PDB-4djz: Catalytic fragment of masp-1 in complex with its specific inhibit...

ID or keywords:

Entry

Database: PDB / ID: 4djz

Title

Catalytic fragment of masp-1 in complex with its specific inhibitor developed by directed evolution on sgci scaffold

Components

Mannan-binding lectin serine protease 1 heavy chain
Mannan-binding lectin serine protease 1 light chain
Protease inhibitor SGPI-2

Keywords

HYDROLASE/HYDROLASE INHIBITOR / in vitro evolution / specific inhibitor / hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex

Function / homology

Function and homology information

Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / negative regulation of complement activation / complement activation, lectin pathway / zymogen activation / Scavenging by Class A Receptors / Initial triggering of complement / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase inhibitor activity / calcium-dependent protein binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Schistocerca gregaria (desert locust)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Heja, D. / Harmat, V. / Fodor, K. / Wilmanns, M. / Dobo, J. / Kekesi, K.A. / Zavodszky, P. / Gal, P. / Pal, G.

Citation

Journal: J.Biol.Chem. / Year: 2012
Title: Monospecific Inhibitors Show That Both Mannan-binding Lectin-associated Serine Protease-1 (MASP-1) and -2 Are Essential for Lectin Pathway Activation and Reveal Structural Plasticity of MASP-2.
Authors: Heja, D. / Harmat, V. / Fodor, K. / Wilmanns, M. / Dobo, J. / Kekesi, K.A. / Zavodszky, P. / Gal, P. / Pal, G.

History

Deposition	Feb 3, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 25, 2012	Provider: repository / Type: Initial release
Revision 1.1	May 9, 2012	Group: Database references
Revision 1.2	Jun 27, 2012	Group: Database references
Revision 1.3	Sep 13, 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 / struct_ref_seq_dif 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 / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4djz.cif.gz	337.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4djz.ent.gz	274.9 KB	Display	PDB format
PDBx/mmJSON format	4djz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4djz_validation.pdf.gz	465.5 KB	Display	wwPDB validaton report
Full document	4djz_full_validation.pdf.gz	472.9 KB	Display
Data in XML	4djz_validation.xml.gz	30 KB	Display
Data in CIF	4djz_validation.cif.gz	41.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dj/4djz ftp://data.pdbj.org/pub/pdb/validation_reports/dj/4djz	HTTPS FTP

-
Related structure data

Related structure data	3tvjC 2xttS 3govS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3gov-d 4kkd-2 4kkd-1 4igd-d 1gpz-1 7e59-2 5ubm-d 1ezj-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	#21 - Sep 2001 Antibodies similarity (2) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #126 - Jun 2010 Epidermal Growth Factor similarity (5) #75 - Mar 2006 Tissue Factor similarity (5) #132 - Dec 2010 Adenovirus similarity (5) #231 - Mar 2019 Measles Virus Proteins similarity (5) #237 - Sep 2019 Nanodiscs and HDL similarity (1) #35 - Nov 2002 Ferritin and Transferrin similarity (1) #136 - Apr 2011 Nanobodies similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#21 - Sep 2001
Antibodies
similarity (2)
#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#126 - Jun 2010
Epidermal Growth Factor
similarity (5)
#75 - Mar 2006
Tissue Factor
similarity (5)
#132 - Dec 2010
Adenovirus
similarity (5)
#231 - Mar 2019
Measles Virus Proteins
similarity (5)
#237 - Sep 2019
Nanodiscs and HDL
similarity (1)
#35 - Nov 2002
Ferritin and Transferrin
similarity (1)
#136 - Apr 2011
Nanobodies
similarity (1)

Deposited unit

A: Mannan-binding lectin serine protease 1 heavy chain

B: Mannan-binding lectin serine protease 1 light chain

C: Mannan-binding lectin serine protease 1 heavy chain

D: Mannan-binding lectin serine protease 1 light chain

H: Protease inhibitor SGPI-2

I: Protease inhibitor SGPI-2

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

1

A: Mannan-binding lectin serine protease 1 heavy chain

B: Mannan-binding lectin serine protease 1 light chain

H: Protease inhibitor SGPI-2

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

2

C: Mannan-binding lectin serine protease 1 heavy chain

D: Mannan-binding lectin serine protease 1 light chain

I: Protease inhibitor SGPI-2

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

Unit cell

Length a, b, c (Å)	71.327, 98.404, 155.531
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	C
1	2	A
2	2	C
1	3	A
2	3	C
1	4	B
2	4	D
1	5	H
2	5	I

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	THR	THR	SER	SER	5	A	A	297 - 328	4 - 35
2	1	1	THR	THR	SER	SER	5	C	C	297 - 328	4 - 35
1	2	1	ASP	ASP	ILE	ILE	5	A	A	343 - 364	50 - 71
2	2	1	ASP	ASP	ILE	ILE	5	C	C	343 - 364	50 - 71
1	1	2	VAL	VAL	SER	SER	5	A	A	365 - 381	72 - 88
2	1	2	VAL	VAL	SER	SER	5	C	C	365 - 381	72 - 88
1	2	2	THR	THR	MET	MET	5	A	A	387 - 404	94 - 111
2	2	2	THR	THR	MET	MET	5	C	C	387 - 404	94 - 111
1	3	2	GLY	GLY	PRO	PRO	5	A	A	410 - 434	117 - 141
2	3	2	GLY	GLY	PRO	PRO	5	C	C	410 - 434	117 - 141
1	1	3	CYS	CYS	SER	SER	5	A	A	436 - 442	143 - 149
2	1	3	CYS	CYS	SER	SER	5	C	C	436 - 442	143 - 149
1	1	4	ILE	ILE	THR	THR	5	B	B	449 - 459	1 - 11
2	1	4	ILE	ILE	THR	THR	5	D	D	449 - 459	1 - 11
1	2	4	THR	THR	VAL	VAL	1	B	B	460 - 680	12 - 232
2	2	4	THR	THR	VAL	VAL	1	D	D	460 - 680	12 - 232
1	3	4	TYR	TYR	ASN	ASN	5	B	B	681 - 699	233 - 251
2	3	4	TYR	TYR	ASN	ASN	5	D	D	681 - 699	233 - 251
1	1	5	PHE	PHE	ARG	ARG	5	H	E	13 - 21	13 - 21
2	1	5	PHE	PHE	ARG	ARG	5	I	F	13 - 21	13 - 21
1	2	5	ALA	ALA	CYS	CYS	5	H	E	29 - 36	29 - 36
2	2	5	ALA	ALA	CYS	CYS	5	I	F	29 - 36	29 - 36

NCS ensembles :

ID
1
2
3
4
5

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(0.995668, 0.019617, 0.090887), (-0.011109, 0.995586, -0.093189), (-0.092314, 0.091776, 0.991491)	15.23153, 35.60927, -26.43845

Details

The asymmetric unit contains two complexes of the activated MASP-1 fragment and SGMI-1. The two chains of the MASP-1 fragment are conneced by a disulphide bridge. Complex 1: chains A,B and I; complex 2: chains C,D and H.

#1: Protein	Mannan-binding lectin serine protease 1 heavy chain / Mannan-binding lectin serine protease 1 / Complement factor MASP-3 / Complement-activating ...Mannan-binding lectin serine protease 1 / Complement factor MASP-3 / Complement-activating component of Ra-reactive factor / Mannose-binding lectin-associated serine protease 1 / MASP-1 / Mannose-binding protein-associated serine protease / Ra-reactive factor serine protease p100 / RaRF / Serine protease 5 Mass: 17508.240 Da / Num. of mol.: 2 / Fragment: Sushi domain residues 298-448 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRARF, CRARF1, MASP1, PRSS5 / Plasmid: PET-17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS References: UniProt: P48740, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Antibody	Mannan-binding lectin serine protease 1 light chain / Mannan-binding lectin serine protease 1 / Complement factor MASP-3 / Complement-activating ...Mannan-binding lectin serine protease 1 / Complement factor MASP-3 / Complement-activating component of Ra-reactive factor / Mannose-binding lectin-associated serine protease 1 / MASP-1 / Mannose-binding protein-associated serine protease / Ra-reactive factor serine protease p100 / RaRF / Serine protease 5 Mass: 28028.900 Da / Num. of mol.: 2 / Fragment: Peptidase S1 domain residues 449-699 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRARF, CRARF1, MASP1, PRSS5 / Plasmid: PET-17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS References: UniProt: P48740, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Protein/peptide	Protease inhibitor SGPI-2 / Protease inhibitor SGPI-2 / Schistocerca gregaria chymotrypsin inhibitor / SGCI Mass: 4088.627 Da / Num. of mol.: 2 / Mutation: A30F,L33R,A35L,P37Y Source method: isolated from a genetically manipulated source Details: expressed as MBP fusion protein / Source: (gene. exp.) Schistocerca gregaria (desert locust) / Gene: Y09605.1 / Plasmid: PMAL-P2G, PMAL-TEV-SGPI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR / References: UniProt: O46162
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.75 Å³/Da / Density % sol: 55.27 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M Hepes, 25% PEG1000, 0.3M NaNO3, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-1 / Wavelength: 0.97942 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2011 / Details: mirror

Radiation

Monochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97942 Å / Relative weight: 1

Reflection

Resolution: 3.2→46.91 Å / Num. all: 18731 / Num. obs: 18731 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -6 / Redundancy: 6.8 % / R_merge(I) obs: 0.238 / Net I/σ(I): 7.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Diffraction-ID	% possible all
3.2-3.37	7.1	0.925	2.3	2683	1	100
10.12-46.91	5.6	0.066	16.4	667	1	98.7

-
Processing

Software

Name	Version	Classification
DNA		data collection
PHASER		phasing
REFMAC	5.6.0117	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entries: 2XTT (structure of SGPI-1) and 3GOV

2xtt

3gov

Resolution: 3.2→46.91 Å / Cor.coef. F_o:F_c: 0.882 / Cor.coef. F_o:F_c free: 0.838 / SU B: 57.255 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.54 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS WERE NOT ADDED TO THE MODEL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27414	951	5.1 %	RANDOM
R_work	0.22808	-	-	-
all	0.23045	17687	-	-
obs	0.23045	17687	99.67 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 44.858 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.99 Å²	-0 Å²	0 Å²
2-	-	-0.29 Å²	0 Å²
3-	-	-	4.28 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→46.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6444	0	0	2	6446

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.02	6654
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.036	1.946	9103
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.583	5	865
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.701	24.286	266
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.913	15	966
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.075	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	1008
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	5126
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
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
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	216	MEDIUM POSITIONAL	0.26	0.5
1	A	171	LOOSE POSITIONAL	0.53	5
1	A	216	MEDIUM THERMAL	1.73	2
1	A	171	LOOSE THERMAL	1.87	10
2	A	240	MEDIUM POSITIONAL	0.23	0.5
2	A	213	LOOSE POSITIONAL	0.55	5
2	A	240	MEDIUM THERMAL	0.73	2
2	A	213	LOOSE THERMAL	0.91	10
3	A	28	MEDIUM POSITIONAL	0.11	0.5
3	A	23	LOOSE POSITIONAL	0.29	5
3	A	28	MEDIUM THERMAL	1.1	2
3	A	23	LOOSE THERMAL	1.05	10
4	B	120	MEDIUM POSITIONAL	0.24	0.5
4	B	126	LOOSE POSITIONAL	0.48	5
4	B	1606	TIGHT THERMAL	1.66	0.5
4	B	120	MEDIUM THERMAL	2.62	2
4	B	126	LOOSE THERMAL	2.27	10
5	H	68	MEDIUM POSITIONAL	0.16	0.5
5	H	62	LOOSE POSITIONAL	0.55	5
5	H	68	MEDIUM THERMAL	0.99	2
5	H	62	LOOSE THERMAL	1.08	10

LS refinement shell

Resolution: 3.2→3.283 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.394	51	-
R_work	0.285	1187	-
obs	-	-	99.92 %

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	11.7596	1.473	-0.168	1.3945	1.5668	3.5379	0.3819	0.6029	-0.9821	-0.1961	-0.2038	0.1128	-0.1601	-0.2325	-0.1781	0.2469	0.0089	-0.1059	0.2253	-0.1581	0.3054	-61.1031	2.4861	-22.3163
2	20.9354	3.2245	7.5787	1.3609	0.5013	3.2998	0.348	0.4115	-0.3397	0.0946	0.0084	0.1154	0.1712	0.1886	-0.3564	0.2178	-0.0038	-0.0497	0.0731	-0.0976	0.3135	-25.0683	2.5843	-12.2793
3	2.8082	0.266	0.3033	2.6076	-0.2238	3.2842	0.1168	-0.2351	0.0023	0.3145	-0.1217	-0.112	-0.0355	0.0694	0.0049	0.1134	-0.0432	0.0029	0.0566	-0.068	0.1923	6.3023	12.992	7.0426
4	15.0589	1.9431	4.1248	2.1653	2.0453	5.1959	-0.0046	0.1754	0.0422	-0.3111	-0.0017	0.2636	0.1331	-0.1476	0.0063	0.2071	-0.0742	-0.0689	0.0587	-0.0548	0.2916	-76.2674	-33.8215	0.354
5	16.3154	3.936	3.6268	3.0951	0.0884	1.545	0.2024	-0.2616	0.1583	0.1531	-0.1343	0.0033	0.1202	-0.142	-0.0681	0.1774	0.0061	-0.0399	0.1103	-0.0504	0.1749	-40.2023	-31.666	10.9991
6	3.694	0.0667	0.0672	3.334	0.0385	3.4205	0.0847	-0.596	-0.0132	0.3079	-0.0765	-0.0295	-0.0519	0.2117	-0.0081	0.1206	-0.0955	-0.0153	0.254	-0.0306	0.0239	-7.716	-18.4666	26.527
7	14.5075	-1.1293	-3.4814	4.1611	2.2104	1.8554	-0.4916	-0.9182	0.3921	0.7013	0.3908	0.0382	0.1761	0.4801	0.1009	0.9166	-0.3918	-0.1713	0.5068	-0.2372	0.7405	17.0804	24.2446	19.0569
8	1.0899	-0.9603	-3.9046	1.0231	3.7416	14.6067	0.1862	-0.402	0.3066	-0.0017	0.4096	-0.0577	-0.613	1.684	-0.5958	0.6333	-0.287	-0.0605	0.7501	-0.0898	0.6928	3.286	-5.5757	35.7595

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	297 - 364
2	X-RAY DIFFRACTION	2	A	365 - 434
3	X-RAY DIFFRACTION	3	B	449 - 699
4	X-RAY DIFFRACTION	3	A	435 - 444
5	X-RAY DIFFRACTION	4	C	297 - 364
6	X-RAY DIFFRACTION	5	C	365 - 434
7	X-RAY DIFFRACTION	6	D	449 - 699
8	X-RAY DIFFRACTION	6	C	435 - 444
9	X-RAY DIFFRACTION	7	H	5 - 38
10	X-RAY DIFFRACTION	8	I	6 - 38

-
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

-
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