PDB-8odo: Structure of human guanylylated RTCB in complex with Archease

ID or keywords:

Entry

Database: PDB / ID: 8odo

Title

Structure of human guanylylated RTCB in complex with Archease

Components

Protein archease
RNA-splicing ligase RtcB homolog

Keywords

LIGASE / archease / RTCB / human / tRNA

Function / homology

Function and homology information

tRNA-splicing ligase complex / 3'-phosphate/5'-hydroxy nucleic acid ligase / RNA ligase (GTP) activity / RNA ligase (ATP) activity / tRNA splicing, via endonucleolytic cleavage and ligation / vinculin binding / tRNA processing in the nucleus / tRNA processing / placenta development / nuclear envelope ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Kopp, J. / Gerber, J.L. / Peschek, J.

Funding support

Germany, 1items

Citation

Journal: Nat Commun / Year: 2024
Title: Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease.
Authors: Gerber, J.L. / Morales Guzman, S.I. / Worf, L. / Hubbe, P. / Kopp, J. / Peschek, J.

History

Deposition	Mar 9, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 27, 2024	Provider: repository / Type: Initial release
Revision 1.1	Apr 17, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8odo.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb8odo.ent.gz	887.7 KB	Display	PDB format
PDBx/mmJSON format	8odo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8odo_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	8odo_full_validation.pdf.gz	1.6 MB	Display
Data in XML	8odo_validation.xml.gz	94.1 KB	Display
Data in CIF	8odo_validation.cif.gz	130.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/od/8odo ftp://data.pdbj.org/pub/pdb/validation_reports/od/8odo	HTTPS FTP

-
Related structure data

Related structure data	8bttC 8btxC 8odpC C: citing same article (ref.)
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	#205 - Jan 2017 Nuclear Pore Complex similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (1)

Deposited unit

A: RNA-splicing ligase RtcB homolog

B: Protein archease

C: RNA-splicing ligase RtcB homolog

D: Protein archease

E: RNA-splicing ligase RtcB homolog

F: Protein archease

G: RNA-splicing ligase RtcB homolog

H: Protein archease

hetero molecules

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

1

A: RNA-splicing ligase RtcB homolog

B: Protein archease

hetero molecules

defined by author&software
Evidence: gel filtration, complex is a hetero dimer of human RTCB and human archease
79 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: RNA-splicing ligase RtcB homolog

D: Protein archease

hetero molecules

defined by author&software
Evidence: gel filtration, complex is a hetero dimer of human RTCB and human archease
79 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: RNA-splicing ligase RtcB homolog

F: Protein archease

hetero molecules

defined by author&software
Evidence: gel filtration, complex is a hetero dimer of human RTCB and human archease
79 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: RNA-splicing ligase RtcB homolog

H: Protein archease

hetero molecules

defined by author&software
Evidence: gel filtration, complex is a hetero dimer of human RTCB and human archease
79 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	99.090, 125.547, 125.733
Angle α, β, γ (deg.)	90.000, 108.510, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

-
Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein	RNA-splicing ligase RtcB homolog / 3'-phosphate/5'-hydroxy nucleic acid ligase Mass: 55412.320 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RTCB, C22orf28, HSPC117 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9Y3I0, 3'-phosphate/5'-hydroxy nucleic acid ligase
#2: Protein	Protein archease Mass: 22997.656 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB8OS / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A8K0B5

#1: Protein

RNA-splicing ligase RtcB homolog / 3'-phosphate/5'-hydroxy nucleic acid ligase

Mass: 55412.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: RTCB, C22orf28, HSPC117 / Production host:

Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y3I0, 3'-phosphate/5'-hydroxy nucleic acid ligase

#2: Protein

Protein archease

Mass: 22997.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: ZBTB8OS / Production host:

Escherichia coli BL21 (bacteria) / References: UniProt: A8K0B5

-
Non-polymers , 4 types, 659 molecules

#3: Chemical	ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₈P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.24 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: protein: RTCB 160 uM, Archease 200 uM, 2 mM manganese chloride, 2 mM GTP reservoir: 10% w/v PEG 8000, 0.1 M HEPES pH 7.5, 8% v/v ethylene glycol drop: 200 nl protein + 200 nl reservoir

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9737 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 3, 2021 / Details: Toroidal mirror
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9737 Å / Relative weight: 1
Reflection	Resolution: 2.2→119.23 Å / Num. obs: 145859 / % possible obs: 99.3 % / Redundancy: 7 % / B_iso Wilson estimate: 44.78 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.11 / R_pim(I) all: 0.045 / Net I/σ(I): 9.2
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 6.3 % / R_merge(I) obs: 1.16 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6868 / CC_1/2: 0.86 / R_pim(I) all: 0.495 / % possible all: 95.2

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS	20210205	data reduction
Aimless	1.12.10	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: D_1292120363

Resolution: 2.2→75.23 Å / SU ML: 0.2795 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8484
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2176	7183	4.94 %
R_work	0.1933	138355	-
obs	0.1945	145538	99.15 %

Solvent computation

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

Displacement parameters

B_iso mean: 65.24 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→75.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20965	0	120	643	21728

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0022	21502
X-RAY DIFFRACTION	f_angle_d	0.4961	29081
X-RAY DIFFRACTION	f_chiral_restr	0.0429	3167
X-RAY DIFFRACTION	f_plane_restr	0.004	3815
X-RAY DIFFRACTION	f_dihedral_angle_d	12.9423	7942

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 (%)
2.2-2.23	0.4266	233	0.3683	4351	X-RAY DIFFRACTION	94.79
2.23-2.26	0.3876	258	0.3489	4577	X-RAY DIFFRACTION	98.23
2.26-2.28	0.4174	250	0.3276	4510	X-RAY DIFFRACTION	98.25
2.28-2.31	0.3442	212	0.3163	4592	X-RAY DIFFRACTION	98.89
2.31-2.34	0.3017	251	0.3023	4543	X-RAY DIFFRACTION	98.46
2.34-2.38	0.3162	252	0.2811	4592	X-RAY DIFFRACTION	98.52
2.38-2.41	0.2985	249	0.2801	4542	X-RAY DIFFRACTION	98.62
2.41-2.45	0.2998	246	0.278	4555	X-RAY DIFFRACTION	98.83
2.45-2.48	0.322	239	0.2889	4576	X-RAY DIFFRACTION	98.93
2.48-2.52	0.3439	239	0.2872	4618	X-RAY DIFFRACTION	99.04
2.52-2.57	0.2869	232	0.2732	4549	X-RAY DIFFRACTION	98.94
2.57-2.61	0.3326	221	0.2673	4714	X-RAY DIFFRACTION	99.14
2.61-2.66	0.3165	239	0.2466	4584	X-RAY DIFFRACTION	99.28
2.66-2.72	0.2798	238	0.2444	4568	X-RAY DIFFRACTION	99.42
2.72-2.78	0.2785	251	0.2286	4629	X-RAY DIFFRACTION	99.39
2.78-2.84	0.3035	216	0.2332	4641	X-RAY DIFFRACTION	99.63
2.84-2.91	0.2398	258	0.2278	4645	X-RAY DIFFRACTION	99.67
2.91-2.99	0.2356	235	0.2223	4621	X-RAY DIFFRACTION	99.57
2.99-3.08	0.2798	232	0.23	4606	X-RAY DIFFRACTION	99.49
3.08-3.18	0.2579	266	0.2229	4579	X-RAY DIFFRACTION	99.61
3.18-3.29	0.2432	263	0.2081	4647	X-RAY DIFFRACTION	99.84
3.29-3.43	0.2179	237	0.196	4662	X-RAY DIFFRACTION	99.84
3.43-3.58	0.2154	242	0.1855	4634	X-RAY DIFFRACTION	99.92
3.58-3.77	0.1786	261	0.1779	4609	X-RAY DIFFRACTION	99.94
3.77-4.01	0.1835	225	0.1656	4688	X-RAY DIFFRACTION	99.92
4.01-4.32	0.1959	218	0.1481	4720	X-RAY DIFFRACTION	99.92
4.32-4.75	0.153	232	0.1372	4666	X-RAY DIFFRACTION	99.94
4.75-5.44	0.1566	198	0.1494	4710	X-RAY DIFFRACTION	99.92
5.44-6.85	0.159	233	0.1641	4709	X-RAY DIFFRACTION	99.68
6.85-75.23	0.1459	257	0.1397	4718	X-RAY DIFFRACTION	98.93

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	1.66638047343	0.177436493529	0.236792557607	0.443841841159	-0.0246385839369	1.22823506578	-0.0705425753569	-0.579239787875	0.441973179665	0.224354066907	-0.167739068895	0.0219499272447	-0.112459556813	-0.372134757716	0.191630535179	0.439596878263	0.0620241170587	0.00800792131438	0.675567088194	-0.170785129251	0.506828063257	18.04	64.505	78.039
2	1.02768822119	0.417720029026	-0.0548259136958	0.677916633969	0.1572883101	1.10076313803	-0.146095201971	-0.0433495645181	0.251621892856	0.0530634622984	0.0383320976911	0.0801340415825	-0.127316989062	-0.164021537878	0.102761646283	0.405006619568	0.0375951271392	-0.0664943252514	0.391993452069	-0.0616255950653	0.470431830865	31.472	65.938	63.276
3	1.36185778157	-0.346293512058	0.653632095001	0.90058183697	-0.0514198521746	1.57591367851	-0.0469308008422	0.169818382367	0.180462398539	0.0505598829356	-0.0893331507139	-0.0686602846516	-0.00511266035626	0.263370106342	0.115899395368	0.427713297882	0.00323918059766	-0.00185653424753	0.469762704928	0.00729999856978	0.48466944041	47.724	61.222	50.717
4	0.940505201542	-0.0425226609473	-0.0534433100303	0.558702565008	-0.363110572961	1.63994665904	-0.0824270533999	-0.125515074039	0.358320387128	0.21866027968	-0.136909763926	-0.0943239755662	-0.369232426113	-0.0816307256292	0.238014178813	0.495012222765	0.0299302505546	-0.136988836899	0.388061901872	-0.0383610116288	0.626378694153	40.346	80.816	59.843
5	1.58025760204	0.117517213811	0.244003022752	0.00702617950258	0.113214816657	1.21576618311	0.0884381816598	-0.107185659759	-0.391524919297	-0.0170757451991	-0.0878318369806	-0.034314308054	0.436982962407	-0.0389676409066	0.0554126645112	0.501119428932	0.00923389987062	-0.00614053002355	0.405674938349	-0.00933375025785	0.487136411618	31.287	46.325	62.42
6	1.00171817582	0.0906448100368	0.126736478757	1.41628633607	-0.434700181848	1.45549514403	-0.123870890958	-0.00569634664906	0.188783175204	0.013616029862	-0.0799876236398	-0.204379632167	-0.136189702173	0.186898629996	0.144416598365	0.420379745607	0.0113549993643	-0.0371312207458	0.397341660214	-0.0245120209521	0.502647326278	44.261	66.249	60.33
7	0.653924139325	0.602523704135	0.257302280246	0.615119190515	-0.0549017029534	1.51435086714	-0.180420511919	-0.0816034271907	0.330036767372	-0.0240697660895	-0.012421932625	0.103824600017	-0.29651129357	-0.165004338121	0.19393338431	0.537960896082	0.0652797158098	-0.0987187675933	0.428264625331	-0.0822677890294	0.620338875395	31.263	76.375	62.978
8	1.06096812865	0.45921672608	-1.0942611174	1.99161291363	-1.11209519495	2.38654595788	0.188659527034	0.115051810269	0.435995045476	-0.0527152492473	-0.271100363268	1.11939845876	-0.242009051095	-0.202056042384	-0.0415058895534	0.598204206962	-0.00838293235586	-0.0544508810387	0.653748214807	0.0111742608138	0.728503974486	4.705	62.396	49.579
9	1.82806975747	0.307234576161	0.332917811064	1.86191925421	0.0198416904688	1.79035746687	0.168323788108	0.370192912943	0.683610121787	-0.661193060292	0.0710699178896	0.00106417264601	-0.40946381131	0.175777623186	-0.0657087957359	0.704856612957	0.0754630326563	-0.0336889490181	0.640979840018	0.103055383091	0.661895099345	17.675	69.063	32.342
10	0.795764514031	0.132427382224	-0.00841230444135	1.05330924862	-0.503760110981	0.238406216743	-0.30922813432	0.242910029785	0.464162636439	-0.175433114638	0.183872494611	0.328037250755	-0.264594683007	0.0346374149142	0.0637914298126	0.440129790892	0.016151133069	-0.01721670072	0.529875555419	0.0119493298148	0.55065699211	13.102	60.388	45.773
11	0.889073980965	0.48606266276	0.0834263031784	0.970505560265	-0.362546313501	0.906837904182	-0.0964625334878	0.048175846871	0.164839033738	-0.152462276426	-0.0226171732121	0.253431610043	-0.0476231621738	-0.172943265287	0.0201388158543	0.442328493056	-0.00361087988521	-0.00334784543837	0.488615359607	-0.0404112855925	0.47349124409	13.9	53.317	46.294
12	1.83665345016	-0.41446233895	-0.407543839637	3.05557720792	0.712096224275	2.18093981996	-0.341240832877	0.228325734827	0.357304697482	-0.344608578118	-0.111690420449	0.414122959746	-0.203539795009	-0.135141553817	0.0243589246238	0.5055913384	-0.0193799261086	-0.0623798780355	0.563270494187	0.0626643148667	0.484580960629	20.025	60.084	32.191
13	0.622494990989	0.388899783689	-0.736794778663	1.78313532157	-2.29131715551	5.80108515442	0.0193680720879	0.123912583318	-0.262401561672	-0.290538908256	-0.360513190442	-0.208271283782	0.615708688137	0.444709392007	0.146950547459	0.523350166895	-0.0166791919654	0.00844246160929	0.490948846124	-0.0204413471816	0.522189958594	23.7	42.426	42.881
14	0.989505726823	0.299055330332	-0.174917951741	1.16447696728	-0.615767373414	1.07224954599	0.00164872635818	0.162058518801	-0.141336607606	-0.102709006268	0.0218824420356	-0.149776318222	0.241516009739	0.0965004001874	0.0657877994683	0.423776964947	0.0111788672615	-0.00200459847576	0.489416088782	-0.0299127223635	0.447684268668	24.221	49.99	43.198
15	1.2575121146	0.0712601663947	0.46617992965	0.840858018745	0.146371933819	1.36595691368	-0.0983877444803	0.168260848888	-0.0204708778214	-0.647383188282	0.181388632003	0.229721568477	0.571769869902	-0.0686518073387	0.0287665765305	0.534423825109	-0.0457674352996	-0.000345068965315	0.45862014503	-0.00328045190947	0.456770124806	18.779	41.813	42.021
16	1.56846839492	0.221178252713	0.506821695626	1.90697884656	0.259442858168	1.05691144149	-0.051802046449	0.104595633989	0.12133851862	-0.187273805933	-0.167549407021	-0.143303862478	-0.456979854364	0.00234188107651	0.0647119729149	0.545505737054	-0.0208216263523	-0.0490161893174	0.435860457674	0.0554955419279	0.558696800799	26.715	65.363	36.059
17	0.678594675495	-0.355739562022	0.250664266833	0.86273336268	0.237733191389	1.65045634145	-0.0223147795755	-0.0425438744605	-0.200670834167	0.117614772713	-0.0618136545685	-0.0670036468743	-0.0755809784772	-0.125301926857	0.0170201283493	0.407458916841	0.0175299386436	-0.00743237391327	0.405053471967	-0.0475345636814	0.44250229082	16.149	52.482	54.275
18	1.3851443961	-0.167814260189	-0.247525130317	1.48733969308	0.285066360248	0.642682871568	-0.0704656890506	0.01554349598	0.0759077946113	-0.108370315221	0.0984270067177	-0.271143178722	-0.062511076012	0.322559056683	-0.0112435180039	0.40406934476	0.00613869628828	0.0448030973173	0.572285561455	-0.105523373982	0.501743594759	-4.575	59.421	64.415
19	0.869189934789	0.328461499212	0.27977800729	1.1605281199	-0.170047164234	0.691477891483	0.0150220679063	-0.0664251586559	-0.0087933424777	0.0180935561841	0.0729560324306	-0.0883740520248	0.0768113915422	0.089752858109	-0.0528991860377	0.397837011663	0.0540516829623	0.023836904666	0.429809483562	-0.0608603891575	0.376991521131	-20.496	46.224	70.652
20	0.669818887821	-0.171685801261	0.549789188138	0.333511874347	0.113697432226	0.833850980236	0.0379699814156	-0.138570841132	-0.130515383906	0.0198821393888	0.0441929180203	0.322958266122	0.202315294368	-0.101183511995	-0.0494230550376	0.531945556592	0.0300731440366	0.0496702331914	0.559931598892	0.0589244630602	0.591800823032	-40.806	37.289	69.064
21	0.978585261772	-0.0636159510448	0.633360530598	0.668089954074	-0.206651632666	1.22223975782	-0.0157097139391	-0.194720832077	-0.127650537156	0.285238286026	0.0487836071841	-0.00247086794886	0.210921775828	-0.077843502081	-0.0954013568931	0.51843746714	0.0227123353756	0.0091251219506	0.454552219756	-0.00426763274053	0.446072756557	-27.51	37.503	75.87
22	1.29358662416	0.40994060223	-0.499405615377	0.191695183629	-0.33779098474	1.26768596393	0.118272532988	0.188777968896	0.289393808699	-0.126799363958	-0.0071492496449	0.127409387343	-0.261842045254	-0.183466185151	-0.0999167627809	0.480756628219	0.0504497246791	0.00900022062366	0.453615658855	-0.039629102166	0.570890616374	-30.406	62.005	61.805
23	1.14961074001	0.136041171808	-0.0179442025856	1.12143484301	-0.17442875511	1.03554926484	-0.0105329332686	-0.233061587705	-0.0472350881029	0.11310546442	0.142060866727	-0.0235845196684	0.090911687589	-0.0883279789808	-0.120805100382	0.435855041625	0.0564222688231	0.00665933949632	0.485102047586	-0.0231030617262	0.434437647076	-29.004	43.284	76.395
24	1.26416138147	0.440109082104	0.650384582142	0.689153209151	-0.0112402310961	0.936827999579	0.0549780762284	-0.0232594360614	-0.137531039704	0.0647415412768	0.102981978474	-0.134097090511	0.191373037588	0.300649719933	-0.0837161000172	0.47933623266	0.0906323731091	-0.0257261926928	0.485606124502	-0.0533208366113	0.463114597559	-13.45	39.229	71.669
25	0.998607369105	0.483714998005	-0.475773665246	0.716021286602	-0.639412736661	0.670298352281	0.134068624033	0.601738233524	0.0294625271914	-0.065256511022	0.296403529087	-0.547782459424	0.114220513334	0.338182676329	-0.0475831882774	0.798404753605	-0.0520825733462	-0.0418546441823	0.883565860198	-0.00933343422504	0.852149744747	-14.786	38.874	42.755
26	2.14800622113	0.0341812338675	0.15385009687	1.26036164944	0.795229998101	2.12896927972	0.0137960722511	0.0208233706332	-0.543054353459	-0.330796708308	-0.258953561605	0.174079703233	0.788541433429	-0.0408991509332	0.00812963050465	0.819427513544	0.0990288760715	-0.132873930531	0.586842451415	-0.115174830406	0.653454749072	-27.01	25.695	37.99
27	1.02559181137	0.597944291596	-0.310634154643	0.860517561925	0.0906551270658	0.58101850844	-0.0327943838695	0.276629220955	-0.0698301386877	-0.2501196936	0.195944301479	-0.0653578087209	0.0343690664403	0.214184716826	-0.145284830562	0.471068721152	-0.00246308075423	-0.0017144173095	0.522497960359	-0.0639427779364	0.428082266315	-22.978	44.797	41.672
28	0.938612577411	-0.00125853707378	0.115064887952	1.22934168847	-0.592144971792	1.18503079239	0.00424548660074	-0.0605028708766	0.180068326094	0.055485742923	-0.00745309829052	0.205712751295	-0.0925897853523	-0.283035979956	0.00497959599181	0.457068595526	0.035756621956	-0.0372673634511	0.49555379886	-0.0452958768269	0.477937810071	-34.388	49.632	45.185
29	1.40672919364	0.419988289189	0.166878310392	1.23578148092	0.267140932012	1.61278408581	-0.243580782039	0.39471487819	0.117639811322	-0.353895302951	0.227935221938	0.296790221284	-0.229710492138	-0.108206471711	0.00496769388657	0.557579863294	0.0380195758907	-0.0528957162505	0.506310331846	-0.0275109810061	0.480134912332	-34.609	54.643	38.397
30	1.17089410563	0.0814668317635	0.193408162408	1.44965952055	0.625706531902	0.962871985038	0.0200075038063	-0.0135587617554	0.177425891598	-0.166153275747	0.0459328656969	0.180060126696	0.0373143112514	0.202971934049	0.0127787997346	0.442781796196	0.0437567510395	-0.0145425547032	0.414769540609	-0.0441405077502	0.433532071261	-23.495	48.42	47.888
31	1.65169413197	-0.560103068335	0.289370735324	1.53321822183	-0.608205477144	1.34504282312	0.132381759007	1.29006966279	-0.171885710781	-0.398744668163	-0.0326388177488	0.159329062852	0.0883798314376	0.394555276014	-0.0990436961635	0.609091160965	0.0764486133473	-0.107318639078	1.08810639262	-0.151218523952	0.500134273668	-9.814	35.745	-3.907
32	1.49819376647	-0.227233096653	0.963581580169	1.36856642433	-0.18598104414	1.45152650225	0.537736706169	0.866918185085	-1.0770806388	-0.158505127743	0.00763339933879	0.0615308576571	0.713482928592	0.453430260061	-0.384658777049	0.963405351407	0.322817435025	-0.315022653877	0.952611389827	-0.542540032707	1.08689162147	9.396	12.738	5.64
33	2.32607471383	-0.688715109563	0.0229107100095	0.411441871481	0.550833834603	1.51027912404	0.268578521952	1.05405758909	0.157808406947	-0.185552872751	-0.165602085965	-0.17176677987	-0.245702081959	0.686184483975	-0.245801456371	0.619683564408	0.0342196637601	0.025216626236	1.31956430195	-0.0536377173845	0.609645089578	10.882	40.58	-1.345
34	2.36116611585	0.15151521335	0.569611857765	0.626056049232	0.161254735577	1.1165040645	0.518890716204	1.12316352005	-1.13798233417	-0.200091005823	0.0797124290404	0.139214373457	0.6858608233	0.320617508494	-0.0111048775141	0.877724640517	0.226660299392	-0.349744282298	0.951387603536	-0.534192941594	0.928597007863	-0.31	16.55	2.44
35	1.32826447826	0.439566999685	0.337284022336	2.12892656729	-0.298391106428	1.62950698394	0.389465482322	-0.109523847965	0.0942192614956	-0.538907216453	0.012672078813	0.793707192388	0.0700807330425	-0.4708011828	-0.21315961118	0.601676734349	0.0219065871001	-0.066858154451	0.562448733096	0.00946903943183	0.749918521166	-0.62	31.309	32.277
36	2.46735883159	-0.131112315817	1.7885265186	1.4267215445	0.156281430473	2.04605015675	-0.104814989135	0.53737384687	-0.0102038862108	-0.051086903005	0.0891903422874	-0.0296898575069	-0.143007965308	0.429198257321	0.0243224488027	0.480041771977	0.0109647753711	-0.0274404625114	0.556594269779	-0.0553812717673	0.424160472985	8.561	39.9	22.486
37	2.50078352904	-0.284935751233	0.951422563016	1.5383107389	0.486412798889	1.63160648025	-0.191485351262	0.526144311638	0.103520849882	-0.0805156440915	0.13930518546	0.150359336513	-0.29389402937	0.29473519664	0.0213227776686	0.566660824078	-0.0243176989177	-0.111891226701	0.586724599198	-0.0202280765101	0.477256280363	13.478	40.518	23.757
38	3.09586719761	-0.319761242492	0.46734406781	1.03445226461	-0.787608080492	2.75560641069	0.138538548731	0.941190683291	0.257531220047	-0.318474339942	-0.272782932091	-0.305890519466	-0.383038803794	0.211975873527	-0.0468914925062	0.535111808766	0.0314056990837	-0.081169242152	0.664246515807	-0.0191045803892	0.454554228204	1.573	43.279	14.383
39	2.41703734887	-0.00435671222178	1.04994497086	0.620120568047	0.241989292803	2.2143811281	-0.00836717631127	0.556958694597	-0.0273463926675	-0.152922431	-0.0832433993839	0.00616626833821	-0.151022290289	0.249515979255	0.0406895015202	0.595085581601	0.0242252433261	-0.151043707032	0.557940079279	-0.0542780059384	0.485401523657	-45.954	39.175	-8.973
40	1.38768437177	0.268807046064	0.630616524424	0.810068021565	0.256299173383	2.6134971217	-0.200654276897	-0.0204422177717	0.426767118946	-0.170442974455	-0.170383353394	0.275365363556	-0.50213072557	-0.532568107426	0.260167627112	0.659730550891	0.160755557416	-0.254154074015	0.661878173595	-0.179827699197	0.7114709024	-62.444	48.027	2.119
41	1.23243197048	0.165453948561	0.584186885055	0.35399150837	0.462899623183	2.20294221256	-0.0822131878419	-0.00903231262242	0.142110619976	-0.241325292777	-0.0816081841196	0.181738876676	-0.264359867799	-0.394566874643	0.178030948268	0.670935432265	0.0749575420196	-0.235770113088	0.597192532185	-0.146455310261	0.685349736965	-61.169	41.411	-1.637
42	1.17317034526	-0.30173094273	0.171130455359	0.935202619938	0.62750706839	1.85972964826	-0.253866794936	0.390825490845	0.404613269893	-0.294934708469	-0.0730802181985	0.0711871205283	-0.61637854894	0.115254184384	0.235646077219	0.881948421139	-0.0103780683103	-0.304703814617	0.561477407985	0.04094795022	0.703754674122	-50.518	51.589	-11.037
43	1.57994881149	-0.095485091756	-0.986001104405	4.17015996951	0.533448809521	1.30934556965	0.187768640848	-0.173489697665	0.482925071103	-0.270706189531	0.353742286032	-0.276605220812	-0.779346734088	0.561943382638	0.00505924993559	0.687185915163	0.0488103397829	-0.185103846443	0.880552055107	-0.0766955864179	0.771749196209	-22.873	47.096	8.928
44	1.63296484832	-0.2725488162	0.32742481979	0.558596327302	-0.770419912682	1.46147091779	-0.0878108191932	0.211361535902	0.586317691588	-0.381377195465	-0.310120840548	0.530944925786	-1.06816141111	-0.325497796281	0.065720575788	0.984134931378	0.0243772666179	-0.413520860761	0.535745633206	-0.106618070199	1.07422955808	-36.595	63.598	17.641
45	1.35577137685	-0.662890336443	0.390328001276	0.998286588269	-0.129945815527	0.842722514134	-0.276879669986	-0.0557014823609	0.515092276094	-0.0612562529847	0.0435356566817	-0.188764366066	-0.463333825636	0.059371497424	0.150624544678	0.625449125735	0.0320151338586	-0.162617034727	0.507603988024	-0.0993718423695	0.595408470342	-34.046	47.28	16.075
46	1.37715948929	-0.0477395465018	1.10218181217	1.50749564639	0.0600341244983	1.41528816618	-0.122051568119	-0.570538989364	0.105623871268	0.0907743550814	0.013805579263	0.246075869633	-0.102448504756	-0.409846318016	0.160652890441	0.563655064803	0.0749803810569	-0.124242860792	0.547774410928	-0.0784381220896	0.529190533853	-43.668	40.91	21.891
47	1.52304953438	0.196776803979	0.50154874741	0.294102214784	0.689216046097	2.35735611542	-0.238809125978	-0.171262293741	0.21089312612	0.0373252621804	0.0695242350866	-0.0787603622286	-0.15689470402	-0.156832457278	0.132554603572	0.567979944917	0.0753074584175	-0.163505162787	0.420458735945	-0.0762280582764	0.510821772718	-38.461	40.933	17.098

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 3:52 )	A	3 - 52
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 53:150 )	A	53 - 150
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 151:218 )	A	151 - 218
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 219:262 )	A	219 - 262
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 263:300 )	A	263 - 300
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 301:375 )	A	301 - 375
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 376:505 )	A	376 - 505
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 11:20 )	B	11 - 20
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 21:35 )	B	21 - 35
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 36:51 )	B	36 - 51
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 52:76 )	B	52 - 76
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 77:85 )	B	77 - 85
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 86:96 )	B	86 - 96
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 97:125 )	B	97 - 125
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 126:143 )	B	126 - 143
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 144:153 )	B	144 - 153
17	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 154:179 )	B	154 - 179
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 3:64 )	C	3 - 64
19	X-RAY DIFFRACTION	19	( CHAIN C AND RESID 65:150 )	C	65 - 150
20	X-RAY DIFFRACTION	20	( CHAIN C AND RESID 151:181 )	C	151 - 181
21	X-RAY DIFFRACTION	21	( CHAIN C AND RESID 182:262 )	C	182 - 262
22	X-RAY DIFFRACTION	22	( CHAIN C AND RESID 263:300 )	C	263 - 300
23	X-RAY DIFFRACTION	23	( CHAIN C AND RESID 301:375 )	C	301 - 375
24	X-RAY DIFFRACTION	24	( CHAIN C AND RESID 376:505 )	C	376 - 505
25	X-RAY DIFFRACTION	25	( CHAIN D AND RESID 12:26 )	D	12 - 26
26	X-RAY DIFFRACTION	26	( CHAIN D AND RESID 27:35 )	D	27 - 35
27	X-RAY DIFFRACTION	27	( CHAIN D AND RESID 36:85 )	D	36 - 85
28	X-RAY DIFFRACTION	28	( CHAIN D AND RESID 86:125 )	D	86 - 125
29	X-RAY DIFFRACTION	29	( CHAIN D AND RESID 126:143 )	D	126 - 143
30	X-RAY DIFFRACTION	30	( CHAIN D AND RESID 144:179 )	D	144 - 179
31	X-RAY DIFFRACTION	31	( CHAIN E AND RESID 3:109 )	E	3 - 109
32	X-RAY DIFFRACTION	32	( CHAIN E AND RESID 110:262 )	E	110 - 262
33	X-RAY DIFFRACTION	33	( CHAIN E AND RESID 263:300 )	E	263 - 300
34	X-RAY DIFFRACTION	34	( CHAIN E AND RESID 301:505 )	E	301 - 505
35	X-RAY DIFFRACTION	35	( CHAIN F AND RESID 12:35 )	F	12 - 35
36	X-RAY DIFFRACTION	36	( CHAIN F AND RESID 36:125 )	F	36 - 125
37	X-RAY DIFFRACTION	37	( CHAIN F AND RESID 126:153 )	F	126 - 153
38	X-RAY DIFFRACTION	38	( CHAIN F AND RESID 154:179 )	F	154 - 179
39	X-RAY DIFFRACTION	39	( CHAIN G AND RESID 3:150 )	G	3 - 150
40	X-RAY DIFFRACTION	40	( CHAIN G AND RESID 151:283 )	G	151 - 283
41	X-RAY DIFFRACTION	41	( CHAIN G AND RESID 284:375 )	G	284 - 375
42	X-RAY DIFFRACTION	42	( CHAIN G AND RESID 376:505 )	G	376 - 505
43	X-RAY DIFFRACTION	43	( CHAIN H AND RESID 10:19 )	H	10 - 19
44	X-RAY DIFFRACTION	44	( CHAIN H AND RESID 20:35 )	H	20 - 35
45	X-RAY DIFFRACTION	45	( CHAIN H AND RESID 36:85 )	H	36 - 85
46	X-RAY DIFFRACTION	46	( CHAIN H AND RESID 86:125 )	H	86 - 125
47	X-RAY DIFFRACTION	47	( CHAIN H AND RESID 126:179 )	H	126 - 179

-
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

-
Protein , 2 types, 8 molecules ACEGBDFH

-
Non-polymers , 4 types, 659 molecules

-
Details

-
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

-Protein , 2 types, 8 molecules ACEGBDFH

-Non-polymers , 4 types, 659 molecules

-Details

-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

-
Protein , 2 types, 8 molecules ACEGBDFH

-
Non-polymers , 4 types, 659 molecules

-
Details

-
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