PDB-7tj4: Structure of the S. aureus amidase LytH and activator ActH extrac...

ID or keywords:

Entry

Database: PDB / ID: 7tj4

Title

Structure of the S. aureus amidase LytH and activator ActH extracellular domains

Components

ActH
LytH

Keywords

HYDROLASE / amidase

Function / homology

Function and homology information

rhomboid protease / N-acetylmuramoyl-L-alanine amidase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / peptidoglycan catabolic process / cell wall organization / membrane => GO:0016020 / serine-type endopeptidase activity / extracellular region
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.8 Å

Authors

Page, J.E. / Skiba, M.A. / Kruse, A.C. / Walker, S.

Funding support

United States, 4items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01 AI139011	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01 AI148752	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	T32 GM007753	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	F30 AI156972	United States

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Metal cofactor stabilization by a partner protein is a widespread strategy employed for amidase activation.
Authors: Page, J.E. / Skiba, M.A. / Do, T. / Kruse, A.C. / Walker, S.

History

Deposition	Jan 14, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 6, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2022	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jul 20, 2022	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7tj4.cif.gz	308.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7tj4.ent.gz	208 KB	Display	PDB format
PDBx/mmJSON format	7tj4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7tj4_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	7tj4_full_validation.pdf.gz	1.2 MB	Display
Data in XML	7tj4_validation.xml.gz	25 KB	Display
Data in CIF	7tj4_validation.cif.gz	36.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tj/7tj4 ftp://data.pdbj.org/pub/pdb/validation_reports/tj/7tj4	HTTPS FTP

-
Related structure data

Related structure data	4rn7S S: Starting model for refinement
Similar structure data	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	#140 - Aug 2011 Rhomboid Protease GlpG similarity (4) #141 - Sep 2011 O-GlcNAc Transferase similarity (2) #166 - Oct 2013 Proteasome similarity (2) #230 - Feb 2019 Initiation Factor eIF4E similarity (2)

Deposited unit

A: ActH

B: LytH

C: ActH

D: LytH

hetero molecules

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

1

A: ActH

B: LytH

hetero molecules

defined by author&software
Evidence: gel filtration
33.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: ActH

D: LytH

hetero molecules

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

Unit cell

Length a, b, c (Å)	44.600, 71.260, 190.400
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁
Space group name Hall	P22ab(z,x,y)
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y+1/2,-z+1/2 #4: -x,-y+1/2,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	B-734- HOH

#1: Protein	ActH / Rhomboid protease GluP Mass: 14010.696 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gluP, DD547_01635, RK64_08320 / Plasmid: pETDUET-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2X3YEX3, rhomboid protease
#2: Protein	LytH Mass: 19681.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: lytH / Plasmid: pETDUET-1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O32421, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.27 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 6.3 / Details: 0.1 M ammonium nitrate, 22% (w/v) PEG 3350

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 1.033 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 18, 2021

Radiation

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

Radiation wavelength

Wavelength: 1.033 Å / Relative weight: 1

Reflection

Resolution: 1.8→47.39 Å / Num. obs: 55848 / % possible obs: 97.1 % / Redundancy: 13.106 % / B_iso Wilson estimate: 41.74 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.142 / R_rim(I) all: 0.147 / Χ²: 0.782 / Net I/σ(I): 12

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.8-1.91	12.917	3.542	0.93	8653	0.587	3.687	94.8
1.91-2.04	13.442	1.762	2.16	8305	0.863	1.831	96.2
2.04-2.2	13.546	0.963	4.09	7781	0.939	1.001	97.1
2.2-2.41	13.17	0.542	7.02	7192	0.973	0.564	97
2.41-2.7	13.573	0.268	11.6	6606	0.992	0.279	98
2.7-3.11	13.19	0.145	18.06	5919	0.996	0.151	98.4
3.11-3.81	12.402	0.088	27.49	5040	0.998	0.092	98.7
3.81-5.37	12.582	0.063	37.16	3988	0.998	0.066	99.1
5.37-47.39	11.843	0.053	38.82	2364	0.998	0.056	98.3

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
PHENIX	1.19.2-4158-000	refinement
XDS		data reduction
XSCALE		data scaling
PHASER	2.8.1	phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4RN7

4rn7

Resolution: 1.8→47.39 Å / SU ML: 0.3312 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.7365
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.229	1993	3.58 %
R_work	0.1859	53660	-
obs	0.1875	55653	96.88 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 41.33 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→47.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4717	0	2	319	5038

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0136	4781
X-RAY DIFFRACTION	f_angle_d	1.2502	6445
X-RAY DIFFRACTION	f_chiral_restr	0.0667	721
X-RAY DIFFRACTION	f_plane_restr	0.0098	839
X-RAY DIFFRACTION	f_dihedral_angle_d	14.6418	1823

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.8-1.84	0.5008	133	0.4888	3530	X-RAY DIFFRACTION	90.65
1.84-1.89	0.4417	136	0.3965	3686	X-RAY DIFFRACTION	95.24
1.89-1.95	0.4736	139	0.4064	3667	X-RAY DIFFRACTION	93.79
1.95-2.01	0.2934	140	0.273	3760	X-RAY DIFFRACTION	96.63
2.01-2.08	0.2989	140	0.2595	3765	X-RAY DIFFRACTION	96.75
2.08-2.17	0.2303	140	0.2267	3813	X-RAY DIFFRACTION	97.22
2.17-2.27	0.3064	140	0.2465	3809	X-RAY DIFFRACTION	96.96
2.27-2.39	0.2922	143	0.2078	3842	X-RAY DIFFRACTION	97.67
2.39-2.54	0.2764	143	0.1893	3859	X-RAY DIFFRACTION	97.75
2.54-2.73	0.2365	144	0.1872	3865	X-RAY DIFFRACTION	98.19
2.73-3.01	0.1931	146	0.1862	3928	X-RAY DIFFRACTION	98.33
3.01-3.44	0.2447	145	0.1744	3935	X-RAY DIFFRACTION	98.77
3.44-4.33	0.1984	147	0.1411	3991	X-RAY DIFFRACTION	98.95
4.33-47.39	0.1583	157	0.1417	4210	X-RAY DIFFRACTION	99.09

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	0.61505214025	0.241006883328	-1.88502984964	0.26223603661	-0.49738348443	6.17987830412	0.794211066328	0.953563686404	0.988331211627	-0.417311919579	-0.106978623852	0.101345047343	-1.6009591448	-1.49552769824	-0.58288461144	0.965173107639	0.165881785182	0.0425884311413	0.837064846856	0.262318310936	0.687645313319	-16.0374002666	68.3860606296	120.583339004
2	6.73217644271	2.47028359479	-1.09236062324	8.10640672241	-3.22022851362	8.55234709052	0.0334285254327	-0.113353700848	0.334650703203	0.381341346347	-0.293760156771	-0.509866395989	-0.129699260428	0.823173196878	0.253065335257	0.274309089007	-0.0242403184813	-0.0959766753679	0.288168498807	-0.0239713687442	0.347445387941	3.24968411043	61.3395732312	113.957604959
3	5.42172855492	1.45990317781	-0.931503784671	3.13433818842	-0.806630408181	4.10704452624	-0.116453990798	-0.178144716315	-0.19596207196	0.167831862771	-0.0352939611452	-0.169828186654	0.632693262344	0.199294824428	0.110367664134	0.358219347834	0.0209847923208	-0.0088795455795	0.195383837041	0.030799036261	0.238879946506	-4.81277409918	49.3113744433	112.49204494
4	4.67598181621	1.6105127913	0.00816528081526	6.94499530599	1.49406549091	0.356771700591	-0.501173629294	-0.116795351589	-0.493050206046	0.460611002544	0.0654989482125	0.54781693647	1.29741499906	-0.461547524809	0.388219088544	0.663524482925	-0.263998789027	0.0737468879374	0.500771136898	0.0577749572897	0.339956993217	-17.1409864629	42.2399920586	110.885206062
5	3.57178483744	0.330693327846	1.98558732796	5.51653838769	0.530913372563	4.37581396998	-0.118197132086	0.484767197498	-0.116893518167	0.192816939548	0.180700306431	0.172300270213	0.583133746718	-1.51826542012	-0.00137803167574	0.406728678392	-0.223227274023	0.0820707022014	0.735001287862	0.0326325938172	0.372867231115	-22.5309999979	49.4576737391	107.066701849
6	3.9716975861	0.159405067796	-1.71158922995	2.11448826924	0.0862066644913	5.42834629196	0.0783508027374	-0.147153615341	0.0755973736059	0.0511891614336	0.0361876909629	0.0249990729046	-0.170868609242	-0.239264534517	-0.132526378796	0.198774136875	-0.0244490131551	-0.014989584771	0.190671295909	0.00654221963751	0.218399840099	-5.64253216041	64.9745396494	89.1224825436
7	7.49045237863	-2.46777742324	-1.95925820943	6.33888615714	-0.761634435922	8.78659589003	0.390585868011	0.409565964408	0.653703225312	-0.560027508135	-0.187646049036	-0.162608386117	-0.488990766596	0.164289506018	-0.145509770002	0.283870264849	-0.0392303494602	-0.0108012683179	0.222342285225	-0.00691467390197	0.22817776519	-1.86376501016	62.372400192	79.3049929694
8	2.21456218138	0.836929898864	-1.33516994108	0.801714440899	-0.490066513041	2.2279541111	-0.0991718649179	0.234522474361	-0.0821915405925	-0.0719466056933	0.0722505826876	0.0948045505836	0.702723901099	-0.637526375246	0.0469499065988	0.322114629547	-0.0789988273607	-0.0229094624734	0.308047490383	0.000939674779608	0.284669822656	-5.16749972384	48.8355005733	86.4151118079
9	1.50475028187	-0.243576813422	-2.77834770766	1.1060641341	0.500873289433	6.84625153916	-0.0129984440194	0.140114296157	-0.0906606640719	-0.0330994234713	0.080525984544	0.0332658875205	0.344409755326	-0.397046823653	-0.0403973485957	0.206375734008	-0.0380810091477	-0.0546475974386	0.230678390154	0.0282793119648	0.257962401838	-4.48263825259	53.947148031	89.8487116609
10	4.69585786429	1.69721847258	0.19394116364	5.09444657407	-0.381500746909	4.53162593354	0.311332460952	-1.78220742595	-0.838748662018	1.58116346266	0.333245664961	0.546137894129	-0.290534438833	-0.869908365017	-0.599440627648	0.941168975341	0.0540396693332	0.102865859708	0.739555460499	0.123825701498	0.575040193793	-2.5820622946	41.8558725833	32.0877767751
11	5.15179532728	0.0502487451617	-0.303051375791	6.40392771519	-0.968491751103	8.3781934823	-0.133894041346	0.436093846613	-0.844139647683	-0.538417570727	0.0092905700368	-0.378941710816	1.16766286702	0.716309748441	0.146635267638	0.555126549403	0.101359659624	0.0606656922654	0.374210246411	-0.107732986063	0.420040377231	17.614568456	41.3652390035	37.0415098812
12	4.9527772585	-2.3472473136	-0.403398213149	4.07839507892	-0.530122481058	8.32193438866	-0.063669735409	0.204028092414	0.0661449636328	-0.103998522909	-0.0627792825903	-0.303895000085	-0.308279147824	0.715153906927	0.11762848315	0.29243833888	-0.057811061821	-0.00833513792391	0.228924683032	-0.00527556286802	0.25250273238	14.2977473797	54.3758822661	42.7201612453
13	7.95413684303	1.55991970881	4.78818877401	2.14287003597	1.90331103655	7.60461102773	-0.362615830437	-0.177595827763	0.879837519461	-0.37552390163	0.0640666473938	0.112202854709	-1.87126790275	-0.42906680279	0.413371945681	0.763576321246	0.0796048326475	-0.0256749467253	0.363796626991	0.00781859592443	0.417959991751	5.82121545738	64.5839893542	45.9729250054
14	6.13222088006	1.83135723387	3.32651322352	8.38322549382	2.14947475778	7.9908838812	-0.245455896169	0.130440952951	0.499589208675	-0.466201111229	-0.0612904325403	0.391829824392	-1.26973604368	-1.18073871006	0.35325705297	0.429863896152	0.142366902669	-0.0443722584929	0.479454514707	0.0758717202778	0.323394010114	-2.4770950872	58.886075569	47.6568948906
15	5.6076908257	-3.18541779016	-1.55737654285	6.61369012859	0.834866150333	6.36069170658	0.0892898539346	-0.202566693329	0.543092045947	0.0957087826609	0.0275650869743	-0.984203790119	1.01734748023	1.40314570439	-0.0335329822302	0.516331286895	0.237256844616	-0.0867425057881	0.472594184888	-0.0274460082755	0.471999265049	22.4112491666	35.6454594063	66.3558375251
16	2.21833767094	0.416354524471	-1.76006802611	3.10873378024	-4.18148227085	6.35048756112	-0.0733586111288	0.00366870619043	-0.308977575505	0.221902636135	0.182939154921	0.222266614644	0.94643443516	-1.2127631938	-0.0709708923402	0.537258218714	-0.111707693535	-0.0371661136999	0.463280674865	0.00446057771134	0.379315895599	-1.48543077917	39.9980517488	67.9303054733
17	4.61173794897	-2.57542385339	3.27161540032	8.4756614929	-2.86739445391	5.81469188603	0.0731692192809	0.433736467021	0.0640958042278	-0.46112566416	0.206888748526	0.410653144937	0.734289821378	-2.30601268332	-0.303740297432	0.449827434826	-0.0371223258157	-0.0778217111653	0.785503226258	-0.0496465457165	0.430761597296	-5.94474721814	46.2447228456	56.8843070117
18	8.60808931905	-4.85536466948	-0.92079254335	8.18221589064	0.0834842802555	2.57555961447	0.0214340235154	0.571234886731	-0.572178940443	-0.173700363821	-0.150846386607	-0.110807340186	1.04992135986	0.281877017085	0.113747810492	0.671011255666	0.0879608228972	-0.0631737071533	0.253264753483	-0.0473890829918	0.288012054188	11.1123949997	36.3606617286	59.3534563382
19	4.59102377404	-0.3619820534	0.642375893983	4.53591404865	0.560007101242	3.39309678903	0.147391498298	-0.136578303804	-0.63163293761	0.144915290799	-0.00159394162895	-0.0161981297069	1.27690260458	0.460863769505	-0.128359256794	0.634817954568	0.108175182275	-0.0724295582605	0.276474729719	0.0369501103349	0.324035522093	11.9804474358	34.6892827327	70.3395489028
20	4.7309343465	-0.669620864815	3.99594722538	2.56089029839	-0.569548035711	3.46243553329	0.023520278795	-0.128742323213	-0.0225815118496	-0.238014289823	0.045037136479	0.153065908379	-0.0640069112254	-0.24323275463	-0.00989262523971	0.344324928295	0.0404225022964	-0.00912601523348	0.363512306013	0.0209322830369	0.286334797989	7.68016711482	53.0840996631	68.1359332775
21	8.24883704506	-0.134223548632	3.0598260933	5.00102915309	-1.08263111575	8.83769882806	-0.115131240437	-0.165287948338	0.121270303414	-0.207726193626	0.176043364942	-0.26512815032	-0.703736103352	1.29305055998	0.0145077624667	0.261828767034	-0.0349018321407	-0.0185692775883	0.464724293989	-0.0744645492069	0.339288845122	21.7191657653	50.4805542642	68.5867883176
22	2.01002106774	0.154818147304	0.268798169573	5.15545800732	0.425393088964	7.62923831239	0.127967613527	0.144113030429	0.22914158533	-0.392704927372	0.07906567824	-0.0376317503369	-1.32145304983	0.115515080426	-0.201204966504	0.303831756491	-0.018014219257	-0.0149683568799	0.323980803108	0.0290208565395	0.30003965207	15.0623908682	54.8861039251	62.4775361461
23	3.53946667887	2.71264477721	-1.05821526698	2.91433335958	1.08006088945	4.92672147972	0.0609387974136	-0.448896564236	-0.119341284573	0.42262450242	0.0548861103253	-0.0490846003111	0.50214734306	0.190901457475	-0.0869187914596	0.358808054091	0.108422647344	-0.0282548155079	0.24191667578	0.018758755869	0.256561108795	13.4615348431	44.6518381643	74.9818851568
24	4.85044640226	-5.12199715357	-4.68068338773	8.86223329804	2.2669610175	6.68406335449	-0.0386220146655	0.32502963194	-0.126907430219	-0.326072620948	-0.0835851905643	0.0275269073771	0.0671924998265	-0.47186873202	0.140760351625	0.31782703012	-0.0337547593052	-0.0322508106232	0.335782602009	0.00777210779147	0.29008191924	2.90373514359	50.1482051689	56.412849788
25	6.5670495744	-0.733857193767	5.78034898541	4.469487451	-0.5816804169	7.72666593909	0.258341882922	0.53979766942	-0.134618304721	-0.177324491644	-0.113753972837	-0.464823956799	0.569524480625	1.23408247362	-0.188103630127	0.319743897086	0.117001412892	0.0394512040824	0.398927774519	0.00740054404569	0.268686078305	19.8463940687	43.4663259126	58.1992363192

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid -7 through 368 )	A	A	-7 - 368	1 - 11
2	2	chain 'A' and (resid 369 through 395 )	A	A	369 - 395	12 - 38
3	3	chain 'A' and (resid 396 through 450 )	A	A	396 - 450	39 - 93
4	4	chain 'A' and (resid 451 through 464 )	A	A	451 - 464	94 - 107
5	5	chain 'A' and (resid 465 through 479 )	A	A	465 - 479	108 - 122
6	6	chain 'B' and (resid -1 through 179 )	B	B	-1 - 179	1 - 64
7	7	chain 'B' and (resid 180 through 193 )	B	B	180 - 193	65 - 78
8	8	chain 'B' and (resid 194 through 228 )	B	B	194 - 228	79 - 113
9	9	chain 'B' and (resid 229 through 291 )	B	B	229 - 291	114 - 176
10	10	chain 'C' and (resid -7 through 368 )	C	D	-7 - 368	1 - 11
11	11	chain 'C' and (resid 369 through 400 )	C	D	369 - 400	12 - 43
12	12	chain 'C' and (resid 401 through 448 )	C	D	401 - 448	44 - 91
13	13	chain 'C' and (resid 449 through 464 )	C	D	449 - 464	92 - 107
14	14	chain 'C' and (resid 465 through 479 )	C	D	465 - 479	108 - 122
15	15	chain 'D' and (resid -1 through 126 )	D	E	-1 - 126	1 - 11
16	16	chain 'D' and (resid 127 through 136 )	D	E	127 - 136	12 - 21
17	17	chain 'D' and (resid 137 through 144 )	D	E	137 - 144	22 - 29
18	18	chain 'D' and (resid 145 through 162 )	D	E	145 - 162	30 - 47
19	19	chain 'D' and (resid 163 through 193 )	D	E	163 - 193	48 - 78
20	20	chain 'D' and (resid 194 through 211 )	D	E	194 - 211	79 - 96
21	21	chain 'D' and (resid 212 through 226 )	D	E	212 - 226	97 - 111
22	22	chain 'D' and (resid 227 through 238 )	D	E	227 - 238	112 - 123
23	23	chain 'D' and (resid 239 through 256 )	D	E	239 - 256	124 - 141
24	24	chain 'D' and (resid 257 through 270 )	D	E	257 - 270	142 - 155
25	25	chain 'D' and (resid 271 through 290 )	D	E	271 - 290	156 - 175

-
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