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- PDB-9o07: Structure of human MAIT A-F7 TCR in complex with human MR1-lumiflavin -

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Open data

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Basic information

Entry

Database: PDB / ID: 9o07

Title

Structure of human MAIT A-F7 TCR in complex with human MR1-lumiflavin

Components

Beta-2-microglobulin
Major histocompatibility complex class I-related gene protein
TCR-alpha
TCR-beta

Keywords

IMMUNE SYSTEM / receptor

Function / homology

Function and homology information

positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.97 Å

Authors

Abdelaal, M. / Rossjohn, J. / Awad, W.

Funding support

Australia, 1items

Citation

Journal: To Be Published
Title: Major histocompatibility complex class I-related gene protein / TCR alpha /TCR beta / Beta-2-microglobulin complex
Authors: Abdelaal, M. / Rossjohn, J. / Awad, W.

History

Deposition	Apr 2, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 19, 2025	Provider: repository / Type: Initial release

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	9o07.cif.gz	841.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9o07.ent.gz	573.8 KB	Display	PDB format
PDBx/mmJSON format	9o07.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9o07_validation.pdf.gz	991.4 KB	Display	wwPDB validaton report
Full document	9o07_full_validation.pdf.gz	1002.6 KB	Display
Data in XML	9o07_validation.xml.gz	86.8 KB	Display
Data in CIF	9o07_validation.cif.gz	117.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o0/9o07 ftp://data.pdbj.org/pub/pdb/validation_reports/o0/9o07	HTTPS FTP

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Related structure data

Related structure data	9o05C 9o06C 9o08C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#62 - Feb 2005 Major Histocompatibility Complex similarity (1) #63 - Mar 2005 T-Cell Receptor similarity (1)

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Assembly

Deposited unit

C: Major histocompatibility complex class I-related gene protein

D: TCR-alpha

E: TCR-beta

F: Beta-2-microglobulin

A: Major histocompatibility complex class I-related gene protein

B: TCR-alpha

G: TCR-beta

H: Beta-2-microglobulin

hetero molecules

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

C: Major histocompatibility complex class I-related gene protein

D: TCR-alpha

E: TCR-beta

F: Beta-2-microglobulin

hetero molecules

defined by author
Evidence: surface plasmon resonance
94.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

A: Major histocompatibility complex class I-related gene protein

B: TCR-alpha

G: TCR-beta

H: Beta-2-microglobulin

hetero molecules

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

Unit cell

Length a, b, c (Å)	212.712, 69.293, 141.169
Angle α, β, γ (deg.)	90.000, 103.481, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

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Components

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Protein , 4 types, 8 molecules CADBEGFH

#1: Protein	Major histocompatibility complex class I-related gene protein / MHC class I-related gene protein / Class I histocompatibility antigen-like protein Mass: 31711.670 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95460
#2: Protein	TCR-alpha Mass: 22781.268 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein	TCR-beta Mass: 27677.760 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Protein	Beta-2-microglobulin Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Non-polymers , 4 types, 1413 molecules

#5: Chemical	ChemComp-LFN / LUMIFLAVIN / 7,8,10-TRIMETHYLBENZO[G]PTERIDINE-2,4(3H,10H)-DIONE Mass: 256.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₃H₁₂N₄O₂ / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1409 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experimental details

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54.26 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: Bis-Tris-propane, PEG3350 and sodium acetate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953739 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 3, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.953739 Å / Relative weight: 1
Reflection	Resolution: 1.97→49.32 Å / Num. obs: 141041 / % possible obs: 99.66 % / Redundancy: 2 % / B_iso Wilson estimate: 37.75 Å² / CC_1/2: 0.999 / Net I/σ(I): 11.03
Reflection shell	Resolution: 1.97→1.99 Å / Num. unique obs: 4650 / CC_1/2: 0.618

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Processing

Software

Name	Version	Classification
PHENIX	1.21_5207	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.97→49.32 Å / SU ML: 0.209 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.1257
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1945	7154	5.07 %
R_work	0.157	133873	-
obs	0.1589	141027	99.66 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 43.75 Å²

Refinement step

Cycle: LAST / Resolution: 1.97→49.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12689	0	45	1410	14144

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0068	13499
X-RAY DIFFRACTION	f_angle_d	0.8445	18476
X-RAY DIFFRACTION	f_chiral_restr	0.0554	1983
X-RAY DIFFRACTION	f_plane_restr	0.0071	2435
X-RAY DIFFRACTION	f_dihedral_angle_d	13.3858	4924

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 (%)
1.97-1.99	0.2665	222	0.2428	4428	X-RAY DIFFRACTION	99.51
1.99-2.02	0.2789	244	0.239	4395	X-RAY DIFFRACTION	99.49
2.02-2.04	0.2628	236	0.2238	4487	X-RAY DIFFRACTION	99.58
2.04-2.07	0.2819	245	0.2191	4373	X-RAY DIFFRACTION	99.55
2.07-2.09	0.2392	247	0.2119	4432	X-RAY DIFFRACTION	99.53
2.09-2.12	0.2432	220	0.2032	4429	X-RAY DIFFRACTION	99.68
2.12-2.15	0.2489	246	0.1943	4502	X-RAY DIFFRACTION	99.77
2.15-2.18	0.242	244	0.1899	4399	X-RAY DIFFRACTION	99.74
2.18-2.22	0.2405	226	0.1865	4434	X-RAY DIFFRACTION	99.76
2.22-2.26	0.2488	221	0.18	4478	X-RAY DIFFRACTION	99.85
2.26-2.29	0.2623	214	0.1895	4438	X-RAY DIFFRACTION	99.96
2.29-2.34	0.227	264	0.1844	4459	X-RAY DIFFRACTION	99.92
2.34-2.38	0.2464	226	0.1755	4502	X-RAY DIFFRACTION	99.87
2.38-2.43	0.1994	212	0.1717	4434	X-RAY DIFFRACTION	99.79
2.43-2.48	0.2272	242	0.1761	4486	X-RAY DIFFRACTION	99.83
2.48-2.54	0.2147	225	0.1753	4454	X-RAY DIFFRACTION	99.85
2.54-2.6	0.241	267	0.1766	4427	X-RAY DIFFRACTION	99.87
2.6-2.67	0.2352	259	0.1824	4466	X-RAY DIFFRACTION	99.81
2.67-2.75	0.2396	247	0.1861	4431	X-RAY DIFFRACTION	99.74
2.75-2.84	0.2239	265	0.1836	4408	X-RAY DIFFRACTION	99.79
2.84-2.94	0.2201	239	0.1693	4477	X-RAY DIFFRACTION	99.66
2.94-3.06	0.2164	260	0.1615	4422	X-RAY DIFFRACTION	99.53
3.06-3.2	0.2149	238	0.1559	4470	X-RAY DIFFRACTION	99.39
3.2-3.37	0.1855	250	0.1567	4443	X-RAY DIFFRACTION	99.53
3.37-3.58	0.1719	238	0.1391	4485	X-RAY DIFFRACTION	99.6
3.58-3.86	0.1541	223	0.1303	4512	X-RAY DIFFRACTION	99.66
3.86-4.24	0.153	219	0.1236	4522	X-RAY DIFFRACTION	99.66
4.24-4.86	0.1394	248	0.1126	4508	X-RAY DIFFRACTION	99.73
4.86-6.12	0.1697	237	0.1397	4536	X-RAY DIFFRACTION	99.65
6.12-49.32	0.1869	230	0.1714	4636	X-RAY DIFFRACTION	98.7

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	2.58092906804	0.275414426591	0.319014155808	2.77128435072	0.0511635965118	2.80025580847	0.148383997384	0.162779464771	-0.0368594396547	-0.0503753772989	-0.0536359884933	0.214927778559	0.0830978118898	-0.0314042848666	-0.0855057630043	0.207976614944	-0.00425145688219	0.00649514963072	0.207520977924	-0.00955655900467	0.208381966142	30.2651360733	-5.71579044172	20.7830402727
2	2.58743806899	-0.596002385995	0.0929611164635	2.92145140361	-1.69081864896	2.05281092347	0.188025686978	-0.053456910931	-0.186351493655	0.28380848773	-0.154376033111	-0.107813005093	0.135960321453	0.13820405209	-0.0250123295103	0.27209796261	-0.0368203357911	-0.0056646603873	0.230519952648	-0.0129951024179	0.16714460376	38.1686762728	-13.569851423	31.3515552492
3	2.30665644125	0.612437283383	-0.340980485227	2.37577400792	0.484587470857	2.11331969855	-0.00572176749205	-0.18617426398	-0.198474509787	-0.00606425868207	-0.0196543162979	0.175749476872	0.155952324033	-0.123626691566	0.0373971446153	0.267690467038	0.00250309083265	0.0354015261931	0.199924563515	-0.00537100066814	0.319557896643	15.1862721967	2.74311331827	50.3249392065
4	2.21046770394	0.457433945723	1.23801398128	3.56924535853	0.14874409162	3.52107326539	0.0931162603982	-0.293906938273	-0.144941173838	0.344865625514	-0.0180813477728	0.336044674322	0.186702482194	-0.48496554176	-0.103060157779	0.253270719548	-0.0155751151177	0.0818350672038	0.249012831568	0.0146661074396	0.333258654987	15.3619322401	3.8641903786	56.6297422852
5	5.89158795372	-2.63368857937	0.0838308050109	4.084927547	-0.891554905785	1.52062711015	-0.109373816554	0.231670562246	0.0221940708407	0.166420427828	0.149660544276	0.0862581782118	0.0740860180119	0.30204116608	-0.0305584443796	0.322943051479	-0.00930542790158	-0.0507897577696	0.495139978029	0.0334093067853	0.282004927966	70.0376827965	-2.27534153221	17.8792597797
6	2.06669190503	0.19520262702	-0.582818078763	1.23260876871	0.104108016248	0.673514208086	0.0840004732613	-0.0722783741063	0.0579913780927	0.00351707024973	0.0108824497577	-0.072746634406	-0.038790066967	0.193453198194	-0.0619631811484	0.317354598969	0.0146976826722	-0.00530276978895	0.370394940069	0.0445480506283	0.258028419011	60.5597987819	-7.58128930467	19.5706627082
7	5.78886577191	-0.909168463839	-2.04108621435	2.22556920134	-0.506698908429	3.97740911864	0.108190832203	-0.191280613072	-0.335553298329	0.0468941645129	-0.0307527678356	-0.122779480844	0.29106390902	0.596668669315	-0.0740966240106	0.359235087723	0.0084794711578	-0.0528833979466	0.468665577341	0.00741496267135	0.299412512591	64.638477918	-9.61875337768	27.1047597135
8	5.74709290507	-1.72796535448	-1.53275074282	2.16305511613	1.24818794785	2.42856562677	-0.176824427062	0.168500538987	-0.179192883489	0.0993235145791	0.212927737384	-0.196269333951	0.34347036098	0.458540330542	-0.0226409433111	0.333328733817	0.0451502899829	-0.00486462185811	0.471463604055	-0.000944181695163	0.246589919076	69.0012020003	-11.3575308144	16.4979562167
9	3.58077076595	-0.312703701075	-2.46347253479	0.837166702031	0.477485093047	1.61659783739	0.00903764079058	-0.107550139351	0.0941480085792	-0.170124120766	0.0965382777376	-0.280729663726	0.073780074029	0.227231077967	-0.109758559597	0.37014374616	0.0361547957887	-0.0060899280399	0.47018808268	0.0193380005759	0.327503227591	78.2587032357	-7.56529998345	7.43502950906
10	4.48422075796	0.269523665312	-0.0652615927753	2.06231905186	0.0363921313754	4.83502361044	0.108794692171	-0.204764277079	0.642907691225	-0.152060369171	-0.0082526289201	-0.413493034429	-0.227036944646	0.588591847787	-0.0822717721213	0.437276223831	0.03860468163	0.110375262003	0.394386827539	-0.0396624107205	0.536548680697	88.3746013046	-6.15522895536	0.0079592219073
11	5.70779264907	-0.0379468846953	0.904855259531	7.95476501557	0.731165626603	8.21361676468	0.0902081828812	-0.760807370743	0.691441580023	0.101726202584	-0.646982344421	-0.798000918139	-0.507700226791	1.04869438474	0.584655429923	0.462445290894	-0.122736951155	0.0751542362249	0.74437365963	-0.0430944828123	0.936984234821	99.3752439024	-4.25713523399	2.94345836801
12	3.15188712197	0.0919753944474	-2.06048616996	1.79223863936	-0.430948659313	2.18677335641	0.0262414559848	0.255364630229	0.0543426237556	-0.339717366423	-0.000444851101682	0.230989415488	0.244930210251	-0.460067853326	-0.027469344077	0.41688392923	-0.0319462949751	-0.0679317621326	0.486430654125	0.0531796877337	0.286540847054	49.3864609881	-7.39628645204	0.0953315925897
13	1.66680184464	-0.0142689480276	-0.371757219524	1.3128754085	-0.201854394691	1.17564772336	0.130361746436	0.0738573276453	0.0316197691631	-0.204199927244	-0.0202013689996	-0.228266725913	0.140983994962	0.199626379136	-0.112114470265	0.458511562131	0.0265374896715	-0.00662779523545	0.268498469682	-0.0364880402269	0.269101945214	69.5831281297	-10.6773729541	-3.27568704536
14	2.35821312313	0.0524269367094	0.846465904054	2.01774569541	-0.0117438062367	2.97972363301	0.160487457221	0.144862922851	-0.325329075705	-0.387230877286	0.0561687494448	-0.00351812144019	0.524096878406	0.226945435789	-0.165791725913	0.553179025095	0.0664112459135	0.0307609523734	0.295200089116	-0.0393063831791	0.265602114885	77.1064230196	-13.7295635035	-10.9810175831
15	3.33488148676	-1.78453641726	0.114509605126	6.39430608493	0.0374989639728	1.90673889491	-0.0174099272373	0.188478722432	-0.372793226578	0.631966755906	-0.18346360634	-0.106982959633	0.444837530073	0.0152881123197	0.208854312126	0.294305731096	-0.0440902565669	-0.0206929872227	0.233748315063	-0.0012163434965	0.378019566785	11.9899498032	-11.5062551242	34.5651766786
16	3.16973690725	-0.674314581397	0.832434042304	3.61785992303	-0.443233184635	3.86874196419	-0.222411538567	-0.108679526293	0.593545064177	0.42036825557	-0.236872039218	0.720201058384	-0.808964098768	-0.869644514287	0.433392292291	0.615907272877	0.0920178344605	0.0421226010958	0.371146780744	-0.0950792500695	0.687136753748	2.80106085794	11.4205132327	39.6372151197
17	2.42513111812	-1.41827587724	-0.575850979246	4.31553134289	1.68821858247	2.10208150165	-0.044825321409	0.2804706374	0.27107124951	-0.0249225077398	-0.111109172511	-0.115394586263	-0.40924495033	-0.0682543792847	0.148357220641	0.401416294713	-0.0535283734778	-0.0458051336215	0.291616634257	0.0115561971338	0.35998346364	9.80618165348	-0.159534203286	33.3311360588
18	6.1638709601	-3.78269617373	-0.937015002136	4.86587105351	0.972789552353	2.54912997887	-0.00678880176323	0.669300000307	-0.167241048823	-0.563348031863	-0.237986424462	0.313832410327	-0.0985891997169	-0.332716238088	0.216079080596	0.411692314578	-0.103025090449	-0.0566819128829	0.409839921653	0.0172857234399	0.355346603622	8.36415496702	-8.14148375289	25.7780118841
19	2.0054139429	0.414988798871	0.0860241916608	2.22838891169	-0.00382925746302	3.02254037035	-0.109846657168	0.81338704788	0.693806147139	-0.8300230994	0.0360787762244	0.263136081526	-0.0817295027271	0.148234766994	0.118229400788	0.600878268106	0.0235928817184	-0.115776520335	0.48280158836	0.04616763459	0.477386039022	3.00837719649	1.56752968991	24.0400654349
20	4.63944676093	-2.01756870919	0.881342089314	5.80781431629	-1.8967752941	4.44943025471	-0.116078030537	0.350925653903	0.0947601864352	-0.465879389196	0.265386986359	-0.0445495490825	0.317832202909	0.0580743310817	-0.119675911488	0.402878234213	-0.0754373530846	0.0249080299944	0.322504877899	-0.0458561054396	0.356136275206	22.4762488182	-8.54660391569	30.0766401504
21	6.3460057511	-3.69846408042	-0.570866997025	5.05037980327	0.907896390928	2.52426942065	0.0284580876924	0.306396670915	0.658729485062	-0.407244356189	-0.0375988460185	-0.0459353920892	-0.456512720052	-0.223809593841	0.0292842786894	0.43546873721	-0.0386254073654	-0.0551876851655	0.320437499286	0.00415391402961	0.388381603822	10.3842510154	1.25171729399	29.7400668387
22	0.675437014344	-0.451664656199	-0.205837746403	0.30755086181	0.145666206952	0.0691146984739	0.321450345481	0.306471503023	0.611295126119	-0.0974433333116	-0.100662110452	0.808948153811	-0.0857059074525	-0.34442921704	-0.188700485176	0.509240659285	0.127143959638	-0.119802337985	0.543757077839	-0.108261142478	1.09516159342	-6.62963731942	5.88642128259	35.2164521465
23	3.19127907445	-3.0344214689	-0.785076442983	6.22346828963	-0.380099076226	1.73140812463	0.183112423183	0.387667685821	-0.207438424695	-1.13698313602	-0.577507545009	0.900991382657	-0.01466569475	-0.418507601421	0.364829934193	0.352793656766	-0.00947215621488	-0.114311546454	0.410098563764	-0.111846706513	0.468122817661	4.23962316881	-11.5410052287	28.3040779607
24	6.91259226281	-1.14206804821	-0.401713993161	9.50419242119	3.09886448869	8.61816177902	0.452253547239	-0.839936154974	0.616256353826	0.676125040068	-0.267045548953	0.666622613188	-0.6431416894	-0.656766067558	-0.255028631495	0.416730306218	-0.0516628479309	0.0856154786677	0.519157553057	0.00897626373755	0.544715933979	0.0430079216315	-2.45388923749	38.5004068309
25	2.01665010261	0.364637481155	-0.51458036854	2.43411469696	-0.425904251925	1.42561516506	0.0183373601032	0.000983459573012	0.26352924491	-0.0272159429666	-0.00805552493569	0.074167509684	-0.117331051416	0.00537642453576	-0.000192328062247	0.184713432866	0.0365344021347	-0.0342412475208	0.284982698171	-0.0128245378098	0.288037468568	-9.84136739889	-25.1302454967	48.7471105267
26	1.13903028118	-1.08967255893	0.0160087330565	2.23323751333	-0.796088383271	1.19667293859	0.158192213673	0.18425377299	-0.317410489616	-0.00253089440745	-0.0817622153007	-0.41897084466	0.0585818132316	-0.0131289150662	-0.0768519438416	0.221232585247	0.0373767029889	0.0220296708587	0.256492534124	-0.00772902669059	0.158907331848	-5.4655945542	-32.8176622944	42.6993470373
27	2.37088254841	0.398763647178	-0.869046283823	2.22025491655	0.150899626734	2.37521899683	-0.0349664479744	0.429340099534	0.462837465271	-0.26390623856	0.0297561796778	0.0216533114872	-0.507793661447	0.205598460187	-0.00309791482817	0.386436370735	-0.0438905249336	-0.119616690993	0.510503008201	0.0626712646111	0.444635604279	-30.5225515918	-24.2570806363	20.871723949
28	2.13972656488	-1.17890848741	0.0189037022204	1.65411661661	-0.209847018659	1.75817053075	-0.0033336473962	-0.100076073567	-0.139929890383	-0.0381011293888	0.0817501206815	0.0717091368573	0.158990075648	-0.0446022919595	-0.0712468213501	0.201254695785	0.00544921550853	0.0131518126665	0.23408797243	-0.00793496683712	0.278211204116	14.0212429187	-46.8913252955	55.1703421729
29	3.14694974644	-1.46071594823	1.27685224971	1.73444675034	-0.524515541936	2.32638057618	-0.062754550016	-0.038027957186	0.140121937526	-0.044089413289	-0.00520459280829	-0.129277533303	-0.0261347466748	0.0691079533633	0.063215958169	0.213187903464	0.00197337188417	0.00724427754431	0.20387813516	-0.0128247976253	0.264006166556	16.0915207989	-45.7334111497	53.9293521426
30	4.71972118282	-1.00951504558	1.70583838351	3.07857209087	1.10506105689	1.36504985761	0.0987323794328	0.587581987605	0.193597564421	-0.0328822572538	-0.281680906346	-0.333414965544	0.359038471961	0.400355481827	0.185414175275	0.27613710597	0.0508473952999	0.0200927994436	0.289113897868	-0.0530579772314	0.402228262473	43.4064463285	-58.2980861332	68.7365193742
31	3.57441846565	-0.794348377314	-0.708066282764	3.05140103954	1.23915500895	4.30760053224	-0.0238738323749	0.0775513774064	-0.276309896949	0.458952131835	-0.00236005450032	-0.0345289199474	0.430424996107	0.00375655007695	0.0329664473163	0.347190782895	0.0232189423569	-0.00985178731039	0.218347406586	-0.0275605273155	0.339360145878	37.1673106428	-60.4425075148	76.9614964182
32	1.94682252431	-0.0652695724272	-0.35449231277	2.48132115504	-1.34651000958	2.13169723947	0.00753260402447	-0.308416761811	0.171572347491	0.349223279664	-0.122653405827	-0.14817972224	-0.416293046964	0.0547086754284	0.0694384297898	0.273454044198	0.0238570392093	-0.0149292073961	0.390013055547	-0.0352475126234	0.285593013953	7.00194478778	-35.4352629958	76.0106968802
33	2.45951602533	-0.137733913143	-0.59896130437	2.4203297906	-1.01671685551	2.33509743297	-0.0555955832107	-0.151171108143	-0.0079049054857	0.0413421305823	0.00643766695083	0.163987171238	-0.108617111151	-0.241521877622	0.0527917427447	0.194891729152	0.0320207874032	-0.0163783866402	0.272346949984	-0.0477366076801	0.227205663808	2.09816281095	-37.040586335	70.4364031389
34	2.9217459486	-1.12746762329	1.75798163112	1.47413119815	-0.720234723119	2.45894697502	0.0366254615591	-0.00681062130058	-0.31334508279	-0.187400716066	0.0325931258795	0.133893765473	0.419050786088	-0.579344459373	-0.0201566048479	0.286410423151	-0.00865930445016	0.0342425286774	0.385413384888	-0.00769822981467	0.292744532	11.7253648205	-49.5675663358	88.141264665
35	3.92879716603	-0.226566339092	-1.26002408851	2.24869640313	0.571475916365	3.21426111452	0.064384932261	0.271069640407	-0.0942890347259	0.113012708713	-0.0561788651343	0.110532704984	-0.0828949067563	-0.198484619405	-0.0045800270462	0.272072694045	0.0372926954961	-0.0074632473672	0.207909923375	-0.00455359430295	0.217833608679	33.3945012453	-50.1181640135	81.1035741703
36	4.68266974159	0.752208251308	-2.26798791535	0.682084088479	0.0707261902315	1.64196417333	0.337156443075	-0.0217777796734	0.201792848332	0.0577878368806	-0.105040789702	-0.0662692458453	-0.259713899462	-0.0673360800764	-0.179377644178	0.322416074544	0.0370871836431	-0.0353245556117	0.293086202218	-0.0343700231629	0.2863540157	29.0214105983	-43.7605142491	91.407924279
37	2.24733961265	-1.77610185083	-2.66097401255	5.90035153285	0.666776810219	5.29997249896	0.000466458468639	-0.361353695013	1.27956920539	-0.402758522916	0.276710100682	-0.473091572425	-0.539772416535	0.53174926893	-0.291443182154	0.612778714406	-0.020635215308	-0.0433704523669	0.548184484366	0.0508111473217	0.941568374948	-15.878404556	-7.23738789455	41.1874176923
38	3.05884733732	-0.527520777641	-0.569506197858	1.81355578979	-0.113720294824	1.76169123059	-0.257115390169	0.330433077745	0.472979232129	-0.276657242583	0.129872823886	0.896377204483	-0.00593418820076	-0.585946258247	0.149738571669	0.402137761319	0.059132183997	-0.158576880063	0.60272090592	-0.0431579499461	0.735005928983	-36.1658508344	-19.7073617916	37.9565439358
39	2.89452064446	-0.106889536135	1.07487550128	0.16088891437	-0.339872372499	0.947437477053	-0.233308243923	-0.847348981819	0.854934093453	0.113139917418	0.00521242316026	0.508273691137	-0.520297446375	-0.294177235809	0.194356553505	0.47353062042	0.170597112485	-0.102297797184	0.618484790561	-0.218020445326	0.861085931943	-28.7339370767	-11.1400036504	47.3752842306
40	6.1488686429	-1.69489628752	-0.00189643030181	1.1145757035	0.736202815524	1.24554914709	0.00373086910583	-0.4532140356	-0.113153796648	0.277724104519	-0.139865693881	0.879015167919	-0.140429724695	-0.303967222732	0.11685226114	0.52499323734	0.219350323751	0.0802399180123	0.861310302112	-0.0385549696309	0.984066991653	-38.9503054078	-14.807367135	49.5499750316
41	7.5707054111	-0.764469269918	-4.6803017907	3.56817016128	0.341124588817	5.22601226709	-0.209795291339	-0.564479877083	-0.576585020323	0.178023052084	0.0609052814271	0.191441217993	-0.502034251919	0.321488421072	0.142916218714	0.432880837611	0.0297775271434	-0.115280113524	0.514874263585	-0.00693982711123	0.437695859416	-21.7068149913	-21.8787494177	47.5118456396
42	2.1240877497	2.32915686614	0.897091142472	5.31993553594	-1.3906340666	7.62161191454	0.101328234238	0.501099034273	0.096563211479	-0.460315605045	0.32658091289	0.590894390381	0.0230049514294	-0.617587042304	-0.420698449772	0.313732298155	0.029616102281	-0.0976843467724	0.342364511267	0.00895580983401	0.477462727073	-13.4436438041	-18.6596788985	39.9455093955
43	2.03577794044	-1.02928645175	-0.504597380838	1.43364835396	0.0962062274088	2.33166191182	-0.598744711777	-1.04354420139	0.282155693745	0.207285689245	0.1892739436	0.507719043317	0.131828517552	-0.534773791762	0.417727126068	0.383197354209	0.0695306183736	-0.0141145486208	0.612308429196	-0.0700571071366	0.658278944914	-33.2936095704	-20.0985210797	44.3558603262
44	0.000318924271938	-0.00103857985287	-0.00169454024069	0.000782785058095	0.00209838960378	0.000161216057393	-0.401005952708	-0.319763415745	0.416201646509	-0.240531512487	-0.305982461822	0.366863332624	-0.538865860673	-0.369533352492	0.651750385027	0.605953874387	0.133329059272	-0.302904128904	1.19332400854	-0.0216525269028	1.21515234958	-49.5162828379	-13.9558015526	38.4635929987
45	5.14964650216	0.197948263698	0.537581629775	0.944636947963	0.412920067842	1.95091163109	0.240625927883	-0.281580243831	0.531521124525	0.0639432714311	0.324291570488	0.0572949992238	-0.214839797105	0.0213956213553	-0.4406889465	0.385341798621	0.157020036314	-0.0269153274971	0.621825953294	-0.2046350217	1.35545685297	-35.2577503857	-9.36584900127	43.8998903802
46	3.39700260038	-2.96704018584	1.29382159521	2.5911633783	-1.13403844765	0.49654354392	0.0549091368843	-0.0308080399781	0.259512102471	0.166989423959	-0.038308009323	0.836124776165	-0.62810054629	-0.483148857591	-0.0403454187508	0.545788750395	0.130251843679	-0.111305858466	0.567486541905	-0.16455917122	1.26640031845	-24.4478114293	-2.91624742031	44.6743189521
47	2.30253059734	2.53999456876	-0.224311210923	6.33805383557	0.844290400055	1.41815840222	-0.145094120392	0.170016105417	0.131825888405	-0.608008489748	-0.0762743218728	0.0620601717064	-0.10112389234	-0.139161508745	0.161102295694	0.552729660655	0.206910846409	-0.259977046119	0.500310596927	-0.0432028278888	1.15171143412	-36.993102257	-9.52371494717	36.7765618238

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 'C' and (resid 1 through 83 )	C	A	1 - 83	1 - 83
2	2	chain 'C' and (resid 84 through 171 )	C	A	84 - 171	84 - 171
3	3	chain 'C' and (resid 172 through 237 )	C	A	172 - 237	172 - 237
4	4	chain 'C' and (resid 238 through 270 )	C	A	238 - 270	238 - 266
5	5	chain 'D' and (resid 1 through 17 )	D	C	1 - 17	1 - 17
6	6	chain 'D' and (resid 18 through 52 )	D	C	18 - 52	18 - 52
7	7	chain 'D' and (resid 53 through 75 )	D	C	53 - 75	53 - 75
8	8	chain 'D' and (resid 76 through 91 )	D	C	76 - 91	76 - 91
9	9	chain 'D' and (resid 92 through 135 )	D	C	92 - 135	92 - 129
10	10	chain 'D' and (resid 136 through 188 )	D	C	136 - 188	130 - 181
11	11	chain 'D' and (resid 189 through 199 )	D	C	189 - 199	182 - 192
12	12	chain 'E' and (resid 3 through 94 )	E	D	3 - 94	1 - 92
13	13	chain 'E' and (resid 95 through 140 )	E	D	95 - 140	93 - 138
14	14	chain 'E' and (resid 141 through 244 )	E	D	141 - 244	139 - 242
15	15	chain 'F' and (resid 0 through 11 )	F	E	0 - 11	1 - 12
16	16	chain 'F' and (resid 12 through 19 )	F	E	12 - 19	13 - 20
17	17	chain 'F' and (resid 20 through 30 )	F	E	20 - 30	21 - 31
18	18	chain 'F' and (resid 31 through 41 )	F	E	31 - 41	32 - 42
19	19	chain 'F' and (resid 42 through 51 )	F	E	42 - 51	43 - 52
20	20	chain 'F' and (resid 52 through 61 )	F	E	52 - 61	53 - 62
21	21	chain 'F' and (resid 62 through 71 )	F	E	62 - 71	63 - 72
22	22	chain 'F' and (resid 72 through 77 )	F	E	72 - 77	73 - 78
23	23	chain 'F' and (resid 78 through 90 )	F	E	78 - 90	79 - 91
24	24	chain 'F' and (resid 91 through 99 )	F	E	91 - 99	92 - 100
25	25	chain 'A' and (resid 0 through 133 )	A	F	0 - 133	1 - 134
26	26	chain 'A' and (resid 134 through 182 )	A	F	134 - 182	135 - 183
27	27	chain 'A' and (resid 183 through 270 )	A	F	183 - 270	184 - 264
28	28	chain 'B' and (resid 1 through 52 )	B	H	1 - 52	1 - 52
29	29	chain 'B' and (resid 53 through 108 )	B	H	53 - 108	53 - 108
30	30	chain 'B' and (resid 109 through 120 )	B	H	109 - 120	109 - 120
31	31	chain 'B' and (resid 121 through 200 )	B	H	121 - 200	121 - 200
32	32	chain 'G' and (resid 2 through 37 )	G	I	2 - 37	2 - 37
33	33	chain 'G' and (resid 38 through 109 )	G	I	38 - 109	38 - 109
34	34	chain 'G' and (resid 110 through 124 )	G	I	110 - 124	110 - 124
35	35	chain 'G' and (resid 125 through 202 )	G	I	125 - 202	125 - 202
36	36	chain 'G' and (resid 203 through 244 )	G	I	203 - 244	203 - 244
37	37	chain 'H' and (resid 0 through 5 )	H	J	0 - 5	1 - 6
38	38	chain 'H' and (resid 6 through 30 )	H	J	6 - 30	7 - 31
39	39	chain 'H' and (resid 31 through 41 )	H	J	31 - 41	32 - 42
40	40	chain 'H' and (resid 42 through 51 )	H	J	42 - 51	43 - 52
41	41	chain 'H' and (resid 52 through 56 )	H	J	52 - 56	53 - 57
42	42	chain 'H' and (resid 57 through 61 )	H	J	57 - 61	58 - 62
43	43	chain 'H' and (resid 62 through 71 )	H	J	62 - 71	63 - 72
44	44	chain 'H' and (resid 72 through 77 )	H	J	72 - 77	73 - 78
45	45	chain 'H' and (resid 78 through 83 )	H	J	78 - 83	79 - 84
46	46	chain 'H' and (resid 84 through 90 )	H	J	84 - 90	85 - 91
47	47	chain 'H' and (resid 91 through 96 )	H	J	91 - 96	92 - 97

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About Yorodumi

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News

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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

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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

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Protein , 4 types, 8 molecules CADBEGFH

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