PDB-9emy: P. falciparum FIKK13 in complex with ATPgammaS

ID or keywords:

Entry

Database: PDB / ID: 9emy

Title

P. falciparum FIKK13 in complex with ATPgammaS

Components

Nanobody 2G9
Nanobody 9F10
non-specific serine/threonine protein kinase

Keywords

PEPTIDE BINDING PROTEIN / Malaria / kinase

Function / homology

Function and homology information

non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding / membrane
Similarity search - Function

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.814 Å

Authors

Purkiss, A.G. / Ogrodowicz, R.W. / Christodoulou, E. / Kjaer, S.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: Evolution and inhibition of the FIKK effector kinase family in P. falciparum
Authors: Purkiss, A.G. / Ogrodowicz, R.W. / Christodoulou, E. / Kjaer, S. / Belda, H. / Bradley, D. / Nofal, S.D. / Broncel, M. / Jones, D.A. / Davies, H. / Bertran, M.T. / Joshi, D. / OReilly, N. / ...

History

Deposition	Mar 11, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 26, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9emy.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb9emy.ent.gz	806.6 KB	Display	PDB format
PDBx/mmJSON format	9emy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/em/9emy ftp://data.pdbj.org/pub/pdb/validation_reports/em/9emy	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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1)

Deposited unit

A: non-specific serine/threonine protein kinase

B: non-specific serine/threonine protein kinase

C: Nanobody 9F10

D: Nanobody 9F10

E: Nanobody 2G9

F: Nanobody 2G9

G: non-specific serine/threonine protein kinase

H: non-specific serine/threonine protein kinase

I: Nanobody 9F10

J: Nanobody 9F10

K: Nanobody 2G9

L: Nanobody 2G9

hetero molecules

318 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: non-specific serine/threonine protein kinase

C: Nanobody 9F10

E: Nanobody 2G9

hetero molecules

defined by author
Evidence: homology, Apo structure is a pair of trimers. Each trimer comprising one copy each of FIKK13 and the two nanobodies., PISA analysis suggests the interface between FIKK monomers is much ...Evidence: homology, Apo structure is a pair of trimers. Each trimer comprising one copy each of FIKK13 and the two nanobodies., PISA analysis suggests the interface between FIKK monomers is much weaker than between FIKK monomers and each nanobody.
79.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: non-specific serine/threonine protein kinase

D: Nanobody 9F10

F: Nanobody 2G9

hetero molecules

defined by author
79.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: non-specific serine/threonine protein kinase

I: Nanobody 9F10

K: Nanobody 2G9

hetero molecules

defined by author
79.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

H: non-specific serine/threonine protein kinase

J: Nanobody 9F10

L: Nanobody 2G9

hetero molecules

defined by author
79.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	82.397, 121.657, 151.059
Angle α, β, γ (deg.)	90, 90.02, 90
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	TYR	TYR	LYS	LYS	A	A	158 - 560	10 - 412
2	1	1	TYR	TYR	LYS	LYS	B	B	158 - 560	10 - 412
3	2	2	SER	SER	SER	SER	A	A	157 - 558	9 - 410
4	2	2	SER	SER	SER	SER	G	G	157 - 558	9 - 410
5	3	3	TYR	TYR	LYS	LYS	A	A	158 - 560	10 - 412
6	3	3	TYR	TYR	LYS	LYS	H	H	158 - 560	10 - 412
7	4	4	TYR	TYR	SER	SER	B	B	158 - 559	10 - 411
8	4	4	TYR	TYR	SER	SER	G	G	158 - 559	10 - 411
9	5	5	TYR	TYR	LYS	LYS	B	B	158 - 560	10 - 412
10	5	5	TYR	TYR	LYS	LYS	H	H	158 - 560	10 - 412
11	6	6	GLU	GLU	SER	SER	C	C	4 - 128	2 - 126
12	6	6	GLU	GLU	SER	SER	D	D	4 - 128	2 - 126
13	7	7	GLU	GLU	SER	SER	C	C	4 - 128	2 - 126
14	7	7	GLU	GLU	SER	SER	I	I	4 - 128	2 - 126
15	8	8	GLN	GLN	SER	SER	C	C	5 - 128	3 - 126
16	8	8	GLN	GLN	SER	SER	J	J	5 - 128	3 - 126
17	9	9	GLU	GLU	SER	SER	D	D	4 - 128	2 - 126
18	9	9	GLU	GLU	SER	SER	I	I	4 - 128	2 - 126
19	10	10	GLN	GLN	SER	SER	D	D	5 - 128	3 - 126
20	10	10	GLN	GLN	SER	SER	J	J	5 - 128	3 - 126
21	11	11	GLU	GLU	SER	SER	E	E	8 - 126	6 - 124
22	11	11	GLU	GLU	SER	SER	F	F	8 - 126	6 - 124
23	12	12	VAL	VAL	SER	SER	E	E	4 - 126	2 - 124
24	12	12	VAL	VAL	SER	SER	K	K	4 - 126	2 - 124
25	13	13	GLU	GLU	SER	SER	E	E	8 - 126	6 - 124
26	13	13	GLU	GLU	SER	SER	L	L	8 - 126	6 - 124
27	14	14	GLU	GLU	SER	SER	F	F	8 - 127	6 - 125
28	14	14	GLU	GLU	SER	SER	K	K	8 - 127	6 - 125
29	15	15	GLU	GLU	SER	SER	F	F	8 - 127	6 - 125
30	15	15	GLU	GLU	SER	SER	L	L	8 - 127	6 - 125
31	16	16	TYR	TYR	SER	SER	G	G	158 - 559	10 - 411
32	16	16	TYR	TYR	SER	SER	H	H	158 - 559	10 - 411
33	17	17	GLN	GLN	SER	SER	I	I	5 - 128	3 - 126
34	17	17	GLN	GLN	SER	SER	J	J	5 - 128	3 - 126
35	18	18	GLU	GLU	SER	SER	K	K	8 - 126	6 - 124
36	18	18	GLU	GLU	SER	SER	L	L	8 - 126	6 - 124

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30
16	Local NCS retraints between domains: 31 32
17	Local NCS retraints between domains: 33 34
18	Local NCS retraints between domains: 35 36

-
Protein , 1 types, 4 molecules ABGH

#1: Protein	non-specific serine/threonine protein kinase Mass: 49764.645 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: CK202_4380, CYL21_5595 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: A0A2I0BRS6, non-specific serine/threonine protein kinase

#1: Protein

non-specific serine/threonine protein kinase

Mass: 49764.645 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Plasmodium falciparum (malaria parasite P. falciparum)
Gene: CK202_4380, CYL21_5595 / Production host:

Escherichia coli BL21 (bacteria)
References: UniProt: A0A2I0BRS6, non-specific serine/threonine protein kinase

-
Antibody , 2 types, 8 molecules CDIJEFKL

#2: Antibody	Nanobody 9F10 Mass: 14703.017 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Antibody	Nanobody 2G9 Mass: 14476.922 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21 (bacteria)

-
Non-polymers , 3 types, 23 molecules

#4: Chemical	ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₂P₃S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Chemical	ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₈ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.71 Å³/Da / Density % sol: 27.96 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M LiCl, 20% w/v PEG 6,000, 10% v/v Ethylene Glycol, 0.1M HEPES

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.81→64.17 Å / Num. obs: 72257 / % possible obs: 99.8 % / Redundancy: 7 % / B_iso Wilson estimate: 55.6 Å² / CC_1/2: 0.995 / R split: 0.212 / R_merge(I) obs: 0.196 / R_pim(I) all: 0.079 / Net I/σ(I): 6.8
Reflection shell	Resolution: 2.81→2.86 Å / Redundancy: 7.3 % / R_merge(I) obs: 2.123 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 3451 / CC_1/2: 0.614 / R_pim(I) all: 0.844 / R_rim(I) all: 2.286 / % possible all: 96.1

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.88)	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.814→64.169 Å / Cor.coef. F_o:F_c: 0.917 / Cor.coef. F_o:F_c free: 0.869 / WR_factor R_free: 0.246 / WR_factor R_work: 0.202 / SU B: 66.896 / SU ML: 0.534 / Average fsc free: 0.9301 / Average fsc work: 0.9516 / Cross valid method: THROUGHOUT / ESU R Free: 0.434 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2862	3699	5.126 %
R_work	0.2423	68457	-
all	0.245	-	-
obs	-	72156	99.686 %

Solvent computation

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

Displacement parameters

B_iso mean: 74.501 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.124 Å²	-0 Å²	-0.015 Å²
2-	-	-0.963 Å²	0 Å²
3-	-	-	1.086 Å²

Refinement step

Cycle: LAST / Resolution: 2.814→64.169 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19014	0	148	18	19180

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	19651
X-RAY DIFFRACTION	r_angle_refined_deg	1.549	1.796	26740
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.796	5	2436
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	23.05	5	64
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.576	10	2966
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.689	10	846
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	2901
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	15316
X-RAY DIFFRACTION	r_nbd_refined	0.235	0.2	8248
X-RAY DIFFRACTION	r_nbtor_refined	0.314	0.2	13230
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.147	0.2	485
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.32	0.2	24
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.238	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	2.219	2.402	9840
X-RAY DIFFRACTION	r_mcangle_it	3.694	4.304	12244
X-RAY DIFFRACTION	r_scbond_it	2.632	2.488	9811
X-RAY DIFFRACTION	r_scangle_it	4.189	4.541	14496
X-RAY DIFFRACTION	r_lrange_it	7.863	28.642	80690
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.077	0.05	12224
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.059	0.05	12587
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.077	0.05	12208
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.082	0.05	12087
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.042	0.05	12739
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.116	0.05	3207
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.049	0.05	3626
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.121	0.05	3154
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.106	0.05	3233
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.084	0.05	3332
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.119	0.05	2932
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.091	0.05	3539
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.132	0.05	2964
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.115	0.05	2992
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.075	0.05	3046
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.082	0.05	12094
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.109	0.05	3190
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.123	0.05	3022

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07654	0.0501
1	2	B	X-RAY DIFFRACTION	Local ncs	0.07654	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.05911	0.05011
2	4	G	X-RAY DIFFRACTION	Local ncs	0.05911	0.05011
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07722	0.0501
3	6	H	X-RAY DIFFRACTION	Local ncs	0.07722	0.0501
4	7	B	X-RAY DIFFRACTION	Local ncs	0.08186	0.0501
4	8	G	X-RAY DIFFRACTION	Local ncs	0.08186	0.0501
5	9	B	X-RAY DIFFRACTION	Local ncs	0.04218	0.05011
5	10	H	X-RAY DIFFRACTION	Local ncs	0.04218	0.05011
6	11	C	X-RAY DIFFRACTION	Local ncs	0.11643	0.05011
6	12	D	X-RAY DIFFRACTION	Local ncs	0.11643	0.05011
7	13	C	X-RAY DIFFRACTION	Local ncs	0.04932	0.05013
7	14	I	X-RAY DIFFRACTION	Local ncs	0.04932	0.05013
8	15	C	X-RAY DIFFRACTION	Local ncs	0.12116	0.0501
8	16	J	X-RAY DIFFRACTION	Local ncs	0.12116	0.0501
9	17	D	X-RAY DIFFRACTION	Local ncs	0.10591	0.05011
9	18	I	X-RAY DIFFRACTION	Local ncs	0.10591	0.05011
10	19	D	X-RAY DIFFRACTION	Local ncs	0.08362	0.05011
10	20	J	X-RAY DIFFRACTION	Local ncs	0.08362	0.05011
11	21	E	X-RAY DIFFRACTION	Local ncs	0.11877	0.05009
11	22	F	X-RAY DIFFRACTION	Local ncs	0.11877	0.05009
12	23	E	X-RAY DIFFRACTION	Local ncs	0.09057	0.05011
12	24	K	X-RAY DIFFRACTION	Local ncs	0.09057	0.05011
13	25	E	X-RAY DIFFRACTION	Local ncs	0.13242	0.05009
13	26	L	X-RAY DIFFRACTION	Local ncs	0.13242	0.05009
14	27	F	X-RAY DIFFRACTION	Local ncs	0.11547	0.0501
14	28	K	X-RAY DIFFRACTION	Local ncs	0.11547	0.0501
15	29	F	X-RAY DIFFRACTION	Local ncs	0.07518	0.05011
15	30	L	X-RAY DIFFRACTION	Local ncs	0.07518	0.05011
16	31	G	X-RAY DIFFRACTION	Local ncs	0.08229	0.0501
16	32	H	X-RAY DIFFRACTION	Local ncs	0.08229	0.0501
17	33	I	X-RAY DIFFRACTION	Local ncs	0.10898	0.05011
17	34	J	X-RAY DIFFRACTION	Local ncs	0.10898	0.05011
18	35	K	X-RAY DIFFRACTION	Local ncs	0.1226	0.0501
18	36	L	X-RAY DIFFRACTION	Local ncs	0.1226	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.814-2.887	0.417	285	0.395	4900	0.396	5334	0.873	0.893	97.2066	0.397
2.887-2.966	0.434	241	0.368	4964	0.371	5216	0.86	0.913	99.7891	0.364
2.966-3.052	0.366	247	0.357	4796	0.357	5051	0.914	0.917	99.8416	0.346
3.052-3.146	0.398	270	0.331	4600	0.335	4879	0.886	0.932	99.8155	0.312
3.146-3.249	0.323	213	0.314	4484	0.314	4708	0.929	0.939	99.7664	0.287
3.249-3.362	0.339	242	0.275	4356	0.279	4607	0.932	0.954	99.8046	0.243
3.362-3.489	0.31	278	0.266	4161	0.268	4443	0.938	0.958	99.91	0.232
3.489-3.631	0.259	212	0.239	4033	0.24	4247	0.953	0.967	99.9529	0.204
3.631-3.792	0.294	190	0.233	3931	0.236	4122	0.942	0.969	99.9757	0.197
3.792-3.976	0.274	192	0.208	3775	0.211	3968	0.949	0.975	99.9748	0.174
3.976-4.191	0.251	179	0.197	3530	0.2	3712	0.957	0.977	99.9192	0.161
4.191-4.444	0.231	214	0.189	3297	0.192	3513	0.969	0.98	99.9431	0.159
4.444-4.749	0.223	165	0.181	3174	0.182	3340	0.971	0.981	99.9701	0.15
4.749-5.127	0.216	145	0.196	2951	0.197	3096	0.97	0.977	100	0.161
5.127-5.613	0.266	121	0.21	2745	0.213	2867	0.943	0.974	99.9651	0.168
5.613-6.269	0.262	154	0.23	2435	0.232	2592	0.954	0.972	99.8843	0.184
6.269-7.227	0.288	127	0.243	2161	0.245	2289	0.941	0.968	99.9563	0.198
7.227-8.824	0.192	104	0.192	1858	0.192	1962	0.977	0.977	100	0.164
8.824-12.362	0.266	75	0.183	1459	0.187	1535	0.958	0.98	99.9349	0.173
12.362-64.169	0.527	45	0.402	847	0.408	895	0.854	0.902	99.6648	0.37

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	1.5254	0.0751	-0.4022	1.7357	-0.1936	0.8591	-0.0787	-0.0412	-0.1213	0.0375	0.0985	-0.1706	0.0997	0.1913	-0.0198	0.8972	0.0493	-0.0485	0.4066	-0.0503	0.0355	22.9319	-6.8028	22.5341
2	1.3787	-0.2132	-0.1698	1.4341	0.564	1.4718	-0.113	-0.0784	0.0856	0.0467	0.1135	0.1262	0.1374	-0.0411	-0.0004	0.9948	0.0851	0.053	0.4536	0.0578	0.029	-3.8799	19.3371	54.7435
3	2.2584	1.2856	3.1272	2.3233	1.7901	4.9265	-0.0021	0.3414	-0.3622	-0.0539	0.1116	0.1264	-0.0096	0.0915	-0.1095	0.7757	0.0654	0.0181	0.4691	-0.1951	0.4728	-2.2749	-23.5419	2.2867
4	2.268	-0.249	-0.6503	1.3435	-0.5689	2.6657	-0.0022	-0.0372	-0.788	-0.3538	-0.0768	0.4028	0.2118	-0.5337	0.079	1.1295	-0.0403	0.0222	0.6906	0.0437	0.5346	-31.6432	-1.7055	63.6093
5	3.7465	-3.0766	-0.0958	4.0341	0.944	2.1556	-0.0202	0.4304	0.076	-0.1921	-0.1393	0.475	-0.2871	-0.2576	0.1595	0.8619	0.0277	-0.0235	0.5312	0.0223	0.2461	-9.9687	10.523	16.573
6	1.3086	-1.1375	-0.945	4.5397	0.7322	2.1606	-0.0142	-0.3785	-0.2236	0.2196	-0.0481	0.25	0.1456	-0.0144	0.0623	0.8886	0.0227	0.0757	0.519	0.0863	0.1788	2.8845	-17.7403	53.6404
7	1.283	-0.2258	0.418	1.6275	-0.2533	1.0431	-0.0676	-0.0308	0.1318	-0.0393	0.1026	-0.1761	-0.0797	0.1808	-0.0349	0.8907	-0.0543	0.0164	0.4042	-0.0683	0.0418	64.2235	67.4122	53.1029
8	1.2739	0.1748	0.2101	1.5892	0.5614	1.1941	-0.1248	0.1046	-0.0376	-0.0641	0.1142	0.128	-0.136	-0.0476	0.0106	0.9839	-0.0916	-0.067	0.4508	0.0544	0.0221	37.1105	41.7229	20.6311
9	2.0858	-1.263	-2.9618	2.7464	1.686	4.9737	-0.0147	-0.3011	0.3558	0.0721	0.0874	0.1904	0.0122	0.0393	-0.0727	0.7784	-0.0424	-0.0238	0.4809	-0.1936	0.4654	38.8601	84.3926	73.2982
10	2.4533	0.3784	0.4854	1.5335	-0.7887	1.5374	0.0941	-0.0013	0.8459	0.4041	-0.1463	0.3553	-0.1825	-0.5596	0.0521	1.1384	0.026	-0.0446	0.7156	0.0438	0.503	9.4779	62.3207	11.9507
11	4.1313	3.1744	0.0825	4.4474	0.8506	1.9759	-0.0521	-0.3116	-0.098	0.22	-0.087	0.4583	0.2948	-0.1988	0.1391	0.853	-0.0312	0.009	0.529	0.0076	0.1973	31.3502	50.0893	58.8446
12	0.8075	1.322	1.1067	5.4195	1.4711	2.7107	0.0289	0.3232	0.1458	-0.2389	-0.0569	0.21	-0.149	-0.0583	0.0281	0.8663	-0.0083	-0.0658	0.574	0.1139	0.1949	43.8873	78.5425	21.7848

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	Ap	157 - 601
2	X-RAY DIFFRACTION	2	ALL	Bp	158 - 602
3	X-RAY DIFFRACTION	3	ALL	Cp	4 - 128
4	X-RAY DIFFRACTION	4	ALL	Dp	4 - 129
5	X-RAY DIFFRACTION	5	ALL	Ep	3 - 127
6	X-RAY DIFFRACTION	6	ALL	Fp	8 - 127
7	X-RAY DIFFRACTION	7	ALL	Gp	157 - 601
8	X-RAY DIFFRACTION	8	ALL	Hp	158 - 601
9	X-RAY DIFFRACTION	9	ALL	Ip	4 - 128
10	X-RAY DIFFRACTION	10	ALL	Jp	5 - 129
11	X-RAY DIFFRACTION	11	ALL	Kp	4 - 127
12	X-RAY DIFFRACTION	12	ALL	Lp	8 - 127

-
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

-
Protein , 1 types, 4 molecules ABGH

-
Antibody , 2 types, 8 molecules CDIJEFKL

-
Non-polymers , 3 types, 23 molecules

-
Details

-
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

-Protein , 1 types, 4 molecules ABGH

-Antibody , 2 types, 8 molecules CDIJEFKL

-Non-polymers , 3 types, 23 molecules

-Details

-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

-
Protein , 1 types, 4 molecules ABGH

-
Antibody , 2 types, 8 molecules CDIJEFKL

-
Non-polymers , 3 types, 23 molecules

-
Details

-
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