PDB-5u1b: Ferritin with Gc MtrE loop2 inserted at the N-terminus

ID or keywords:

Entry

Database: PDB / ID: 5u1b

Title

Ferritin with Gc MtrE loop2 inserted at the N-terminus

Components

MtrE protein,Ferritin chimera

Keywords

OXIDOREDUCTASE / chimera / nanoparticle / 24mer cage / immunogen

Function / homology

Function and homology information

bacterial non-heme ferritin / efflux transmembrane transporter activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Neisseria gonorrhoeae (bacteria)

Helicobacter pylori (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.81 Å

Authors

Wang, S.

Citation

Journal: FEBS Open Bio / Year: 2017
Title: Structure-based design of ferritin nanoparticle immunogens displaying antigenic loops of Neisseria gonorrhoeae.
Authors: Wang, L. / Xing, D. / Le Van, A. / Jerse, A.E. / Wang, S.

History

Deposition	Nov 28, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 11, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5u1b.cif.gz	528.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5u1b.ent.gz	439.4 KB	Display	PDB format
PDBx/mmJSON format	5u1b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5u1b_validation.pdf.gz	480.8 KB	Display	wwPDB validaton report
Full document	5u1b_full_validation.pdf.gz	488.6 KB	Display
Data in XML	5u1b_validation.xml.gz	42.5 KB	Display
Data in CIF	5u1b_validation.cif.gz	59.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u1/5u1b ftp://data.pdbj.org/pub/pdb/validation_reports/u1/5u1b	HTTPS FTP

-
Related structure data

Related structure data	5u1aC 3bvfS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3qz3-1 3ka8-1 1eum-1 4xgs-1 3bve-1 1vlg-1 3egm-1 5u1a-1 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	#222 - Jun 2018 Proteins and Nanoparticles similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (3) #35 - Nov 2002 Ferritin and Transferrin similarity (6) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #114 - Jun 2009 Vaults similarity (1) #57 - Sep 2004 Catalase similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#222 - Jun 2018
Proteins and Nanoparticles
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (3)
#35 - Nov 2002
Ferritin and Transferrin
similarity (6)
#261 - Sep 2021
DNA-Sequencing Nanopores
similarity (1)
#114 - Jun 2009
Vaults
similarity (1)
#57 - Sep 2004
Catalase
similarity (1)
#22 - Oct 2001
Photosystem I
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#29 - May 2002
Penicillin-binding Proteins
similarity (1)

Deposited unit

A: MtrE protein,Ferritin chimera

B: MtrE protein,Ferritin chimera

C: MtrE protein,Ferritin chimera

D: MtrE protein,Ferritin chimera

E: MtrE protein,Ferritin chimera

F: MtrE protein,Ferritin chimera

G: MtrE protein,Ferritin chimera

H: MtrE protein,Ferritin chimera

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

1

A: MtrE protein,Ferritin chimera

B: MtrE protein,Ferritin chimera

C: MtrE protein,Ferritin chimera

D: MtrE protein,Ferritin chimera

E: MtrE protein,Ferritin chimera

F: MtrE protein,Ferritin chimera

G: MtrE protein,Ferritin chimera

H: MtrE protein,Ferritin chimera

A: MtrE protein,Ferritin chimera

B: MtrE protein,Ferritin chimera

C: MtrE protein,Ferritin chimera

D: MtrE protein,Ferritin chimera

E: MtrE protein,Ferritin chimera

F: MtrE protein,Ferritin chimera

G: MtrE protein,Ferritin chimera

H: MtrE protein,Ferritin chimera

A: MtrE protein,Ferritin chimera

B: MtrE protein,Ferritin chimera

C: MtrE protein,Ferritin chimera

D: MtrE protein,Ferritin chimera

E: MtrE protein,Ferritin chimera

F: MtrE protein,Ferritin chimera

G: MtrE protein,Ferritin chimera

H: MtrE protein,Ferritin chimera

defined by author&software
517 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	124.514, 124.514, 314.885
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-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	MET	MET	ARG	ARG	A	A	1 - 165	23 - 187
2	1	MET	MET	ARG	ARG	B	B	1 - 165	23 - 187
1	2	MET	MET	ARG	ARG	A	A	1 - 165	23 - 187
2	2	MET	MET	ARG	ARG	C	C	1 - 165	23 - 187
1	3	MET	MET	ARG	ARG	A	A	1 - 165	23 - 187
2	3	MET	MET	ARG	ARG	D	D	1 - 165	23 - 187
1	4	MET	MET	ARG	ARG	A	A	1 - 165	23 - 187
2	4	MET	MET	ARG	ARG	E	E	1 - 165	23 - 187
1	5	MET	MET	ARG	ARG	A	A	1 - 165	23 - 187
2	5	MET	MET	ARG	ARG	F	F	1 - 165	23 - 187
1	6	MET	MET	ARG	ARG	A	A	1 - 165	23 - 187
2	6	MET	MET	ARG	ARG	G	G	1 - 165	23 - 187
1	7	ASP	ASP	LYS	LYS	A	A	-1 - 166	21 - 188
2	7	ASP	ASP	LYS	LYS	H	H	-1 - 166	21 - 188
1	8	MET	MET	LYS	LYS	B	B	1 - 166	23 - 188
2	8	MET	MET	LYS	LYS	C	C	1 - 166	23 - 188
1	9	MET	MET	LYS	LYS	B	B	1 - 166	23 - 188
2	9	MET	MET	LYS	LYS	D	D	1 - 166	23 - 188
1	10	MET	MET	LYS	LYS	B	B	1 - 166	23 - 188
2	10	MET	MET	LYS	LYS	E	E	1 - 166	23 - 188
1	11	MET	MET	LYS	LYS	B	B	1 - 166	23 - 188
2	11	MET	MET	LYS	LYS	F	F	1 - 166	23 - 188
1	12	MET	MET	LYS	LYS	B	B	1 - 166	23 - 188
2	12	MET	MET	LYS	LYS	G	G	1 - 166	23 - 188
1	13	MET	MET	ARG	ARG	B	B	1 - 165	23 - 187
2	13	MET	MET	ARG	ARG	H	H	1 - 165	23 - 187
1	14	MET	MET	LYS	LYS	C	C	1 - 166	23 - 188
2	14	MET	MET	LYS	LYS	D	D	1 - 166	23 - 188
1	15	MET	MET	LYS	LYS	C	C	1 - 166	23 - 188
2	15	MET	MET	LYS	LYS	E	E	1 - 166	23 - 188
1	16	MET	MET	LYS	LYS	C	C	1 - 166	23 - 188
2	16	MET	MET	LYS	LYS	F	F	1 - 166	23 - 188
1	17	MET	MET	LYS	LYS	C	C	1 - 166	23 - 188
2	17	MET	MET	LYS	LYS	G	G	1 - 166	23 - 188
1	18	MET	MET	ARG	ARG	C	C	1 - 165	23 - 187
2	18	MET	MET	ARG	ARG	H	H	1 - 165	23 - 187
1	19	MET	MET	LYS	LYS	D	D	1 - 166	23 - 188
2	19	MET	MET	LYS	LYS	E	E	1 - 166	23 - 188
1	20	MET	MET	LYS	LYS	D	D	1 - 166	23 - 188
2	20	MET	MET	LYS	LYS	F	F	1 - 166	23 - 188
1	21	MET	MET	LYS	LYS	D	D	1 - 166	23 - 188
2	21	MET	MET	LYS	LYS	G	G	1 - 166	23 - 188
1	22	MET	MET	ARG	ARG	D	D	1 - 165	23 - 187
2	22	MET	MET	ARG	ARG	H	H	1 - 165	23 - 187
1	23	MET	MET	LYS	LYS	E	E	1 - 166	23 - 188
2	23	MET	MET	LYS	LYS	F	F	1 - 166	23 - 188
1	24	MET	MET	LYS	LYS	E	E	1 - 166	23 - 188
2	24	MET	MET	LYS	LYS	G	G	1 - 166	23 - 188
1	25	MET	MET	ARG	ARG	E	E	1 - 165	23 - 187
2	25	MET	MET	ARG	ARG	H	H	1 - 165	23 - 187
1	26	MET	MET	LYS	LYS	F	F	1 - 166	23 - 188
2	26	MET	MET	LYS	LYS	G	G	1 - 166	23 - 188
1	27	MET	MET	ARG	ARG	F	F	1 - 165	23 - 187
2	27	MET	MET	ARG	ARG	H	H	1 - 165	23 - 187
1	28	MET	MET	ARG	ARG	G	G	1 - 165	23 - 187
2	28	MET	MET	ARG	ARG	H	H	1 - 165	23 - 187

NCS ensembles :

#1: Protein	MtrE protein,Ferritin chimera Mass: 21552.273 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria), (gene. exp.) Helicobacter pylori (bacteria) Gene: mtrE, pfr, AB991_00330, ACM31_07775, AEY53_00945 / Plasmid: pET28 / Production host: Escherichia coli #1/H766 (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q51006, UniProt: O69434, bacterial non-heme ferritin
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

MtrE protein,Ferritin chimera

Mass: 21552.273 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Neisseria gonorrhoeae (bacteria), (gene. exp.)

Helicobacter pylori (bacteria)
Gene: mtrE, pfr, AB991_00330, ACM31_07775, AEY53_00945 / Plasmid: pET28 / Production host:

Escherichia coli #1/H766 (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q51006, UniProt: O69434, bacterial non-heme ferritin

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.72 Å³/Da / Density % sol: 54.85 % / Description: hexagonal plate
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: ammonium sulfate, tris

-
Data collection

Diffraction

Mean temperature: 137 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å

Detector

Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 14, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.545
1	1	K, H, -L	2	0.455

Reflection

Resolution: 2.8→20 Å / Num. obs: 41284 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / R_merge(I) obs: 0.166 / Net I/av σ(I): 10.105 / Net I/σ(I): 7.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	Diffraction-ID	% possible all
2.8-2.85	4.5	0.796	2197	0.551	1	99.9
2.85-2.9	4.6	0.752		0.597	1	100
2.9-2.96	4.7	0.682		0.635	1	100
2.96-3.02	4.7	0.605		0.666	1	100
3.02-3.08	4.7	0.525		0.708	1	100
3.08-3.15	4.7	0.472		0.816	1	100
3.15-3.23	4.7	0.386		0.851	1	100
3.23-3.32	4.7	0.391		0.864	1	100
3.32-3.41	4.7	0.4		0.876	1	100
3.41-3.52	4.7	0.285		0.9	1	100
3.52-3.65	4.1	0.373		0.892	1	45.7
3.65-3.79	3.7	0.456		0.898	1	39.6
3.79-3.97	3.9	0.16		0.951	1	82.2
3.97-4.17	4.6	0.172		0.966	1	99.6
4.17-4.43	4.8	0.151		0.959	1	100
4.43-4.77	4.8	0.106		0.981	1	100
4.77-5.24	4.8	0.102		0.981	1	100
5.24-5.98	4.8	0.114		0.976	1	100
5.98-7.47	4.8	0.087		0.985	1	100
7.47-20	4.6	0.069		0.984	1	100

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	7.83 Å	19.89 Å
Translation	7.83 Å	19.89 Å

-
Processing

Software

Name	Version	Classification
HKL-2000		data scaling
PHASER	2.6.1	phasing
REFMAC	5.8.0155	refinement
PDB_EXTRACT	3.2	data extraction
HKL-2000		data reduction
HKL		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3BVF

3bvf

Resolution: 2.81→19.89 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.912 / SU B: 18.82 / SU ML: 0.177 / SU R Cruickshank DPI: 0.0592 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.074
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2247	2273	5.5 %	RANDOM
R_work	0.1771	-	-	-
obs	0.1797	38919	92.41 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 158.02 Å² / B_iso mean: 62.184 Å² / B_iso min: 18.38 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-18.25 Å²	0 Å²	0 Å²
2-	-	-18.25 Å²	0 Å²
3-	-	-	36.5 Å²

Refinement step

Cycle: final / Resolution: 2.81→19.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10884	0	0	11	10895
B_iso mean	-	-	-	38.64	-
Num. residues	-	-	-	-	1332

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.019	11126
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	10416
X-RAY DIFFRACTION	r_angle_refined_deg	1.653	1.93	15004
X-RAY DIFFRACTION	r_angle_other_deg	0.969	3	24048
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.144	5	1324
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.165	26.02	588
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.647	15	2044
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	7.879	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	1620
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	12640
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2628
X-RAY DIFFRACTION	r_mcbond_it	5.52	5.411	5320
X-RAY DIFFRACTION	r_mcbond_other	5.5	5.41	5319
X-RAY DIFFRACTION	r_mcangle_it	7.938	8.104	6636

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	11200	0.07
1	2	B	11200	0.07
2	1	A	11204	0.08
2	2	C	11204	0.08
3	1	A	11264	0.07
3	2	D	11264	0.07
4	1	A	11304	0.05
4	2	E	11304	0.05
5	1	A	11208	0.07
5	2	F	11208	0.07
6	1	A	11232	0.08
6	2	G	11232	0.08
7	1	A	11360	0.08
7	2	H	11360	0.08
8	1	B	11174	0.07
8	2	C	11174	0.07
9	1	B	11240	0.07
9	2	D	11240	0.07
10	1	B	11230	0.07
10	2	E	11230	0.07
11	1	B	11358	0.05
11	2	F	11358	0.05
12	1	B	11270	0.07
12	2	G	11270	0.07
13	1	B	11188	0.07
13	2	H	11188	0.07
14	1	C	11216	0.08
14	2	D	11216	0.08
15	1	C	11212	0.07
15	2	E	11212	0.07
16	1	C	11266	0.07
16	2	F	11266	0.07
17	1	C	11298	0.07
17	2	G	11298	0.07
18	1	C	11140	0.09
18	2	H	11140	0.09
19	1	D	11274	0.08
19	2	E	11274	0.08
20	1	D	11302	0.07
20	2	F	11302	0.07
21	1	D	11282	0.08
21	2	G	11282	0.08
22	1	D	11272	0.07
22	2	H	11272	0.07
23	1	E	11264	0.07
23	2	F	11264	0.07
24	1	E	11328	0.07
24	2	G	11328	0.07
25	1	E	11194	0.08
25	2	H	11194	0.08
26	1	F	11258	0.07
26	2	G	11258	0.07
27	1	F	11226	0.07
27	2	H	11226	0.07
28	1	G	11200	0.08
28	2	H	11200	0.08

LS refinement shell

Resolution: 2.806→2.879 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.291	208	-
R_work	0.214	2878	-
all	-	3086	-
obs	-	-	92.62 %

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	0.0503	0.0575	-0.1812	0.1215	-0.0775	0.9945	-0.004	-0.0116	0.0071	-0.0022	-0.0061	0.0037	0.0016	0.0562	0.0101	0.028	-0.0035	-0.0059	0.0156	-0.0144	0.062	-111.9234	188.0915	12.262
2	0.1733	0.0177	-0.0444	0.0632	-0.0762	0.4386	0.0015	0.0007	-0.0167	0.0005	0.0017	-0.0121	0.022	-0.0314	-0.0032	0.0319	0.012	-0.0025	0.0184	-0.0027	0.0556	-109.0572	162.8439	15.1133
3	0.1868	-0.1211	0.0503	0.4371	-0.2494	0.1504	-0.0273	0.0081	-0.0151	-0.0194	-0.0025	-0.0294	0.0055	0.001	0.0298	0.0452	0.0029	0.0029	0.0197	-0.0038	0.0331	-73.8549	160.9783	-31.8518
4	0.1593	-0.2091	0.0422	1.1378	-0.1714	0.0328	-0.0545	-0.0052	-0.0029	0.0161	0.0726	-0.0005	-0.0081	-0.0183	-0.0181	0.0452	0.0072	0.0003	0.0218	0.0134	0.0443	-96.4442	166.2189	-20.5796
5	0.3117	0.016	0.0752	0.9758	-0.3342	0.1356	-0.0414	-0.0114	0.0053	0.0207	0.0245	-0.0545	-0.0192	-0.0144	0.0169	0.0397	-0.0034	0.0199	0.0318	-0.0007	0.0192	-76.9439	196.0638	58.8502
6	0.4049	0.0175	0.1111	0.219	0.0052	0.1095	0	-0.0339	-0.0182	-0.0004	0.0554	0.006	-0.0008	-0.0096	-0.0554	0.0515	0.0045	0.0044	0.0181	0.0039	0.0332	-98.4733	187.0713	47.825
7	0.5317	0.3208	0.131	0.1939	0.0775	0.2805	0.0095	0.0778	-0.0177	0.0048	0.0491	-0.0079	0.0221	0.0176	-0.0586	0.0163	-0.0065	0.0023	0.0213	-0.0027	0.0725	-87.9684	220.8943	1.1201
8	0.3512	0.2741	0.0648	0.3204	0.0783	0.2276	0.0315	-0.0016	-0.0054	0.0161	-0.0279	-0.0017	0.0011	0.0125	-0.0036	0.0168	-0.0163	-0.0046	0.0334	0.0085	0.0555	-92.7256	217.5269	26.0318

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 166
2	X-RAY DIFFRACTION	2	B	1 - 166
3	X-RAY DIFFRACTION	3	C	1 - 166
4	X-RAY DIFFRACTION	4	D	1 - 166
5	X-RAY DIFFRACTION	5	E	1 - 166
6	X-RAY DIFFRACTION	6	F	1 - 166
7	X-RAY DIFFRACTION	7	G	1 - 166
8	X-RAY DIFFRACTION	8	H	-1 - 166

-
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://pdbjlvh1.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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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