PDB-6s9n: Designed Armadillo Repeat protein Lock2 fused to target peptide K...

ID or keywords:

Entry

Database: PDB / ID: 6s9n

Title

Designed Armadillo Repeat protein Lock2 fused to target peptide KRKRKAKLSF

Components

Lock2_KRKRKAKLSF

Keywords

DE NOVO PROTEIN / peptide binder / repeat protein / designed armadillo repeat protein

Function / homology

Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Ernst, P. / Zosel, F. / Reichen, C. / Schuler, B. / Pluckthun, A.

Citation

Journal: Acs Chem.Biol. / Year: 2020
Title: Structure-Guided Design of a Peptide Lock for Modular Peptide Binders.
Authors: Ernst, P. / Zosel, F. / Reichen, C. / Nettels, D. / Schuler, B. / Pluckthun, A.

History

Deposition	Jul 15, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 19, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 4, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	May 15, 2024	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_struct_conn_angle / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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PDBx/mmCIF format	6s9n.cif.gz	666.4 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s9/6s9n ftp://data.pdbj.org/pub/pdb/validation_reports/s9/6s9n	HTTPS FTP

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Related structure data

Related structure data	6s9lC 6s9mC 6s9oC 6s9pC C: citing same article (ref.)
Similar structure data	6s9m-5 6s9m-3 6s9m-2 5aei-3 6s9l-2 5mfn-1 3zfw-2 5aei-2 4l7m-1 4v3o-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) 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 - HomologyF&H Search

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Lock2_KRKRKAKLSF

B: Lock2_KRKRKAKLSF

C: Lock2_KRKRKAKLSF

D: Lock2_KRKRKAKLSF

E: Lock2_KRKRKAKLSF

F: Lock2_KRKRKAKLSF

hetero molecules

189 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Lock2_KRKRKAKLSF

hetero molecules

defined by author
Evidence: assay for oligomerization, fluorescence anisotropy and FRET kinetic experiments
31.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Lock2_KRKRKAKLSF

hetero molecules

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

3

C: Lock2_KRKRKAKLSF

hetero molecules

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

4

D: Lock2_KRKRKAKLSF

hetero molecules

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

5

E: Lock2_KRKRKAKLSF

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

6

F: Lock2_KRKRKAKLSF

hetero molecules

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

Unit cell

Length a, b, c (Å)	55.260, 85.500, 194.030
Angle α, β, γ (deg.)	90.000, 96.330, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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	SER	SER	SER	SER	A	A	11 - 308	4 - 301
2	1	SER	SER	SER	SER	B	B	11 - 308	4 - 301
1	2	SER	SER	SER	SER	A	A	11 - 308	4 - 301
2	2	SER	SER	SER	SER	C	C	11 - 308	4 - 301
1	3	SER	SER	SER	SER	A	A	11 - 308	4 - 301
2	3	SER	SER	SER	SER	D	D	11 - 308	4 - 301
1	4	GLY	GLY	SER	SER	A	A	10 - 308	3 - 301
2	4	GLY	GLY	SER	SER	E	E	10 - 308	3 - 301
1	5	SER	SER	SER	SER	A	A	11 - 308	4 - 301
2	5	SER	SER	SER	SER	F	F	11 - 308	4 - 301
1	6	SER	SER	PHE	PHE	B	B	11 - 309	4 - 302
2	6	SER	SER	PHE	PHE	C	C	11 - 309	4 - 302
1	7	SER	SER	PHE	PHE	B	B	11 - 309	4 - 302
2	7	SER	SER	PHE	PHE	D	D	11 - 309	4 - 302
1	8	SER	SER	SER	SER	B	B	11 - 308	4 - 301
2	8	SER	SER	SER	SER	E	E	11 - 308	4 - 301
1	9	SER	SER	PHE	PHE	B	B	11 - 309	4 - 302
2	9	SER	SER	PHE	PHE	F	F	11 - 309	4 - 302
1	10	SER	SER	PHE	PHE	C	C	11 - 309	4 - 302
2	10	SER	SER	PHE	PHE	D	D	11 - 309	4 - 302
1	11	SER	SER	SER	SER	C	C	11 - 308	4 - 301
2	11	SER	SER	SER	SER	E	E	11 - 308	4 - 301
1	12	SER	SER	PHE	PHE	C	C	11 - 309	4 - 302
2	12	SER	SER	PHE	PHE	F	F	11 - 309	4 - 302
1	13	SER	SER	SER	SER	D	D	11 - 308	4 - 301
2	13	SER	SER	SER	SER	E	E	11 - 308	4 - 301
1	14	SER	SER	PHE	PHE	D	D	11 - 309	4 - 302
2	14	SER	SER	PHE	PHE	F	F	11 - 309	4 - 302
1	15	SER	SER	SER	SER	E	E	11 - 308	4 - 301
2	15	SER	SER	SER	SER	F	F	11 - 308	4 - 301

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	Lock2_KRKRKAKLSF Mass: 31449.340 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1174 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.43 Å³/Da / Density % sol: 49.34 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion Details: 22.5 % PEG smear medium 0.1 M CaCl2, 0.1 M MgCl2, 0.1 M Pipes pH 7

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06SA / Wavelength: 1.000041 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2017

Radiation

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

Radiation wavelength

Wavelength: 1.000041 Å / Relative weight: 1

Reflection

Resolution: 2.1→45.61 Å / Num. obs: 199596 / % possible obs: 96.8 % / Redundancy: 2.793 % / B_iso Wilson estimate: 34.209 Å² / CC_1/2: 0.972 / R_merge(I) obs: 0.213 / R_rim(I) all: 0.264 / Χ²: 0.902 / Net I/σ(I): 4.89 / Num. measured all: 557469 / Scaling rejects: 1136

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.1-2.15	2.375	0.998	0.96	34129	15244	14371	0.507	1.252	94.3
2.15-2.21	2.532	0.864	1.2	36709	14972	14496	0.617	1.072	96.8
2.21-2.28	2.863	0.801	1.43	40623	14353	14188	0.675	0.975	98.9
2.28-2.35	2.861	0.654	1.74	39482	13974	13798	0.746	0.797	98.7
2.35-2.42	2.863	0.541	2.11	38770	13722	13542	0.798	0.66	98.7
2.42-2.51	2.865	0.467	2.4	36837	13164	12859	0.862	0.572	97.7
2.51-2.6	2.866	0.435	2.62	35607	12695	12424	0.854	0.532	97.9
2.6-2.71	2.899	0.425	2.83	34331	12142	11842	0.851	0.52	97.5
2.71-2.83	2.858	0.342	3.4	32543	11779	11386	0.897	0.42	96.7
2.83-2.97	2.846	0.29	4.04	30273	11178	10636	0.913	0.358	95.2
2.97-3.13	2.847	0.267	4.85	28929	10596	10160	0.922	0.33	95.9
3.13-3.32	2.813	0.232	6.04	27400	10136	9739	0.929	0.29	96.1
3.32-3.55	2.766	0.197	7.37	25127	9448	9084	0.928	0.247	96.1
3.55-3.83	2.658	0.156	9.33	22137	8784	8330	0.94	0.198	94.8
3.83-4.2	2.407	0.124	10.71	18102	8140	7520	0.956	0.158	92.4
4.2-4.7	3.031	0.106	14.2	21763	7328	7180	0.973	0.131	98
4.7-5.42	3.061	0.124	12.48	19587	6467	6398	0.969	0.154	98.9
5.42-6.64	3.057	0.127	11.71	16459	5455	5384	0.966	0.158	98.7
6.64-9.39	3.018	0.067	16.86	12452	4231	4126	0.993	0.083	97.5
9.39-45.61	2.911	0.054	21.07	6209	2289	2133	0.994	0.066	93.2

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
REFMAC	5.8.0189	refinement
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→45.61 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.917 / SU B: 15.527 / SU ML: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.216
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2616	5177	5 %	RANDOM
R_work	0.2234	-	-	-
obs	0.2253	98361	98.65 %	-

Solvent computation

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

Displacement parameters

B_iso max: 113 Å² / B_iso mean: 33.651 Å² / B_iso min: 11.79 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.22 Å²	-0 Å²	-1.01 Å²
2-	-	-0.72 Å²	0 Å²
3-	-	-	-0.27 Å²

Refinement step

Cycle: final / Resolution: 2.1→45.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13191	0	22	1174	14387
B_iso mean	-	-	38.2	40.38	-
Num. residues	-	-	-	-	1797

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.019	13444
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	12674
X-RAY DIFFRACTION	r_angle_refined_deg	1.8	1.981	18259
X-RAY DIFFRACTION	r_angle_other_deg	1.066	3	29718
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.149	5	1815
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	43.034	28.583	593
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.992	15	2384
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.326	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.109	0.2	2155
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	15362
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2020

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	18460	0.08
1	2	B	18460	0.08
2	1	A	18294	0.09
2	2	C	18294	0.09
3	1	A	18294	0.08
3	2	D	18294	0.08
4	1	A	18242	0.09
4	2	E	18242	0.09
5	1	A	18136	0.09
5	2	F	18136	0.09
6	1	B	18548	0.08
6	2	C	18548	0.08
7	1	B	18462	0.08
7	2	D	18462	0.08
8	1	B	18340	0.08
8	2	E	18340	0.08
9	1	B	18356	0.09
9	2	F	18356	0.09
10	1	C	18528	0.08
10	2	D	18528	0.08
11	1	C	18404	0.08
11	2	E	18404	0.08
12	1	C	18500	0.09
12	2	F	18500	0.09
13	1	D	18284	0.08
13	2	E	18284	0.08
14	1	D	18286	0.09
14	2	F	18286	0.09
15	1	E	18130	0.09
15	2	F	18130	0.09

LS refinement shell

Resolution: 2.1→2.154 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.346	369	-
R_work	0.341	7010	-
all	-	7379	-
obs	-	-	95.82 %

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	0.0485	0.1195	-0.0741	0.3824	-0.0371	0.3558	0.0003	-0.0131	-0.0098	0.0275	-0.0291	-0.0151	0.041	-0.0035	0.0288	0.2832	0.0079	0.0976	0.2462	0.0095	0.0358	-2.0912	35.6265	-47.7333
2	0.0885	0.166	-0.0418	0.3636	-0.2272	0.5648	-0.0105	-0.0018	-0.0097	0.0176	-0.0482	-0.0244	-0.0407	0.0024	0.0586	0.3279	0.0065	0.1003	0.221	0.0026	0.0395	-24.8031	-8.2806	-16.0646
3	0.2809	-0.208	0.2839	0.2812	0.0035	0.6473	-0.005	0.0139	0.0224	0.0016	-0.0212	-0.011	-0.0315	-0.0081	0.0262	0.3006	0.0025	0.1169	0.2562	-0.0033	0.0482	-30.0312	-16.7742	-52.0557
4	0.2085	-0.1551	-0.0079	0.128	0.1364	1.7218	0.0122	0.0754	0.0544	0.0294	-0.0581	-0.0315	0.1665	-0.2206	0.0458	0.3434	-0.025	0.0761	0.2999	0.0149	0.0299	11.6323	38.8608	-12.8961
5	0.011	-0.018	-0.0744	0.2061	-0.1075	0.8038	-0.0097	-0.008	-0.008	-0.0268	-0.0004	0.0436	0.0998	0.0456	0.0101	0.3272	0.0213	0.0945	0.2406	-0.0129	0.042	-8.2965	26.7378	-78.0131
6	0.5301	-0.0209	0.5399	0.1554	0.0838	0.6417	-0.0694	0.02	0.036	-0.0385	0.0301	-0.0265	-0.023	0.0186	0.0393	0.3311	0.0024	0.0992	0.2502	0.012	0.0373	-28.6275	-22.9539	-83.6393

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 309
2	X-RAY DIFFRACTION	2	B	11 - 309
3	X-RAY DIFFRACTION	3	C	11 - 309
4	X-RAY DIFFRACTION	4	D	11 - 309
5	X-RAY DIFFRACTION	5	E	9 - 309
6	X-RAY DIFFRACTION	6	F	11 - 309

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