PDB-4mec: Crystal structure of RAT Heme oxygenase-1 in complex with ZN(II)-...

ID or keywords:

Entry

Database: PDB / ID: 4mec

Title

Crystal structure of RAT Heme oxygenase-1 in complex with ZN(II)-Protoporphyrin IX

Components

Heme oxygenase 1

Keywords

OXIDOREDUCTASE / All Alpha / Oxygenase / Heme Binding

Function / homology

Function and homology information

arachidonate omega-hydroxylase activity / Regulation of HMOX1 expression and activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonate / heme metabolic process / heme oxygenase (biliverdin-producing) ...arachidonate omega-hydroxylase activity / Regulation of HMOX1 expression and activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonate / heme metabolic process / heme oxygenase (biliverdin-producing) / heme oxidation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / heme oxygenase (decyclizing) activity / negative regulation of muscle cell apoptotic process / wound healing involved in inflammatory response / cellular response to cisplatin / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / cellular response to arsenic-containing substance / negative regulation of epithelial cell apoptotic process / cellular response to nutrient / heme catabolic process / negative regulation of mast cell cytokine production / positive regulation of epithelial cell apoptotic process / phospholipase D activity / epithelial cell apoptotic process / negative regulation of ferroptosis / erythrocyte homeostasis / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of macroautophagy / small GTPase-mediated signal transduction / cellular response to cadmium ion / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of macroautophagy / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / phospholipid metabolic process / liver regeneration / response to nicotine / positive regulation of smooth muscle cell proliferation / macroautophagy / negative regulation of smooth muscle cell proliferation / response to hydrogen peroxide / caveola / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / response to estrogen / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of angiogenesis / cellular response to heat / angiogenesis / negative regulation of neuron apoptotic process / response to oxidative stress / intracellular iron ion homeostasis / response to hypoxia / intracellular signal transduction / response to xenobiotic stimulus / negative regulation of cell population proliferation / heme binding / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / structural molecule activity / enzyme binding / endoplasmic reticulum / protein homodimerization activity / metal ion binding / identical protein binding / nucleus / cytosol
Similarity search - Function

Biological species

Rattus norvegicus (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Sugishima, M.

Citation

Journal: Biochemistry / Year: 2015
Title: Distal regulation of heme binding of heme oxygenase-1 mediated by conformational fluctuations
Authors: Harada, E. / Sugishima, M. / Harada, J. / Fukuyama, K. / Sugase, K.

History

Deposition	Aug 26, 2013	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Aug 27, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jun 1, 2016	Group: Database references
Revision 1.2	Nov 8, 2023	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_conn / struct_ncs_dom_lim / struct_site 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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4mec.cif.gz	595.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4mec.ent.gz	498.3 KB	Display	PDB format
PDBx/mmJSON format	4mec.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/me/4mec ftp://data.pdbj.org/pub/pdb/validation_reports/me/4mec	HTTPS FTP

-
Related structure data

Related structure data	1dveS S: Starting model for refinement
Similar structure data	1s13-2 6eha-2 1oze-2 1ubb-d 1n3u-1 4g7l-d 1ozw-1 1xk0-1 1xjz-1 3k4f-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) 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

1dveS

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#167 - Nov 2013 SNARE Proteins similarity (1)

Deposited unit

A: Heme oxygenase 1

B: Heme oxygenase 1

C: Heme oxygenase 1

D: Heme oxygenase 1

E: Heme oxygenase 1

F: Heme oxygenase 1

G: Heme oxygenase 1

hetero molecules

192 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Heme oxygenase 1

hetero molecules

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

2

B: Heme oxygenase 1

hetero molecules

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

3

C: Heme oxygenase 1

hetero molecules

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

4

D: Heme oxygenase 1

hetero molecules

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

5

E: Heme oxygenase 1

hetero molecules

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

6

F: Heme oxygenase 1

hetero molecules

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

7

G: Heme oxygenase 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	40.059, 73.167, 148.757
Angle α, β, γ (deg.)	86.41, 87.62, 86.25
Int Tables number	1
Space group name H-M	P1

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	GLN	GLN	THR	THR	A	A	11 - 222	11 - 222
2	1	GLN	GLN	THR	THR	B	B	11 - 222	11 - 222
1	2	GLN	GLN	THR	THR	A	A	11 - 222	11 - 222
2	2	GLN	GLN	THR	THR	C	C	11 - 222	11 - 222
1	3	SER	SER	THR	THR	A	A	10 - 222	10 - 222
2	3	SER	SER	THR	THR	D	D	10 - 222	10 - 222
1	4	SER	SER	GLU	GLU	A	A	10 - 223	10 - 223
2	4	SER	SER	GLU	GLU	E	E	10 - 223	10 - 223
1	5	ASP	ASP	GLU	GLU	A	A	12 - 212	12 - 212
2	5	ASP	ASP	GLU	GLU	F	F	12 - 212	12 - 212
1	6	ASP	ASP	ALA	ALA	A	A	12 - 219	12 - 219
2	6	ASP	ASP	ALA	ALA	G	G	12 - 219	12 - 219
1	7	GLN	GLN	THR	THR	B	B	11 - 222	11 - 222
2	7	GLN	GLN	THR	THR	C	C	11 - 222	11 - 222
1	8	GLN	GLN	THR	THR	B	B	11 - 222	11 - 222
2	8	GLN	GLN	THR	THR	D	D	11 - 222	11 - 222
1	9	GLN	GLN	THR	THR	B	B	11 - 222	11 - 222
2	9	GLN	GLN	THR	THR	E	E	11 - 222	11 - 222
1	10	ASP	ASP	GLU	GLU	B	B	12 - 212	12 - 212
2	10	ASP	ASP	GLU	GLU	F	F	12 - 212	12 - 212
1	11	ASP	ASP	ALA	ALA	B	B	12 - 219	12 - 219
2	11	ASP	ASP	ALA	ALA	G	G	12 - 219	12 - 219
1	12	GLN	GLN	THR	THR	C	C	11 - 222	11 - 222
2	12	GLN	GLN	THR	THR	D	D	11 - 222	11 - 222
1	13	GLN	GLN	GLU	GLU	C	C	11 - 223	11 - 223
2	13	GLN	GLN	GLU	GLU	E	E	11 - 223	11 - 223
1	14	ASP	ASP	GLU	GLU	C	C	12 - 212	12 - 212
2	14	ASP	ASP	GLU	GLU	F	F	12 - 212	12 - 212
1	15	ASP	ASP	ALA	ALA	C	C	12 - 219	12 - 219
2	15	ASP	ASP	ALA	ALA	G	G	12 - 219	12 - 219
1	16	SER	SER	GLU	GLU	D	D	10 - 223	10 - 223
2	16	SER	SER	GLU	GLU	E	E	10 - 223	10 - 223
1	17	ASP	ASP	GLU	GLU	D	D	12 - 212	12 - 212
2	17	ASP	ASP	GLU	GLU	F	F	12 - 212	12 - 212
1	18	ASP	ASP	ALA	ALA	D	D	12 - 219	12 - 219
2	18	ASP	ASP	ALA	ALA	G	G	12 - 219	12 - 219
1	19	ASP	ASP	GLU	GLU	E	E	12 - 212	12 - 212
2	19	ASP	ASP	GLU	GLU	F	F	12 - 212	12 - 212
1	20	ASP	ASP	ALA	ALA	E	E	12 - 219	12 - 219
2	20	ASP	ASP	ALA	ALA	G	G	12 - 219	12 - 219
1	21	ASP	ASP	GLU	GLU	F	F	12 - 212	12 - 212
2	21	ASP	ASP	GLU	GLU	G	G	12 - 212	12 - 212

NCS ensembles :

#1: Protein	Heme oxygenase 1 / HO-1 / HSP32 Mass: 26833.406 Da / Num. of mol.: 7 / Fragment: UNP residues 1-232 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hmox1 / Plasmid: PET21A / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P06762, heme oxygenase (biliverdin-producing)
#2: Chemical	ChemComp-ZNH / PROTOPORPHYRIN IX CONTAINING ZN Mass: 626.051 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃₄H₃₂N₄O₄Zn

#1: Protein

Heme oxygenase 1 / HO-1 / HSP32

Mass: 26833.406 Da / Num. of mol.: 7 / Fragment: UNP residues 1-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Rattus norvegicus (Norway rat) / Gene: Hmox1 / Plasmid: PET21A / Production host:

Escherichia Coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P06762, heme oxygenase (biliverdin-producing)

#2: Chemical

ChemComp-ZNH / PROTOPORPHYRIN IX CONTAINING ZN

Mass: 626.051 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃₄H₃₂N₄O₄Zn

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.31 Å³/Da / Density % sol: 46.75 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 4000, 0.2M Sodium Acetate, 0.1M Tris-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SPring-8

/ Beamline: BL38B1 / Wavelength: 1.2 / Wavelength: 1.2 Å

Detector

Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 21, 2009

Radiation

Monochromator: SI(111) DOUBLE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.2	1
2	1.2	1

Reflection

Resolution: 3.2→50 Å / Num. all: 27085 / Num. obs: 27085 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / R_sym value: 0.06 / Net I/σ(I): 14.4

Reflection shell

Resolution: 3.2→3.31 Å / Mean I/σ(I) obs: 2.7 / R_sym value: 0.27 / % possible all: 94

-
Processing

Software

Name	Version	Classification
MOLREP		phasing
REFMAC	5.6.0117	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DVE

1dve

Resolution: 3.2→38.94 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.913 / SU B: 81.531 / SU ML: 0.627 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.658 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.299	1347	5 %	RANDOM
R_work	0.249	-	-	-
all	0.252	25650	-	-
obs	0.252	25650	96.8 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 127.92 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.22 Å²	0.23 Å²	0.05 Å²
2-	-	-0.03 Å²	-0.13 Å²
3-	-	-	0.24 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→38.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11320	0	185	0	11505

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.02	11833
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.865	2.002	16182
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.757	5	1466
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.551	24.044	544
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.175	15	1724
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.552	15	61
X-RAY DIFFRACTION	r_chiral_restr	0.054	0.2	1740
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	9266
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_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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 / Type: interatomic distance / Weight position: 0.05

LS refinement shell

Resolution: 3.19→3.28 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.434	98	-
R_work	0.318	1662	-
obs	-	-	85.19 %

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	3.1049	1.0511	0.7162	3.7672	1.6622	6.64	0.008	0.2354	0.23	-0.0511	0.1648	0.0246	-0.2302	-0.3633	-0.1728	0.1949	0.2513	0.0111	0.3655	-0.0648	0.824	0.096	-0.454	0.323
2	5.276	1.9222	1.387	4.0794	1.0718	4.4427	0.0835	-0.0245	-0.6656	0.4013	-0.0686	0.1152	0.2889	-0.2078	-0.0149	0.3187	0.3044	0.0402	0.398	-0.0071	0.8338	-20.626	-27.004	17
3	5.3468	-0.5237	2.4821	2.1293	0.0011	6.3898	0.0953	-0.2628	-0.0084	0.4461	-0.1645	0.2562	-0.1784	0.0311	0.0692	0.5406	0.0933	0.129	0.1097	-0.1175	0.7505	-29.726	-52.76	39.87
4	3.5194	1.4254	1.1184	3.7753	0.5952	12.0391	0.4089	-0.1056	0.0269	1.2273	0.0484	0.1249	1.213	-0.2481	-0.4573	1.2632	0.1376	0.0297	0.0718	-0.1032	0.4148	-46.13	-84.273	56.432
5	2.7842	0.2211	-1.1508	2.4236	2.9861	15.8919	0.4228	-0.0626	0.2479	-1.1141	0.0363	0.1457	1.1596	-0.0248	-0.459	1.6293	0.1784	-0.3046	0.1565	-0.0762	0.3694	-37.667	-79.101	103.433
6	6.3128	2.143	5.1093	2.5365	1.6513	15.3038	-0.161	0.4183	0.0198	0.4292	0.1216	-0.0492	0.5567	0.1596	0.0393	0.9082	0.1133	-0.1328	0.1808	-0.2323	0.3832	-46.158	-117.938	77.868
7	2.4132	-0.4009	3.8323	4.2783	4.5042	17.1795	0.2339	0.0463	0.0367	-0.991	-0.4416	0.1717	0.969	0.2024	0.2076	1.0859	0.1658	-0.033	0.2655	-0.1217	0.5636	-31.568	-111.321	123.642

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 223
2	X-RAY DIFFRACTION	1	A	300
3	X-RAY DIFFRACTION	2	B	11 - 225
4	X-RAY DIFFRACTION	2	B	300
5	X-RAY DIFFRACTION	3	C	11 - 223
6	X-RAY DIFFRACTION	3	C	300
7	X-RAY DIFFRACTION	4	D	9 - 223
8	X-RAY DIFFRACTION	4	D	300
9	X-RAY DIFFRACTION	5	E	10 - 223
10	X-RAY DIFFRACTION	5	E	300
11	X-RAY DIFFRACTION	6	F	12 - 213
12	X-RAY DIFFRACTION	6	F	300
13	X-RAY DIFFRACTION	7	G	12 - 220
14	X-RAY DIFFRACTION	7	G	300

-
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