 4u0b

Title

Hexamer HIV-1 CA in complex with CPSF6 peptide, P212121 crystal form

Components

Capsid protein p24
Cleavage and polyadenylation specificity factor subunit 6

Keywords

VIRAL PROTEIN /

Capsid /

Complex

Function / homology

Function and homology information

exon-exon junction complex binding / : / positive regulation of RNA export from nucleus / mRNA cleavage factor complex /

interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation /

paraspeckles ...
Similarity search - Function

Biological species

Human immunodeficiency virus type 1 group M subtype B

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Price, A.J. / Jacques, D.A. / James, L.C.

Citation

Journal: Plos Pathog. / Year: 2014
Title: Host Cofactors and Pharmacologic Ligands Share an Essential Interface in HIV-1 Capsid That Is Lost upon Disassembly.
Authors: Price, A.J. / Jacques, D.A. / McEwan, W.A. / Fletcher, A.J. / Essig, S. / Chin, J.W. / Halambage, U.D. / Aiken, C. / James, L.C.

History

Deposition	Jul 11, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Nov 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 20, 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	4u0b.cif.gz	999.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4u0b.ent.gz	843.8 KB	Display	PDB format
PDBx/mmJSON format	4u0b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u0/4u0b ftp://data.pdbj.org/pub/pdb/validation_reports/u0/4u0b	HTTPS FTP

-
Related structure data

Related structure data	4u0aSC 4u0cC 4u0dC 4u0eC 4u0fC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4wym-1 6v2f-2 4wym-2 6v2f-3 3h4e-2 5hgl-d 5tsx-2 4u0d-1 4u0e-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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#163 - Jul 2013 HIV Capsid similarity (3) #87 - Mar 2007 Zinc Fingers similarity (2) #122 - Feb 2010 Enhanceosome similarity (1) #148 - Apr 2012 Ras Protein similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1)

Deposited unit

A: Capsid protein p24

B: Capsid protein p24

C: Capsid protein p24

D: Capsid protein p24

E: Capsid protein p24

F: Capsid protein p24

G: Capsid protein p24

H: Capsid protein p24

I: Capsid protein p24

J: Capsid protein p24

K: Capsid protein p24

L: Capsid protein p24

M: Cleavage and polyadenylation specificity factor subunit 6

N: Cleavage and polyadenylation specificity factor subunit 6

O: Cleavage and polyadenylation specificity factor subunit 6

P: Cleavage and polyadenylation specificity factor subunit 6

Q: Cleavage and polyadenylation specificity factor subunit 6

R: Cleavage and polyadenylation specificity factor subunit 6

S: Cleavage and polyadenylation specificity factor subunit 6

T: Cleavage and polyadenylation specificity factor subunit 6

U: Cleavage and polyadenylation specificity factor subunit 6

V: Cleavage and polyadenylation specificity factor subunit 6

W: Cleavage and polyadenylation specificity factor subunit 6

X: Cleavage and polyadenylation specificity factor subunit 6

324 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Capsid protein p24

B: Capsid protein p24

C: Capsid protein p24

D: Capsid protein p24

E: Capsid protein p24

F: Capsid protein p24

M: Cleavage and polyadenylation specificity factor subunit 6

N: Cleavage and polyadenylation specificity factor subunit 6

O: Cleavage and polyadenylation specificity factor subunit 6

P: Cleavage and polyadenylation specificity factor subunit 6

Q: Cleavage and polyadenylation specificity factor subunit 6

R: Cleavage and polyadenylation specificity factor subunit 6

defined by author&software
162 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: Capsid protein p24

H: Capsid protein p24

I: Capsid protein p24

J: Capsid protein p24

K: Capsid protein p24

L: Capsid protein p24

S: Cleavage and polyadenylation specificity factor subunit 6

T: Cleavage and polyadenylation specificity factor subunit 6

U: Cleavage and polyadenylation specificity factor subunit 6

V: Cleavage and polyadenylation specificity factor subunit 6

W: Cleavage and polyadenylation specificity factor subunit 6

X: Cleavage and polyadenylation specificity factor subunit 6

defined by author&software
162 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	135.130, 135.890, 208.190
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	1 - 145
2	1	1	4	B	1 - 145
3	1	1	4	C	1 - 145
4	1	1	4	D	1 - 145
5	1	1	4	E	1 - 145
6	1	1	4	F	1 - 145
7	1	1	4	G	1 - 145
8	1	1	4	H	1 - 145
9	1	1	4	I	1 - 145
10	1	1	4	J	1 - 145
11	1	1	4	K	1 - 145
12	1	1	4	L	1 - 145
1	1	2	4	A	146 - 999
2	1	2	4	B	146 - 999
3	1	2	4	C	146 - 999
4	1	2	4	D	146 - 999
5	1	2	4	E	146 - 999
6	1	2	4	F	146 - 999
7	1	2	4	G	146 - 999
8	1	2	4	H	146 - 999
9	1	2	4	I	146 - 999
10	1	2	4	J	146 - 999
11	1	2	4	K	146 - 999
12	1	2	4	L	146 - 999

NCS ensembles :

ID
1
2

#1: Protein	Capsid protein p24 / / Pr55Gag Mass: 25461.271 Da / Num. of mol.: 12 / Mutation: yes Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B Strain: isolate NY5 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12493
#2: Protein/peptide	Cleavage and polyadenylation specificity factor subunit 6 / / Cleavage and polyadenylation specificity factor 68 kDa subunit / CPSF 68 kDa subunit / Pre-mRNA ...Cleavage and polyadenylation specificity factor 68 kDa subunit / CPSF 68 kDa subunit / Pre-mRNA cleavage factor Im 68 kDa subunit / Protein HPBRII-4/7 Mass: 1550.796 Da / Num. of mol.: 12 / Fragment: UNP residues 276-290 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16630

#1: Protein

Capsid protein p24 /

/ Pr55Gag

Mass: 25461.271 Da / Num. of mol.: 12 / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Human immunodeficiency virus type 1 group M subtype B
Strain: isolate NY5 / Gene: gag / Plasmid: pET11a / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12493

#2: Protein/peptide

Cleavage and polyadenylation specificity factor subunit 6 /

/ Cleavage and polyadenylation specificity factor 68 kDa subunit / CPSF 68 kDa subunit / Pre-mRNA ...

Mass: 1550.796 Da / Num. of mol.: 12 / Fragment: UNP residues 276-290 / Source method: obtained synthetically / Source: (synth.)

Homo sapiens (human) / References: UniProt: Q16630

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.95 Å³/Da / Density % sol: 58.28 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% v/v PEG 300, 10% v/v glycerol, 5% w/v PEG 8K, 0.1 M TRIS

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9686 Å / Relative weight: 1
Reflection	Resolution: 2.8→48.6 Å / Num. obs: 89373 / % possible obs: 95.1 % / Redundancy: 3.6 % / R_merge(I) obs: 0.069 / Net I/σ(I): 11.7
Reflection shell	Resolution: 2.8→2.95 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.588 / % possible all: 97.6

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing
PDB_EXTRACT	3.14	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4U0A

4u0a

Resolution: 2.8→48.6 Å / Cor.coef. F_o:F_c: 0.928 / Cor.coef. F_o:F_c free: 0.91 / SU B: 36.856 / SU ML: 0.315 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.33 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2619	4479	5 %	RANDOM
R_work	0.2295	84854	-	-
obs	0.2311	89333	94.13 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 229.13 Å² / B_iso mean: 85.338 Å² / B_iso min: 37.05 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.17 Å²	0 Å²	-0 Å²
2-	-	0.39 Å²	-0 Å²
3-	-	-	-0.21 Å²

Refinement step

Cycle: final / Resolution: 2.8→48.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19931	0	0	0	19931
Num. residues	-	-	-	-	2596

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.019	20452
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	19496
X-RAY DIFFRACTION	r_angle_refined_deg	0.739	1.964	27838
X-RAY DIFFRACTION	r_angle_other_deg	0.67	3.001	44943
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.927	5	2569
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.126	24.847	848
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.242	15	3355
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.779	15	110
X-RAY DIFFRACTION	r_chiral_restr	0.04	0.2	3130
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	22972
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4372
X-RAY DIFFRACTION	r_mcbond_it	3.202	7.254	10357
X-RAY DIFFRACTION	r_mcbond_other	3.201	7.254	10356
X-RAY DIFFRACTION	r_mcangle_it	5.172	12.225	12872

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1995	MEDIUM POSITIONAL	0.16	0.5
1	2	B	1995	MEDIUM POSITIONAL	0.15	0.5
1	3	C	1995	MEDIUM POSITIONAL	0.13	0.5
1	4	D	1995	MEDIUM POSITIONAL	0.11	0.5
1	5	E	1995	MEDIUM POSITIONAL	0.11	0.5
1	6	F	1995	MEDIUM POSITIONAL	0.11	0.5
1	7	G	1995	MEDIUM POSITIONAL	0.21	0.5
1	8	H	1995	MEDIUM POSITIONAL	0.18	0.5
1	9	I	1995	MEDIUM POSITIONAL	0.1	0.5
1	10		1995	MEDIUM POSITIONAL	0.11	0.5
1	11	A	1995	MEDIUM POSITIONAL	0.1	0.5
1	12	B	1995	MEDIUM POSITIONAL	0.13	0.5
1	1	A	1995	MEDIUM THERMAL	7.3	2
1	2	B	1995	MEDIUM THERMAL	7.44	2
1	3	C	1995	MEDIUM THERMAL	6.97	2
1	4	D	1995	MEDIUM THERMAL	5.84	2
1	5	E	1995	MEDIUM THERMAL	6.28	2
1	6	F	1995	MEDIUM THERMAL	5.15	2
1	7	G	1995	MEDIUM THERMAL	6.86	2
1	8	H	1995	MEDIUM THERMAL	7.18	2
1	9	I	1995	MEDIUM THERMAL	5.74	2
1	10		1995	MEDIUM THERMAL	5.82	2
1	11	A	1995	MEDIUM THERMAL	9.21	2
1	12	B	1995	MEDIUM THERMAL	5.25	2
2	1	A	976	MEDIUM POSITIONAL	0.23	0.5
2	2	B	976	MEDIUM POSITIONAL	0.16	0.5
2	3	C	976	MEDIUM POSITIONAL	0.14	0.5
2	4	D	976	MEDIUM POSITIONAL	0.13	0.5
2	5	E	976	MEDIUM POSITIONAL	0.13	0.5
2	6	F	976	MEDIUM POSITIONAL	0.25	0.5
2	7	G	976	MEDIUM POSITIONAL	0.18	0.5
2	8	H	976	MEDIUM POSITIONAL	0.2	0.5
2	9	I	976	MEDIUM POSITIONAL	0.13	0.5
2	10		976	MEDIUM POSITIONAL	0.21	0.5
2	11	A	976	MEDIUM POSITIONAL	0.18	0.5
2	12	B	976	MEDIUM POSITIONAL	0.26	0.5
2	1	A	976	MEDIUM THERMAL	13.37	2
2	2	B	976	MEDIUM THERMAL	11.69	2
2	3	C	976	MEDIUM THERMAL	8.02	2
2	4	D	976	MEDIUM THERMAL	7.87	2
2	5	E	976	MEDIUM THERMAL	7.14	2
2	6	F	976	MEDIUM THERMAL	12.78	2
2	7	G	976	MEDIUM THERMAL	8.7	2
2	8	H	976	MEDIUM THERMAL	10.56	2
2	9	I	976	MEDIUM THERMAL	6.93	2
2	10		976	MEDIUM THERMAL	15.3	2
2	11	A	976	MEDIUM THERMAL	8.83	2
2	12	B	976	MEDIUM THERMAL	12.66	2

LS refinement shell

Resolution: 2.8→2.873 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.381	369	-
R_work	0.331	6359	-
all	-	6728	-
obs	-	-	97.07 %

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	2.3446	0.7865	0.0512	2.9161	0.9851	1.2424	-0.2898	0.1115	0.3486	-0.2397	0.0186	0.4319	0.1106	-0.0094	0.2713	0.1159	0.0004	-0.0144	0.1081	-0.0074	0.1846	-17.4358	47.0768	-5.2531
2	1.3959	-0.1094	-0.505	2.3314	-0.2019	3.061	-0.275	-0.0179	-0.3416	0.1241	-0.0021	0.5871	0.5529	-0.1454	0.2771	0.1991	-0.002	0.2286	0.0543	-0.0035	0.4122	-30.905	30.6052	9.6332
3	1.1391	-0.0388	1.093	0.5027	-0.2691	3.8461	-0.3521	-0.388	-0.3887	0.175	0.1319	0.1495	0.1916	-0.2465	0.2202	0.337	0.243	0.3329	0.2213	0.2322	0.341	-27.0824	29.155	36.2981
4	0.6789	0.6229	-0.796	1.2482	-0.9235	1.8562	-0.2434	-0.5387	-0.1965	0.1607	-0.1422	0.0238	0.2282	0.6205	0.3856	0.3288	0.4171	0.1758	0.6373	0.2629	0.197	-10.1865	45.3271	47.7056
5	3.2567	1.4957	-2.3897	0.9773	-0.8345	3.8163	0.0979	-0.4696	0.3126	0.234	0.0594	0.1708	-0.2375	1.0426	-0.1573	0.1819	0.089	0.0171	0.4962	0.0221	0.0707	4.5755	62.1282	32.566
6	1.2176	-0.6333	-0.0203	0.794	1.5377	5.3716	-0.1182	0.0224	0.1989	-0.2368	0.0537	-0.0951	-0.9916	0.0546	0.0645	0.231	-0.0047	-0.054	0.1497	-0.0077	0.1232	0.5394	64.1908	5.9816
7	1.9646	-0.0571	0.6329	0.6876	0.0588	2.3727	-0.0414	-0.0141	-0.4286	-0.0209	-0.163	0.3005	0.1563	-0.4564	0.2044	0.0418	0.009	-0.008	0.2249	-0.2388	0.3923	-71.3846	70.2836	42.9009
8	0.8523	-0.1109	-0.2643	1.5714	-1.1714	3.1213	0.1744	0.3053	-0.0129	-0.454	-0.2886	0.325	0.4333	-0.1364	0.1142	0.2325	0.2192	-0.1716	0.3463	-0.265	0.2976	-72.7871	73.6115	16.0921
9	1.3999	0.3469	0.4593	1.9879	-0.1049	1.8006	0.0525	0.4752	-0.097	-0.4918	-0.2701	0.1262	-0.3209	-0.0665	0.2176	0.3522	0.2787	-0.1049	0.3841	-0.0651	0.1185	-56.8069	89.9427	4.3329
10	1.0911	1.2846	1.0554	2.0511	2.0262	4.598	0.0156	0.3644	-0.1503	-0.2535	0.2066	-0.2006	-1.2933	0.3245	-0.2222	0.504	0.0109	-0.0093	0.241	-0.0375	0.0821	-40.4334	106.2529	19.4308
11	0.3694	-0.5255	-0.5706	1.1302	0.2618	5.9544	0.1144	-0.0263	0.0352	-0.0584	-0.1633	-0.0484	-0.3143	0.8419	0.0488	0.0958	-0.0496	0.0192	0.1744	0.0072	0.0227	-38.2415	102.3287	45.7227
12	3.3648	0.6411	-1.2812	2.4801	0.1434	1.3488	-0.0171	-0.3207	-0.4819	0.0816	-0.2892	-0.1611	-0.043	-0.1089	0.3063	0.0279	0.0084	0.0012	0.134	-0.0187	0.1441	-54.7317	84.211	57.5394
13	7.7402	-5.7892	-2.4221	5.149	1.3862	0.9791	0.0927	0.1358	0.8188	-0.1677	-0.116	-1.159	0.0114	-0.0378	0.0233	0.307	-0.1193	-0.1053	0.1013	0.1123	0.5931	-5.3985	66.8271	-6.974
14	7.2824	0.2246	-4.6207	1.2909	-1.9923	5.5985	0.0255	0.3725	0.4018	-0.3378	-0.3511	-0.3661	0.4744	0.3064	0.3256	0.2088	0.0645	0.0023	0.2029	0.0772	0.3332	-29.5989	40.45	-9.7373
15	1.1038	-1.1093	-1.5969	1.1636	1.527	2.4387	-0.0315	0.0834	-0.0311	-0.0501	-0.0133	0.0404	0.2075	-0.2017	0.0448	0.2189	-0.0717	0.0771	0.1988	0.0616	0.2626	-40.2044	23.8903	18.0164
16	10.6818	-5.1694	-1.8119	2.5454	1.1392	1.8869	-0.2048	-0.2185	-0.8325	0.1625	0.0975	0.3987	0.3989	0.0018	0.1073	0.2975	0.0242	0.1314	0.2248	0.1693	0.2223	-27.673	32.1015	51.069
17	2.7639	0.6842	-0.6361	0.1856	-0.1566	0.1471	0.2597	-0.9223	0.1447	0.117	-0.2263	0.078	-0.0453	0.2207	-0.0334	0.3966	0.0261	0.1025	0.5295	-0.0195	0.1432	-2.1791	56.1967	53.6181
18	9.6507	-7.2403	3.25	5.4319	-2.4384	1.201	-0.4968	-0.7857	0.0014	0.3705	0.5896	-0	-0.273	-0.0829	-0.0928	0.4585	-0.1707	-0.0133	0.3767	-0.1494	0.1161	9.0118	73.7634	24.9523
19	3.1501	4.3813	4.1508	6.1503	5.8324	5.5324	0.4636	-0.4016	-0.1375	0.4575	-0.3369	-0.1978	0.4064	-0.3771	-0.1266	0.5452	-0.0857	0.058	0.6527	0.0743	0.2913	-60.9009	71.8696	62.4532
20	4.3485	-0.3125	-0.8097	7.5868	4.2471	2.4764	-0.4585	-0.381	0.3693	0.5373	0.3264	0.4531	0.3809	0.2315	0.1322	0.3493	-0.1357	-0.065	0.3682	-0.0208	0.3729	-77.3107	60.5149	34.2406
21	2.0026	-2.4076	-0.8314	3.6874	-0.3192	2.5521	0.6017	0.4193	-0.9643	-0.9668	-0.4217	1.5187	0.1637	-0.3859	-0.18	0.3414	0.0167	-0.3461	0.4395	-0.2671	0.671	-69.8497	73.1254	1.4049
22	3.4385	-3.8443	-0.6575	4.3358	0.7507	0.1336	0.508	0.5019	-0.178	-0.6815	-0.5251	0.161	-0.1523	-0.0984	0.0171	0.4846	0.0511	0.0702	0.3208	-0.0309	0.0781	-46.5265	99.1712	-1.4468
23	7.562	-5.5703	-0.1347	4.1086	0.1111	0.0301	0.6515	0.7814	0.361	-0.5538	-0.5688	-0.28	-0.1274	0.0575	-0.0827	0.5461	-0.2595	0.1967	0.4543	0.0471	0.1723	-28.5926	110.8205	27.0704
24	6.9596	-5.9399	-3.9711	5.1435	3.3822	2.3097	0.3233	-0.3483	1.2973	-0.1546	0.1818	-1.1887	-0.1392	0.1813	-0.5051	0.1162	-0.1635	-0.0256	0.5173	0.0044	0.9343	-35.2581	96.6047	59.2038

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 220
2	X-RAY DIFFRACTION	2	B	1 - 220
3	X-RAY DIFFRACTION	3	C	1 - 220
4	X-RAY DIFFRACTION	4	D	1 - 220
5	X-RAY DIFFRACTION	5	E	1 - 220
6	X-RAY DIFFRACTION	6	F	1 - 220
7	X-RAY DIFFRACTION	7	G	1 - 220
8	X-RAY DIFFRACTION	8	H	1 - 220
9	X-RAY DIFFRACTION	9	I	1 - 220
10	X-RAY DIFFRACTION	10	J	1 - 220
11	X-RAY DIFFRACTION	11	K	1 - 220
12	X-RAY DIFFRACTION	12	L	1 - 220
13	X-RAY DIFFRACTION	13	M	313 - 326
14	X-RAY DIFFRACTION	14	N	313 - 325
15	X-RAY DIFFRACTION	15	O	313 - 326
16	X-RAY DIFFRACTION	16	P	313 - 326
17	X-RAY DIFFRACTION	17	Q	313 - 326
18	X-RAY DIFFRACTION	18	R	313 - 326
19	X-RAY DIFFRACTION	19	S	313 - 326
20	X-RAY DIFFRACTION	20	T	313 - 326
21	X-RAY DIFFRACTION	21	U	313 - 326
22	X-RAY DIFFRACTION	22	V	313 - 326
23	X-RAY DIFFRACTION	23	W	313 - 326
24	X-RAY DIFFRACTION	24	X	313 - 326

-
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