PDB-6mzg: Structural Basis of Tubulin Recruitment and Assembly by Microtubu...

ID or keywords:

Entry

Database: PDB / ID: 6mzg

Title

Structural Basis of Tubulin Recruitment and Assembly by Microtubule Polymerases with Tumor Overexpressed Gene (TOG) Domain Arrays

Components

Protein Stu2p/Alp14p
Truncated Darpin-D1
Tubulin alpha-1A chain
Tubulin beta chain

Keywords

CELL CYCLE / Microtubule / Tubulin / Tubulin polymerization / Heat repeats / Microtubule polymerase / Protofilament / TOG arrays / and Unfurled assembly.

Function / homology

Function and homology information

microtubule plus end polymerase / supramolecular complex / establishment or maintenance of microtubule cytoskeleton polarity / microtubule plus-end binding / intracellular non-membrane-bounded organelle / spindle organization / microtubule polymerization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...
Similarity search - Function

Biological species

Lachancea kluyveri NRRL Y-12651 (fungus)

Escherichia coli (E. coli)

Sus scrofa (pig)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.208 Å

Authors

Nithianantham, S. / Al-Bassam, J.

Funding support

United States, 1items

Citation

Journal: Elife / Year: 2018
Title: Structural basis of tubulin recruitment and assembly by microtubule polymerases with Tumor Overexpressed Gene (TOG) domain arrays.
Authors: Nithianantham, S. / Cook, B.D. / Beans, M. / Guo, F. / Chang, F. / Al-Bassam, J.

History

Deposition	Nov 5, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 28, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6mzg.cif.gz	1.8 MB	Display	PDBx/mmCIF format
PDB format	pdb6mzg.ent.gz	1.5 MB	Display	PDB format
PDBx/mmJSON format	6mzg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6mzg_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	6mzg_full_validation.pdf.gz	2.8 MB	Display
Data in XML	6mzg_validation.xml.gz	151.6 KB	Display
Data in CIF	6mzg_validation.cif.gz	202.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mz/6mzg ftp://data.pdbj.org/pub/pdb/validation_reports/mz/6mzg	HTTPS FTP

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Related structure data

Related structure data	6mzeC 6mzfC C: citing same article (ref.)
Similar structure data	6bbn-d 7740 6iqu-1 2g5b-d 6iqs-d 7lkp-d 7jmn-d 3slk-d 7lbe-d 6utk-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#175 - Jul 2014 Microtubules similarity (21) #176 - Aug 2014 Dynein similarity (17) #241 - Jan 2020 Twenty Years of Molecules similarity (17)

Deposited unit

A: Tubulin alpha-1A chain

B: Tubulin beta chain

C: Tubulin alpha-1A chain

D: Tubulin beta chain

E: Protein Stu2p/Alp14p

F: Truncated Darpin-D1

G: Tubulin alpha-1A chain

H: Tubulin beta chain

I: Tubulin alpha-1A chain

J: Tubulin beta chain

K: Protein Stu2p/Alp14p

L: Truncated Darpin-D1

hetero molecules

560 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tubulin alpha-1A chain

B: Tubulin beta chain

C: Tubulin alpha-1A chain

D: Tubulin beta chain

E: Protein Stu2p/Alp14p

F: Truncated Darpin-D1

hetero molecules

defined by author
Evidence: gel filtration, Gel filtration study confirms that skAlp14-tubulin forms unfurled assemblies in solution
280 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: Tubulin alpha-1A chain

H: Tubulin beta chain

I: Tubulin alpha-1A chain

J: Tubulin beta chain

K: Protein Stu2p/Alp14p

L: Truncated Darpin-D1

hetero molecules

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

Unit cell

Length a, b, c (Å)	115.130, 194.990, 149.570
Angle α, β, γ (deg.)	90.000, 90.190, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 4 types, 12 molecules ACGIBDHJEKFL

#1: Protein	Tubulin alpha-1A chain / Alpha-tubulin 1 / Tubulin alpha-1 chain Mass: 50121.266 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Brain / References: UniProt: P02550
#2: Protein	Tubulin beta chain / Beta-tubulin Mass: 49907.770 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Brain / References: UniProt: P02554
#3: Protein	Protein Stu2p/Alp14p Mass: 63099.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Protein was obtained from cDNA (Lachancea kluyveri NRRL Y-12651 chromosome) Source: (gene. exp.) Lachancea kluyveri NRRL Y-12651 (fungus) Gene: SKLU-Cont10078 / Plasmid: pLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A493R6X8*PLUS
#4: Protein	Truncated Darpin-D1 Mass: 14998.981 Da / Num. of mol.: 2 / Mutation: N-terminal truncation (residues 1-40) Source method: isolated from a genetically manipulated source Details: N-terminal residues (1-40) of Darpin-D1 were truncated. Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21

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Non-polymers , 3 types, 16 molecules

#5: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Comment: GTP, energy-carrying molecule*YM
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#7: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.02 Å³/Da / Density % sol: 59.24 % / Description: Rectangular crystal
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50 mM PIPES, 100 mM MgCl2 [pH 7.0], and 10-15% PEG-8000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.9792 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 25, 2014

Radiation

Monochromator: Cryo-Cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection twin

Operator: h,-k,-l / Fraction: 0.49

Reflection

Resolution: 3.2→149.571 Å / Num. obs: 104265 / % possible obs: 96.2 % / Redundancy: 2.9 % / B_iso Wilson estimate: 46.6 Å² / R_pim(I) all: 0.105 / R_rim(I) all: 0.186 / R_sym value: 0.133 / Net I/av σ(I): 5.2 / Net I/σ(I): 5.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	R_pim(I) all	R_rim(I) all	R_sym value	% possible all
3.2-3.37	2.9	0.654	1.1	15435	0.547	0.961	0.654	97.9
3.37-3.58	2.7	0.408	1.8	14072	0.339	0.593	0.408	94
3.58-3.82	2.9	0.261	2.8	13735	0.207	0.364	0.261	97.6
3.82-4.13	2.9	0.167	4.3	12776	0.133	0.236	0.167	97.9
4.13-4.53	2.7	0.112	6.3	11239	0.086	0.151	0.112	93.1
4.53-5.06	3	0.086	8.2	10724	0.065	0.117	0.086	98.8
5.06-5.84	2.8	0.092	7.6	9087	0.072	0.128	0.092	94.3
5.84-7.16	3	0.109	5.9	7947	0.075	0.137	0.109	97.2
7.16-10.12	2.9	0.04	15.3	5925	0.029	0.052	0.04	94.1
10.12-57.565	3	0.029	20.1	3325	0.019	0.035	0.029	94.7

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.3.21	data scaling
PHENIX		refinement
PDB_EXTRACT	3.24	data extraction
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.208→57.565 Å / Cross valid method: THROUGHOUT / σ(F): 1.21 / Phase error: 22.19 / Details: The twin fractions were adjusted during refinement

	R_factor	Num. reflection	% reflection
R_free	0.2341	4535	5.13 %
R_work	0.1753	-	-
obs	0.1802	88337	81.93 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / B_sol: 76.2 Å² / k_sol: 0.34 e/Å³

Displacement parameters

B_iso max: 152.59 Å² / B_iso mean: 48.5489 Å² / B_iso min: 0.63 Å²

Refinement step

Cycle: final / Resolution: 3.208→57.565 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	36617	0	248	0	36865
B_iso mean	-	-	36.43	-	-
Num. residues	-	-	-	-	4660

Refine LS restraints

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	f_bond_d	0.002
X-RAY DIFFRACTION	f_angle_d	0.501
X-RAY DIFFRACTION	f_chiral_restr	0.039
X-RAY DIFFRACTION	f_plane_restr	0.004
X-RAY DIFFRACTION	f_dihedral_angle_d	5.783

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 (%)
3.218-3.2735	0.3176	26	0.2412	421	X-RAY DIFFRACTION	8
3.2735-3.333	0.2352	51	0.2131	1014	X-RAY DIFFRACTION	19
3.333-3.3971	0.3437	91	0.2074	1760	X-RAY DIFFRACTION	33
3.3971-3.4664	0.3034	158	0.2063	3007	X-RAY DIFFRACTION	57
3.4664-3.5417	0.3212	257	0.2018	4662	X-RAY DIFFRACTION	88
3.5417-3.6241	0.2733	230	0.1898	4652	X-RAY DIFFRACTION	87
3.6241-3.7147	0.2701	256	0.1878	5017	X-RAY DIFFRACTION	94
3.7147-3.8151	0.2389	268	0.1805	4949	X-RAY DIFFRACTION	94
3.8151-3.9273	0.2747	256	0.174	4991	X-RAY DIFFRACTION	94
3.9273-4.054	0.2305	294	0.1706	4938	X-RAY DIFFRACTION	92
4.054-4.1989	0.2354	236	0.1668	4875	X-RAY DIFFRACTION	92
4.1989-4.3669	0.2306	228	0.1624	4725	X-RAY DIFFRACTION	88
4.3669-4.5655	0.2107	249	0.157	4689	X-RAY DIFFRACTION	88
4.5655-4.806	0.1801	270	0.1535	5017	X-RAY DIFFRACTION	94
4.806-5.1069	0.2117	257	0.1607	4970	X-RAY DIFFRACTION	93
5.1069-5.5007	0.2384	284	0.176	4894	X-RAY DIFFRACTION	91
5.5007-6.0534	0.2634	224	0.2014	4607	X-RAY DIFFRACTION	86
6.0534-6.9273	0.2593	253	0.2017	5012	X-RAY DIFFRACTION	94
6.9273-8.7201	0.2023	220	0.1801	4840	X-RAY DIFFRACTION	90
8.7201-49.8624	0.1819	262	0.1785	4894	X-RAY DIFFRACTION	90

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	1.4486	-0.2451	0.2141	0.7869	0.1523	1.8871	-0.0029	0.173	0.3714	-0.3559	-0.0895	-0.2194	-0.7419	0.3465	-0.0798	0.3632	-0.1265	0.079	0.4075	0.0219	0.1345	9.561	35.1653	-9.7158
2	0.7404	-0.0219	-0.7602	0.9153	-0.1969	1.7958	-0.0226	-0.1027	-0.0021	0.0916	0.0018	-0.1462	-0.1331	0.4576	-0.0902	0.2296	0.0904	0.0144	0.3909	-0.0588	0.1115	11.2129	20.9893	0.5403
3	0.8838	-0.3995	-0.497	0.5111	0.13	0.5835	0.1004	0.2036	-0.0234	-0.2706	-0.1136	0.0807	-0.1222	-0.1549	0.1755	0.4788	0.2253	0.0281	0.3216	-0.0864	0.2198	-7.3916	31.1736	-1.032
4	1.2958	-0.586	0.3188	1.0324	0.3599	0.9206	0.0386	-0.0549	0.1067	0.0333	-0.0339	0.0778	-0.3499	-0.1998	-0.0122	0.5227	0.1137	0.2319	0.4586	-0.094	0.3525	-5.8346	37.6276	12.8083
5	0.1442	0.0234	-0.519	0.0455	0.0881	2.5425	0.15	-0.1086	0.0416	-0.1159	-0.0996	0.079	0.0331	-0.1279	-0.0231	0.7386	-0.09	0.1026	0.4626	0.0501	0.5787	-6.0062	40.378	11.6582
6	0.1241	-0.0543	-0.0451	0.3995	0.1371	0.2285	-0.0242	-0.1754	0.0256	0.0723	-0.047	0.015	-0.013	-0.0783	-0.1142	0.392	0.1423	0.2029	0.2995	0.0287	0.1075	-0.1946	12.7038	9.8486
7	2.1559	-0.5864	-0.3196	4.1017	-1.1449	1.5658	-0.0073	0.1884	0.3246	-0.229	-0.0006	-0.1137	-0.2324	-0.0368	0.0029	0.6004	0.2272	0.1198	0.4432	0.0552	0.267	-2.7452	9.6828	-33.3477
8	1.1346	0.3329	-0.2336	0.9096	0.4277	0.5411	-0.0528	0.1608	0.0676	-0.1882	-0.063	0.0948	-0.0796	-0.0093	-0.1769	0.2272	0.1202	0.1032	0.3612	-0.0242	0.1243	-2.1655	-6.8539	-28.3641
9	1.5179	0.2094	-0.1222	2.6255	0.1952	1.0786	0.0018	0.3061	0.0923	-0.5997	-0.0774	0.6175	-0.3564	-0.3957	0.0716	0.3598	0.1295	-0.021	0.4061	-0.0506	0.2519	-15.937	3.9576	-16.4982
10	0.2898	0.0114	-0.2494	0.8624	0.7445	0.8923	0.1068	-0.0189	0.1359	0.1106	-0.057	0.2289	-0.1005	-0.0896	0.0149	0.305	0.0146	0.1035	0.3812	-0.0943	0.1279	-11.0499	-7.8477	-12.3076
11	0.689	-0.32	0.1303	0.5346	-0.1066	0.6983	-0.0485	0.0236	0.2756	-0.0185	-0.0728	-0.1841	0.0697	0.1303	0.0818	0.1582	-0.0892	0.115	0.1662	0.0217	0.2116	-0.6823	-38.6096	-53.571
12	1.1884	-0.1356	0.8979	0.1787	-0.4195	1.7879	-0.0448	0.1237	0.342	0.1624	-0.0821	0.0832	-0.1735	-0.1858	-0.1862	0.2457	-0.0772	0.1911	0.19	-0.0379	0.3649	-19.2944	-32.1987	-41.3924
13	0.2743	0.3324	0.1178	0.4756	0.2305	0.2135	-0.0483	-0.0107	0.0823	-0.0043	-0.0578	0.1456	-0.0659	0.072	-0.4777	0.2149	-0.0648	0.123	0.2486	0.098	0.2064	-9.5214	-45.1638	-38.3254
14	1.3443	0.5264	-0.1561	1.8409	-1.2222	2.5794	-0.0218	0.331	0.2535	-0.128	0.0606	0.1963	-0.5257	-0.2939	-0.1606	0.8361	-0.0061	0.1643	0.6322	0.135	0.3025	4.1975	-66.0032	-76.8988
15	0.7285	-0.1169	-0.1527	1.0051	0.1511	0.997	0.0063	0.3978	-0.2664	-0.4113	-0.0594	-0.0385	0.0085	-0.1661	0.0576	0.362	0.0499	0.0969	0.4358	-0.0801	0.2048	9.2256	-79.511	-67.8761
16	1.3592	0.1888	-0.2768	1.1407	-0.2463	0.9243	0.1782	0.7068	-0.142	-0.4201	0.0213	0.4318	-0.2058	-0.4195	-0.0093	0.3338	0.1621	-0.0776	0.4978	-0.1287	0.3957	-11.6839	-70.6478	-60.2389
17	1.1466	-0.4982	-0.4387	0.8889	0.3968	0.8358	-0.0199	-0.0564	-0.092	0.1412	0.0599	0.1049	0.0088	0.0975	0.0535	0.3999	0.1602	0.2371	0.3923	0.0376	0.3316	5.6009	-88.4757	-51.2804
18	3.9694	2.0621	4.0298	1.4005	2.1668	4.5717	0.0536	0.8913	-0.5198	-0.1842	0.2304	-1.0975	0.3333	1.3668	-0.2913	0.5232	0.0635	0.1377	0.3662	-0.0827	0.524	19.8021	-115.1397	-52.3022
19	1.5312	0.3548	-1.5547	0.2986	-0.0384	2.0566	-0.0601	-0.0116	-0.1045	-0.0131	0.0077	-0.1338	0.2179	0.1434	0.0357	0.1711	0.1474	-0.0157	0.2679	-0.0812	0.1354	14.1604	-112.2129	-61.8318
20	8.6505	-5.463	0.8491	5.4091	-1.4426	2.8399	-0.147	0.1117	-0.7154	0.0701	-0.0281	0.8713	0.3045	-0.5217	0.1668	0.2305	0.0386	0.1369	0.412	-0.1475	0.562	12.4235	-120.0535	-68.0832
21	4.0153	-2.5987	-4.9586	1.7297	3.0882	6.435	-0.0159	0.1595	-0.1885	0.1021	-0.1134	0.2547	0.0465	-0.2615	0.1765	0.4954	0.1022	-0.1423	0.3839	0.084	0.2215	11.6657	-118.4142	-53.5613
22	0.8604	0.1824	0.0566	2.386	0.2152	0.0214	0.0096	-0.3134	-0.3135	0.2029	0.2028	0.2373	0.3654	-0.1931	-0.2477	0.4446	0.2068	-0.0124	0.3487	0.0899	0.2455	6.3896	-109.7452	-59.2596
23	1.137	0.143	0.6089	0.4387	0.1863	0.5193	-0.0165	-0.1416	-0.1037	0.0031	-0.0958	0.1082	0.0183	-0.1893	0.0614	0.1503	0.0778	0.1008	0.4469	-0.0487	0.5448	3.0949	-115.2024	-57.0476
24	0.3784	-0.1257	0.1795	2.4639	1.1122	0.6521	-0.0929	0.0976	-0.3081	-0.1544	-0.0896	-0.0496	0.3936	0.1389	0.2	0.4367	0.1989	0.2271	0.4994	-0.0928	0.5892	-0.4539	-105.0611	-56.491
25	0.0655	0.6151	-0.1542	6.3665	-2.1137	1.1237	0.0474	0.0304	0.2795	0.1108	0.2058	0.5849	-0.0796	-0.4196	-0.281	0.3017	-0.0387	0.2402	0.3065	-0.0186	0.6239	-5.5857	-111.5797	-62.2603
26	1.3625	2.1	2.2888	3.2517	3.5316	3.8458	0.0378	0.0342	0.0624	-0.1086	-0.0182	0.0584	-0.0404	0.0197	-0.0116	0.7116	0.0176	-0.1421	0.938	0.1001	0.6926	-4.9226	-108.0926	-46.06
27	5.3379	-2.9535	-1.1756	6.36	-1.4883	1.2292	-0.0206	-0.191	-0.1843	0.1384	0.0335	0.0526	0.2473	-0.1444	-0.018	0.7498	0.1682	0.0435	0.8403	-0.0793	0.8345	-8.5095	-99.5451	-51.7988
28	0.6835	1.3032	0.3624	2.4851	0.6913	0.1934	0.0686	-0.2231	0.2541	0.3316	-0.0195	0.3469	-0.1597	-0.1505	-0.0551	0.8893	0.2917	-0.0533	0.9722	-0.2812	0.9447	-13.3615	-103.4718	-59.2634
29	1.0255	0.0113	0.1207	1.0173	0.1411	0.8913	-0.2181	0.0101	-0.3509	0.0862	-0.0195	-0.2369	0.3781	0.216	0.0133	0.1921	0.0343	0.1944	0.2596	-0.0221	0.2096	29.2613	-15.553	-10.113
30	0.2871	-0.0935	0.0545	0.8886	0.3761	0.3726	-0.1435	0.0428	-0.2967	0.0991	0.2524	-0.5728	0.3366	0.5203	-0.1246	0.5785	0.0897	0.278	0.5201	-0.0103	0.794	44.6691	-82.6608	-49.691
31	2.0411	-1.0031	-0.9159	1.2419	0.2472	1.3144	-0.1161	-0.4503	0.2191	0.0841	0.0051	-0.093	-0.0401	0.2838	-0.0214	0.2573	0.0998	0.0622	0.2229	-0.0067	0.271	31.9591	-65.7179	-39.9058
32	1.3929	0.2753	-0.152	0.4514	-0.5928	0.9926	-0.1393	-0.4225	-0.5987	0.425	0.0842	0.2173	0.2935	0.1958	0.0122	0.4804	0.0812	-0.0363	0.3288	0.0632	0.3629	-48.6861	-66.8734	-65.1224
33	1.3847	-0.6138	0.0792	1.8624	-0.0244	1.9053	-0.1447	-0.3073	-0.1511	0.382	0.1392	-0.1554	0.247	0.018	-0.0389	0.2632	0.141	-0.0754	0.276	0.0519	0.1537	-41.6369	-49.8163	-66.5466
34	1.0394	0.4005	-0.6792	2.1404	1.2031	3.3618	0.1257	0.1317	-0.01	-0.0182	0.0676	-0.1091	0.0483	0.0733	-0.0118	0.2376	0.0452	0.0239	0.2374	-0.0355	0.0712	-44.143	-53.6362	-75.7666
35	0.7616	0.2314	0.3531	0.9818	-0.0368	0.7489	-0.0383	-0.077	-0.0905	0.0666	0.0195	-0.0112	0.0814	0.0255	0.083	0.1822	0.0801	0.1447	0.2867	-0.0548	0.216	-52.5288	-48.8097	-78.8595
36	5.879	1.4935	-1.647	2.246	-1.6806	2.6901	0.0325	-0.1315	0.0957	0.2734	0.1106	0.4253	-0.1551	-0.5222	-0.1314	0.2575	-0.0064	0.0073	0.3599	-0.0038	0.1343	-69.117	-57.2154	-74.3318
37	0.9525	-0.1249	0.515	1.1819	0.3731	1.1484	0.0737	0.216	-0.0376	-0.1144	0.035	-0.1508	0.4513	0.3458	0.0773	0.3681	0.0149	0.1637	0.2494	-0.0125	0.2872	-54.9824	-64.1501	-82.2432
38	0.3634	0.9988	-0.3026	2.9575	-0.878	0.2903	-0.0781	0.2835	-0.2613	-0.0359	0.1913	0.2051	0.5006	-0.397	-0.1006	0.3699	-0.0673	0.1101	0.4775	-0.0216	0.4109	-70.9761	-65.2424	-84.8408
39	0.4896	-0.0332	-0.3085	0.3596	0.113	0.9493	-0.1456	0.108	-0.324	0.0687	-0.2581	0.2603	0.3735	-0.2262	0.1372	0.5106	-0.0129	0.1272	0.3926	-0.1124	0.2485	-63.7508	-71.4385	-88.764
40	0.139	0.0352	-0.0935	0.625	0.0631	0.4007	-0.1183	0.1942	-0.1738	-0.2515	0.0253	0.0172	0.0774	-0.0356	-0.0315	0.2539	-0.0043	0.0436	0.3979	-0.17	0.0708	-57.135	-42.2878	-84.7786
41	1.6295	0.2325	-0.4264	1.7188	-0.1861	2.0619	-0.0971	-0.1527	-0.2319	0.1281	0.0144	0.0529	0.4081	-0.0797	0.2496	0.3066	0.0089	0.1665	0.3439	-0.0134	0.1182	-60.6949	-39.1142	-41.6045
42	1.0566	-0.061	-0.187	0.4097	0.0379	0.7158	-0.0872	-0.062	-0.2255	0.3023	0.0038	0.1806	0.1224	-0.2081	0.0967	0.2478	0.0655	0.1258	0.3408	-0.1081	0.1033	-62.7277	-25.3025	-48.7699
43	1.0468	0.4554	-0.1012	1.1117	0.3262	1.1071	-0.2369	0.182	-0.1146	-0.0494	-0.0084	0.4585	0.2076	-0.1515	0.1083	0.1891	0.0415	0.1306	0.3944	-0.0593	0.2754	-69.8492	-23.4025	-62.3194
44	2.3948	0.9354	-0.6179	0.6637	0.562	3.211	0.1157	-0.2221	-0.7826	0.2098	0.0519	-0.2026	0.7952	0.2118	0.0024	0.3183	-0.0578	-0.1105	0.3593	0.1122	0.3576	-60.6533	-1.3641	-15.2369
45	1.5887	0.1841	-0.0699	2.2529	0.2166	1.5883	0.0428	-0.2983	-0.2095	0.4024	0.0503	-0.1024	0.2491	0.2553	-0.0957	0.1759	-0.0073	-0.0114	0.2	0.0151	0.1883	-51.552	9.324	-19.0306
46	0.7249	0.2981	-0.2934	0.5164	-0.28	0.5503	-0.0236	-0.1613	-0.1323	0.071	-0.0623	0.0942	0.2151	-0.0891	-0.0671	0.2749	-0.2017	0.1236	0.2535	0.028	0.264	-66.5026	10.7641	-28.7916
47	1.6063	0.1999	-0.8037	0.5142	0.1447	1.3922	0.0086	0.2752	0.1224	-0.0613	-0.028	-0.0271	0.0031	-0.0662	-0.347	0.2189	-0.0712	0.2136	0.2434	-0.0761	0.3792	-82.9363	7.7502	-29.84
48	0.4065	0.5487	0.0513	0.9211	-0.0402	0.1453	-0.1214	0.1697	-0.1419	-0.2344	0.1048	0.0663	0.043	0.0027	-0.0591	0.1271	-0.0925	0.0801	0.1774	-0.0786	0.2698	-69.7469	11.9243	-36.4526
49	1.1491	0.2817	-0.9598	1.1398	-1.1155	1.5279	-0.1214	-0.4566	0.0392	0.3149	0.0177	-0.0252	0.0199	0.0197	0.1384	0.8097	-0.2493	0.0083	0.6614	-0.1224	0.3039	-47.6207	43.2486	0.9755
50	1.5118	0.5685	-0.3602	0.3985	-0.3256	1.1553	0.0398	-0.2237	0.0295	0.2809	-0.199	0.2056	0.2366	-0.1766	0.1	0.3994	-0.133	0.0179	0.303	-0.0552	0.3604	-53.5137	50.7295	-10.2631
51	1.979	-0.4247	-0.2951	1.768	0.2496	1.0283	-0.0597	-0.4828	0.0615	0.3902	-0.1041	0.3701	0.2015	-0.2513	0.0634	0.5851	-0.1567	0.0094	0.4916	-0.0573	0.3029	-67.908	43.5369	-13.7426
52	1.6973	-0.3022	-0.154	0.7859	0.2809	2.3415	0.0397	-0.2788	-0.1056	0.365	-0.1031	0.5039	0.1743	-0.6389	-0.0212	0.5345	-0.2406	-0.0511	0.5815	0.0576	0.4174	-73.5222	37.9002	-17.6337
53	2.24	1.2624	0.5743	2.0765	0.3096	0.7669	-0.0216	0.1969	0.119	-0.2032	-0.0391	0.2567	-0.1833	0.2428	0.0218	0.2422	0.0108	0.0717	0.2633	-0.0995	0.2923	-52.001	58.9527	-23.6762
54	0.884	1.154	0.4695	3.7629	1.4618	2.3918	-0.0659	0.1759	-0.1971	-0.2345	0.1668	-0.1584	0.0803	0.0314	-0.2734	0.3813	-0.0362	-0.2654	0.3133	-0.1289	0.6789	-43.1781	86.2192	-12.7511
55	0.3871	0.0496	-0.193	1.2061	-0.1599	0.2547	0.0046	0.0059	0.0328	0.1284	-0.0269	0.0211	-0.045	-0.0033	-0.0736	0.3789	0.1339	-0.242	0.2389	-0.1619	0.4487	-48.7158	85.031	-18.386
56	2.6458	0.9189	0.0876	9.7693	1.0235	0.3447	0.0046	-0.4587	-0.0723	0.6817	-0.0338	0.0782	-0.2129	-0.0234	0.0121	0.382	-0.031	-0.1033	0.4112	-0.2221	0.6815	-54.8562	86.875	-8.5689
57	0.474	-0.0361	-0.575	0.0049	0.0381	0.7114	-0.1209	0.0661	0.0316	0.0562	0.0197	0.0602	-0.0704	-0.1969	0.077	0.4485	0.0198	-0.0784	0.3368	0.14	0.4667	-55.0759	84.3401	-23.0943
58	3.4954	-1.7977	-1.0368	2.5963	1.953	1.6999	0.0202	-0.0014	-0.1907	-0.0208	0.0586	0.2479	0.0241	-0.1614	-0.0301	0.4475	-0.0187	0.1039	0.2493	-0.1535	0.5169	-58.3417	75.1814	-17.4056
59	3.2902	-3.0376	1.1797	4.0311	1.8908	7.7306	0.0074	-0.2306	-0.1998	0.3022	-0.069	-0.0264	0.1912	-0.0148	0.0316	0.3513	-0.0705	-0.0379	0.5618	-0.0177	0.6532	-63.5035	81.7534	-11.4897
60	0.0002	-0.0018	-0.0019	0.0932	0.0933	0.0927	-0.0384	0.121	-0.2414	-0.1067	-0.0623	0.0991	0.2071	-0.0638	0.0421	0.6064	-0.094	-0.2676	0.869	-0.0847	0.7418	-64.8645	74.2258	-24.8044
61	1.1354	2.2922	1.3453	5.5025	3.9484	3.3301	-0.0128	-0.063	-0.3938	0.2068	-0.0186	-0.6827	0.3795	0.5159	0.0296	1.2934	-0.0659	-0.1414	1.2468	0.1198	1.2127	-71.0525	73.3006	-13.8314
62	0.8933	-0.0271	-0.2859	0.8185	0.1605	1.4624	-0.1435	-0.0524	0.0785	0.0083	-0.0259	-0.2124	0.0185	0.0336	0.0904	0.1993	0.0249	0.0353	0.0805	0.0971	0.4201	-28.4793	-13.8744	-64.1591
63	0.388	-0.1312	-0.1489	1.693	0.8058	0.8266	0.0406	-0.1295	0.1806	-0.0462	0.095	-0.618	-0.2908	0.4443	-0.2437	0.3586	-0.0882	-0.0863	0.5008	0.1945	0.6673	-13.6798	53.6338	-23.9779
64	0.9499	0.4169	-0.0736	1.8776	0.6514	1.7125	0.0785	0.0877	-0.1448	-0.0759	0.1795	-0.2084	0.1754	0.4128	-0.1666	0.3413	0.2167	0.054	0.7538	0.0708	0.4617	-24.8602	36.8525	-34.1527

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 2 through 102 )	A	2 - 102
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 103 through 199 )	A	103 - 199
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 200 through 243 )	A	200 - 243
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 244 through 337 )	A	244 - 337
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 338 through 372 )	A	338 - 372
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 373 through 437 )	A	373 - 437
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 63 )	B	1 - 63
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 64 through 243 )	B	64 - 243
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 244 through 324 )	B	244 - 324
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 325 through 441 )	B	325 - 441
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 2 through 243 )	C	2 - 243
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 244 through 337 )	C	244 - 337
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 338 through 439 )	C	338 - 439
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 1 through 64 )	D	1 - 64
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 65 through 243 )	D	65 - 243
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 244 through 373 )	D	244 - 373
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 374 through 441 )	D	374 - 441
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 43 through 49 )	F	43 - 49
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 50 through 59 )	F	50 - 59
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 60 through 68 )	F	60 - 68
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 69 through 82 )	F	69 - 82
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 83 through 92 )	F	83 - 92
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 93 through 115 )	F	93 - 115
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 116 through 125 )	F	116 - 125
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 126 through 135 )	F	126 - 135
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 136 through 148 )	F	136 - 148
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 149 through 158 )	F	149 - 158
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 159 through 167 )	F	159 - 167
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 14 through 253 )	E	14 - 253
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 254 through 395 )	E	254 - 395
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 396 through 543 )	E	396 - 543
32	X-RAY DIFFRACTION	32	chain 'G' and (resid 2 through 88 )	G	2 - 88
33	X-RAY DIFFRACTION	33	chain 'G' and (resid 89 through 128 )	G	89 - 128
34	X-RAY DIFFRACTION	34	chain 'G' and (resid 129 through 160 )	G	129 - 160
35	X-RAY DIFFRACTION	35	chain 'G' and (resid 161 through 199 )	G	161 - 199
36	X-RAY DIFFRACTION	36	chain 'G' and (resid 200 through 223 )	G	200 - 223
37	X-RAY DIFFRACTION	37	chain 'G' and (resid 224 through 273 )	G	224 - 273
38	X-RAY DIFFRACTION	38	chain 'G' and (resid 274 through 311 )	G	274 - 311
39	X-RAY DIFFRACTION	39	chain 'G' and (resid 312 through 372 )	G	312 - 372
40	X-RAY DIFFRACTION	40	chain 'G' and (resid 373 through 437 )	G	373 - 437
41	X-RAY DIFFRACTION	41	chain 'H' and (resid 1 through 64 )	H	1 - 64
42	X-RAY DIFFRACTION	42	chain 'H' and (resid 65 through 295 )	H	65 - 295
43	X-RAY DIFFRACTION	43	chain 'H' and (resid 296 through 441 )	H	296 - 441
44	X-RAY DIFFRACTION	44	chain 'I' and (resid 2 through 47 )	I	2 - 47
45	X-RAY DIFFRACTION	45	chain 'I' and (resid 48 through 160 )	I	48 - 160
46	X-RAY DIFFRACTION	46	chain 'I' and (resid 161 through 273 )	I	161 - 273
47	X-RAY DIFFRACTION	47	chain 'I' and (resid 274 through 311 )	I	274 - 311
48	X-RAY DIFFRACTION	48	chain 'I' and (resid 312 through 439 )	I	312 - 439
49	X-RAY DIFFRACTION	49	chain 'J' and (resid 1 through 127 )	J	1 - 127
50	X-RAY DIFFRACTION	50	chain 'J' and (resid 128 through 243 )	J	128 - 243
51	X-RAY DIFFRACTION	51	chain 'J' and (resid 244 through 324 )	J	244 - 324
52	X-RAY DIFFRACTION	52	chain 'J' and (resid 325 through 373 )	J	325 - 373
53	X-RAY DIFFRACTION	53	chain 'J' and (resid 374 through 441 )	J	374 - 441
54	X-RAY DIFFRACTION	54	chain 'L' and (resid 43 through 68 )	L	43 - 68
55	X-RAY DIFFRACTION	55	chain 'L' and (resid 69 through 92 )	L	69 - 92
56	X-RAY DIFFRACTION	56	chain 'L' and (resid 93 through 101 )	L	93 - 101
57	X-RAY DIFFRACTION	57	chain 'L' and (resid 102 through 115 )	L	102 - 115
58	X-RAY DIFFRACTION	58	chain 'L' and (resid 116 through 125 )	L	116 - 125
59	X-RAY DIFFRACTION	59	chain 'L' and (resid 126 through 135 )	L	126 - 135
60	X-RAY DIFFRACTION	60	chain 'L' and (resid 136 through 158 )	L	136 - 158
61	X-RAY DIFFRACTION	61	chain 'L' and (resid 159 through 167 )	L	159 - 167
62	X-RAY DIFFRACTION	62	chain 'K' and (resid 14 through 253 )	K	14 - 253
63	X-RAY DIFFRACTION	63	chain 'K' and (resid 254 through 388 )	K	254 - 388
64	X-RAY DIFFRACTION	64	chain 'K' and (resid 389 through 543 )	K	389 - 543

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Protein , 4 types, 12 molecules ACGIBDHJEKFL

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-Yorodumi

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Movie

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Structure viewers

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This page

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This web site

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Open data

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Protein , 4 types, 12 molecules ACGIBDHJEKFL

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Non-polymers , 3 types, 16 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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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

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Aug 12, 2020. Covid-19 info

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi