PDB-1wkp: Flowering locus t (ft) from arabidopsis thaliana

ID or keywords:

Entry

Database: PDB / ID: 1wkp

Title

Flowering locus t (ft) from arabidopsis thaliana

Components

FLOWERING LOCUS T protein

Keywords

SIGNALING PROTEIN / cis-peptide / pebp

Function / homology

Function and homology information

meristem determinacy / photoperiodism, flowering / positive regulation of flower development / regulation of flower development / regulation of stomatal movement / flower development / phosphatidylethanolamine binding / cell differentiation / endoplasmic reticulum / nucleus / cytoplasm
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Miller, D. / Banfield, M.J. / Winter, V.J. / Brady, R.L.

Citation

Journal: Embo J. / Year: 2006
Title: A divergent external loop confers antagonistic activity on floral regulators FT and TFL1.
Authors: Ahn, J.H. / Miller, D. / Winter, V.J. / Banfield, M.J. / Lee, J.H. / Yoo, S.Y. / Henz, S.R. / Brady, R.L. / Weigel, D.

History

Deposition	Jun 1, 2004	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 28, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Nov 10, 2021	Group: Database references / Derived calculations / Category: database_2 / 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_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	1wkp.cif.gz	143 KB	Display	PDBx/mmCIF format
PDB format	pdb1wkp.ent.gz	113.2 KB	Display	PDB format
PDBx/mmJSON format	1wkp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wk/1wkp ftp://data.pdbj.org/pub/pdb/validation_reports/wk/1wkp	HTTPS FTP

-
Related structure data

Related structure data	1wkoC 1a44 1bd9 1beh 1fjj 1fux 1kn3 1qou C: citing same article (ref.)
Similar structure data	5rvg-1 1wko-1 7b64-d 6igi-d 5ghi-1 7bf5-3 3ql3-d 3zwg-14 3jzt-3 6vv7-2 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) 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

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: FLOWERING LOCUS T protein

B: FLOWERING LOCUS T protein

C: FLOWERING LOCUS T protein

D: FLOWERING LOCUS T protein

hetero molecules

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

1

A: FLOWERING LOCUS T protein

hetero molecules

defined by author
19.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: FLOWERING LOCUS T protein

hetero molecules

defined by author
19.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: FLOWERING LOCUS T protein

defined by author&software
19.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: FLOWERING LOCUS T protein

defined by author&software
19.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

B: FLOWERING LOCUS T protein

C: FLOWERING LOCUS T protein

hetero molecules

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

6

A: FLOWERING LOCUS T protein

D: FLOWERING LOCUS T protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.973, 61.542, 66.841
Angle α, β, γ (deg.)	75.15, 72.18, 70.55
Int Tables number	1
Space group name H-M	P1

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	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ILE	ILE	SER	SER	1	A	A	10 - 12	13 - 15
2	1	1	ILE	ILE	SER	SER	1	B	B	10 - 12	13 - 15
3	1	1	ILE	ILE	SER	SER	1	C	C	10 - 12	13 - 15
4	1	1	ILE	ILE	SER	SER	1	D	D	10 - 12	13 - 15
5	2	1	ARG	ARG	ILE	ILE	1	A	A	119 - 123	122 - 126
6	2	1	ARG	ARG	ILE	ILE	1	B	B	119 - 123	122 - 126
7	2	1	ARG	ARG	ILE	ILE	1	C	C	119 - 123	122 - 126
8	2	1	ARG	ARG	ILE	ILE	1	D	D	119 - 123	122 - 126
9	3	1	ASN	ASN	SER	SER	1	A	A	141 - 164	144 - 167
10	3	1	ASN	ASN	SER	SER	1	B	B	141 - 164	144 - 167
11	3	1	ASN	ASN	SER	SER	1	C	C	141 - 164	144 - 167
12	3	1	ASN	ASN	SER	SER	1	D	D	141 - 164	144 - 167
13	4	1	VAL	VAL	ASP	ASP	1	A	A	14 - 20	17 - 23
14	4	1	VAL	VAL	ASP	ASP	1	B	B	14 - 20	17 - 23
15	4	1	VAL	VAL	ASP	ASP	1	C	C	14 - 20	17 - 23
16	4	1	VAL	VAL	ASP	ASP	1	D	D	14 - 20	17 - 23
17	5	1	SER	SER	GLU	GLU	1	A	A	107 - 109	110 - 112
18	5	1	SER	SER	GLU	GLU	1	B	B	107 - 109	110 - 112
19	5	1	SER	SER	GLU	GLU	1	C	C	107 - 109	110 - 112
20	5	1	SER	SER	GLU	GLU	1	D	D	107 - 109	110 - 112
21	6	1	ARG	ARG	LEU	LEU	6	A	A	6 - 9	9 - 12
22	6	1	ARG	ARG	LEU	LEU	6	B	B	6 - 9	9 - 12
23	6	1	ARG	ARG	LEU	LEU	6	C	C	6 - 9	9 - 12
24	6	1	ARG	ARG	LEU	LEU	6	D	D	6 - 9	9 - 12
25	7	1	PHE	PHE	SER	SER	1	A	A	64 - 78	67 - 81
26	7	1	PHE	PHE	SER	SER	1	B	B	64 - 78	67 - 81
27	7	1	PHE	PHE	SER	SER	1	C	C	64 - 78	67 - 81
28	7	1	PHE	PHE	SER	SER	1	D	D	64 - 78	67 - 81
29	8	1	ASP	ASP	GLY	GLY	1	A	A	92 - 102	95 - 105
30	8	1	ASP	ASP	GLY	GLY	1	B	B	92 - 102	95 - 105
31	8	1	ASP	ASP	GLY	GLY	1	C	C	92 - 102	95 - 105
32	8	1	ASP	ASP	GLY	GLY	1	D	D	92 - 102	95 - 105
33	9	1	GLN	GLN	GLU	GLU	6	A	A	165 - 167	168 - 170
34	9	1	GLN	GLN	GLU	GLU	6	B	B	165 - 167	168 - 170
35	9	1	GLN	GLN	GLU	GLU	6	C	C	165 - 167	168 - 170
36	9	1	GLN	GLN	GLU	GLU	6	D	D	165 - 167	168 - 170
37	10	1	PRO	PRO	LEU	LEU	1	A	A	45 - 61	48 - 64
38	10	1	PRO	PRO	LEU	LEU	1	B	B	45 - 61	48 - 64
39	10	1	PRO	PRO	LEU	LEU	1	C	C	45 - 61	48 - 64
40	10	1	PRO	PRO	LEU	LEU	1	D	D	45 - 61	48 - 64
41	11	1	THR	THR	LEU	LEU	1	A	A	27 - 43	30 - 46
42	11	1	THR	THR	LEU	LEU	1	B	B	27 - 43	30 - 46
43	11	1	THR	THR	LEU	LEU	1	C	C	27 - 43	30 - 46
44	11	1	THR	THR	LEU	LEU	1	D	D	27 - 43	30 - 46
45	12	1	PRO	PRO	LEU	LEU	1	A	A	80 - 82	83 - 85
46	12	1	PRO	PRO	LEU	LEU	1	B	B	80 - 82	83 - 85
47	12	1	PRO	PRO	LEU	LEU	1	C	C	80 - 82	83 - 85
48	12	1	PRO	PRO	LEU	LEU	1	D	D	80 - 82	83 - 85
49	13	1	GLU	GLU	VAL	VAL	1	A	A	84 - 90	87 - 93
50	13	1	GLU	GLU	VAL	VAL	1	B	B	84 - 90	87 - 93
51	13	1	GLU	GLU	VAL	VAL	1	C	C	84 - 90	87 - 93
52	13	1	GLU	GLU	VAL	VAL	1	D	D	84 - 90	87 - 93
53	14	1	SER	SER	VAL	VAL	3	A	A	12 - 14	15 - 17
54	14	1	SER	SER	VAL	VAL	3	B	B	12 - 14	15 - 17
55	14	1	SER	SER	VAL	VAL	3	C	C	12 - 14	15 - 17
56	14	1	SER	SER	VAL	VAL	3	D	D	12 - 14	15 - 17
57	15	1	ASN	ASN	SER	SER	1	A	A	23 - 25	26 - 28
58	15	1	ASN	ASN	SER	SER	1	B	B	23 - 25	26 - 28
59	15	1	ASN	ASN	SER	SER	1	C	C	23 - 25	26 - 28
60	15	1	ASN	ASN	SER	SER	1	D	D	23 - 25	26 - 28
1	1	2	PHE	PHE	GLY	GLY	1	A	A	125 - 129	128 - 132
2	1	2	PHE	PHE	GLY	GLY	1	B	B	125 - 129	128 - 132
3	2	2	ARG	ARG	ARG	ARG	1	A	A	83	86
4	2	2	ARG	ARG	ARG	ARG	1	B	B	83	86
5	3	2	ASN	ASN	VAL	VAL	1	A	A	103 - 106	106 - 109
6	3	2	ASN	ASN	VAL	VAL	1	B	B	103 - 106	106 - 109
7	4	2	GLN	GLN	GLY	GLY	1	A	A	131 - 137	134 - 140
8	4	2	GLN	GLN	GLY	GLY	1	B	B	131 - 137	134 - 140
9	5	2	ARG	ARG	ARG	ARG	5	A	A	130	133
10	5	2	ARG	ARG	ARG	ARG	5	B	B	130	133
1	1	3	PHE	PHE	GLY	GLY	1	C	C	125 - 137	128 - 140
2	1	3	PHE	PHE	GLY	GLY	1	D	D	125 - 137	128 - 140
3	2	3	ARG	ARG	GLN	GLN	1	C	C	139 - 140	142 - 143
4	2	3	ARG	ARG	GLN	GLN	1	D	D	139 - 140	142 - 143
5	3	3	ARG	ARG	ARG	ARG	1	C	C	83	86
6	3	3	ARG	ARG	ARG	ARG	1	D	D	83	86
7	4	3	ASN	ASN	ILE	ILE	2	C	C	103 - 105	106 - 108
8	4	3	ASN	ASN	ILE	ILE	2	D	D	103 - 105	106 - 108
1	1	4	PRO	PRO	GLY	GLY	5	A	A	111 - 116	114 - 119
2	1	4	PRO	PRO	GLY	GLY	5	C	C	111 - 116	114 - 119
3	1	4	PRO	PRO	GLY	GLY	5	D	D	111 - 116	114 - 119
1	1	5	ASP	ASP	PHE	PHE	4	A	A	20 - 22	23 - 25
2	1	5	ASP	ASP	PHE	PHE	4	B	B	20 - 22	23 - 25
3	2	5	ASN	ASN	THR	THR	1	A	A	23 - 27	26 - 30
4	2	5	ASN	ASN	THR	THR	1	B	B	23 - 27	26 - 30
1	1	6	ASP	ASP	PHE	PHE	4	C	C	20 - 22	23 - 25
2	1	6	ASP	ASP	PHE	PHE	4	D	D	20 - 22	23 - 25
3	2	6	ASN	ASN	THR	THR	1	C	C	23 - 27	26 - 30
4	2	6	ASN	ASN	THR	THR	1	D	D	23 - 27	26 - 30

NCS ensembles :

ID
1
2
3
4
5
6

Details

monomer is biological unit

#1: Protein	FLOWERING LOCUS T protein Mass: 19376.809 Da / Num. of mol.: 4 / Mutation: d42n, c107s, c164s Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FT / Plasmid: pet-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bl21 (de3) / References: UniProt: Q9SXZ2
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.53 Å³/Da / Density % sol: 51.44 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 0.14M Ammonium Sulfate, 38% w/v PEG 5000 MME, 0.1M MES, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 1.488 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 7, 2003
Radiation	Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.488 Å / Relative weight: 1
Reflection	Resolution: 2.6→20 Å / Num. obs: 21870 / % possible obs: 93.2 % / Redundancy: 2.2 % / R_merge(I) obs: 0.076 / Net I/σ(I): 12.05
Reflection shell	Resolution: 2.6→2.72 Å / R_merge(I) obs: 0.17 / Mean I/σ(I) obs: 3.8 / % possible all: 66.2

-
Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: arabidopsis thaliana terminal flower 1 (tfl1)

Resolution: 2.6→20 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.908 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22611	1104	5 %	RANDOM
R_work	0.18129	-	-	-
obs	0.18358	20788	93.74 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 22.073 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.72 Å²	-1.01 Å²	-0.87 Å²
2-	-	0.3 Å²	4.13 Å²
3-	-	-	-0.49 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5202	0	15	195	5412

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	5350
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.4	1.944	7318
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.901	5	645
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	813
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4208
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	2074
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.144	0.2	279
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.228	0.2	58
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.305	0.2	7
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_mcbond_it	0.438	1.5	3249
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.84	2	5328
X-RAY DIFFRACTION	r_scbond_it	1.265	3	2101
X-RAY DIFFRACTION	r_scangle_it	2.115	4.5	1990
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

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	920	tight positional	0.08	0.05
1	2	B	920	tight positional	0.09	0.05
1	3	C	920	tight positional	0.09	0.05
1	4	D	920	tight positional	0.09	0.05
2	1	A	137	tight positional	0.03	0.05
3	1	C	148	tight positional	0.19	0.05
5	1	A	40	tight positional	0.02	0.05
6	1	C	40	tight positional	0.02	0.05
2	1	A	4	medium positional	0.09	0.5
3	1	C	13	medium positional	0.1	0.5
4	1	A	24	medium positional	0.16	0.5
4	2	C	24	medium positional	0.18	0.5
4	3	D	24	medium positional	0.06	0.5
5	1	A	26	medium positional	0.1	0.5
6	1	C	26	medium positional	0.04	0.5
1	1	A	69	loose positional	0.7	5
1	2	B	69	loose positional	0.95	5
1	3	C	69	loose positional	0.72	5
1	4	D	69	loose positional	0.8	5
2	1	A	7	loose positional	0.6	5
4	1	A	12	loose positional	0.59	5
4	2	C	12	loose positional	0.55	5
4	3	D	12	loose positional	0.4	5
1	1	A	920	tight thermal	0.08	0.5
1	2	B	920	tight thermal	0.08	0.5
1	3	C	920	tight thermal	0.08	0.5
1	4	D	920	tight thermal	0.09	0.5
2	1	A	137	tight thermal	0.08	0.5
3	1	C	148	tight thermal	0.07	0.5
5	1	A	40	tight thermal	0.04	0.5
6	1	C	40	tight thermal	0.05	0.5
2	1	A	4	medium thermal	0.28	2
3	1	C	13	medium thermal	0.5	2
4	1	A	24	medium thermal	0.7	2
4	2	C	24	medium thermal	0.39	2
4	3	D	24	medium thermal	0.63	2
5	1	A	26	medium thermal	0.14	2
6	1	C	26	medium thermal	0.32	2
1	1	A	69	loose thermal	2.58	10
1	2	B	69	loose thermal	2.65	10
1	3	C	69	loose thermal	2	10
1	4	D	69	loose thermal	3.04	10
2	1	A	7	loose thermal	3.16	10
4	1	A	12	loose thermal	0.74	10
4	2	C	12	loose thermal	0.39	10
4	3	D	12	loose thermal	0.73	10

LS refinement shell

Resolution: 2.6→2.666 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.291	55
R_work	0.224	1043

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	3.3031	0.203	0.2261	4.5032	-0.0831	3.0139	0.0288	-0.0556	0.0374	0.1161	-0.0989	-0.1668	0.0093	0.0659	0.0701	0.0387	-0.0082	0.0001	0.0752	-0.0011	0.0206	74.4977	10.8268	62.5845
2	3.5304	0.2617	0.2837	2.8529	0.5241	3.8291	-0.0077	0.0718	0.0602	0.0559	-0.0145	0.0305	0.019	-0.1487	0.0222	0.0437	0.0038	-0.0005	0.0268	0.013	0.0549	37.2278	38.4376	34.2762
3	4.8997	0.5384	0.0932	3.6784	-0.5194	3.2149	-0.0153	-0.1325	0.1089	0.0987	0.0025	0.0018	-0.236	0.0783	0.0128	0.0644	0.0038	0.0063	0.0463	-0.0073	0.007	47.7738	56.2162	13.7807
4	4.4938	0.0643	0.6462	2.7746	-0.4329	4.1934	0.0861	0.0712	-0.1606	-0.1675	-0.0743	0.0431	0.2049	0.0878	-0.0118	0.048	0.0109	0.0044	0.0226	0.0105	0.0511	63.9718	25.544	39.7898

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	6 - 167	9 - 170
2	X-RAY DIFFRACTION	2	B	B	6 - 167	9 - 170
3	X-RAY DIFFRACTION	3	C	C	6 - 167	9 - 170
4	X-RAY DIFFRACTION	4	D	D	6 - 167	9 - 170

-
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