PDB-7nbb: Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in c...

ID or keywords:

Entry

Database: PDB / ID: 7nbb

Title

Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with synthetic nanobody NbSL3

Components

(Polyubiquitin- ...) x 2
Synthetic nanobody NbSL3

Keywords

SIGNALING PROTEIN / Ubiquitin / Branched / Heterotypic / Nanobody / Synthetic nanobody

Function / homology

Function and homology information

Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain ...
Similarity search - Domain/homology

Biological species

Homo sapiens (human)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Lange, S.M. / Kulathu, Y.

Funding support

United Kingdom, 2items

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2024
Title: VCP/p97-associated proteins are binders and debranching enzymes of K48-K63-branched ubiquitin chains.
Authors: Lange, S.M. / McFarland, M.R. / Lamoliatte, F. / Carroll, T. / Krshnan, L. / Perez-Rafols, A. / Kwasna, D. / Shen, L. / Wallace, I. / Cole, I. / Armstrong, L.A. / Knebel, A. / Johnson, C. / ...

History

Deposition	Jan 26, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 10, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Jul 31, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7nbb.cif.gz	365.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7nbb.ent.gz	245.4 KB	Display	PDB format
PDBx/mmJSON format	7nbb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7nbb_validation.pdf.gz	483 KB	Display	wwPDB validaton report
Full document	7nbb_full_validation.pdf.gz	488.9 KB	Display
Data in XML	7nbb_validation.xml.gz	34.3 KB	Display
Data in CIF	7nbb_validation.cif.gz	51.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nb/7nbb ftp://data.pdbj.org/pub/pdb/validation_reports/nb/7nbb	HTTPS FTP

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Related structure data

Related structure data	7npoC 8a67C 1ubqS 5vnwS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#136 - Apr 2011 Nanobodies similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: Polyubiquitin-B

B: Polyubiquitin-B

C: Polyubiquitin-B

D: Synthetic nanobody NbSL3

E: Polyubiquitin-B

F: Polyubiquitin-B

G: Polyubiquitin-B

H: Synthetic nanobody NbSL3

hetero molecules

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

1

A: Polyubiquitin-B

B: Polyubiquitin-B

C: Polyubiquitin-B

D: Synthetic nanobody NbSL3

hetero molecules

defined by author
Evidence: gel filtration
39.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Polyubiquitin-B

F: Polyubiquitin-B

G: Polyubiquitin-B

H: Synthetic nanobody NbSL3

hetero molecules

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

Unit cell

Length a, b, c (Å)	54.389, 97.615, 74.967
Angle α, β, γ (deg.)	90.000, 109.959, 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

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Polyubiquitin- ... , 2 types, 6 molecules AEBCFG

#1: Protein	Polyubiquitin-B Mass: 8192.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J3QS39
#2: Protein	Polyubiquitin-B Mass: 8632.859 Da / Num. of mol.: 4 / Mutation: K48R K63R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J3QS39

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Protein , 1 types, 2 molecules DH

#3: Protein	Synthetic nanobody NbSL3 Mass: 14029.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 740 molecules

#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#7: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 722 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.07 % / Description: Rod-shape
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 0.1 M Bis-Tris pH 7.2 0.28 M MgCl2 21% PEG3350 0.15 M NaCl 0.05 M Tris/HCl pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 29, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87313 Å / Relative weight: 1
Reflection	Resolution: 1.274→200 Å / Num. obs: 79157 / % possible obs: 85.3 % / Observed criterion σ(I): 1.2 / Redundancy: 4 % / B_iso Wilson estimate: 18.58 Å² / CC_1/2: 0.992 / R_merge(I) obs: 0.099 / Net I/σ(I): 8
Reflection shell	Resolution: 1.55→1.659 Å / Redundancy: 2.6 % / Num. unique obs: 3958 / CC_1/2: 0.296 / % possible all: 34

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Processing

Software

Name	Version	Classification
PHENIX	1.19rc4_4035	refinement
XDS		data reduction
MxCuBE		data collection
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1UBQ, 5VNW

1ubq

5vnw

Resolution: 1.55→35.95 Å / SU ML: 0.1611 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.1165
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Anisotropic data processing with STARANISO (Global Phasing). Criteria used in determination of diffraction limits: local(I/sigI)>=1.20. Completenes (ellipsoidal) = 85.3

	R_factor	Num. reflection	% reflection
R_free	0.212	3986	5.04 %
R_work	0.1745	75106	-
obs	0.1764	79092	74.31 %

Solvent computation

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

Displacement parameters

B_iso mean: 25.86 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→35.95 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5275	0	28	722	6025

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0075	5487
X-RAY DIFFRACTION	f_angle_d	0.9152	7438
X-RAY DIFFRACTION	f_chiral_restr	0.058	854
X-RAY DIFFRACTION	f_plane_restr	0.008	967
X-RAY DIFFRACTION	f_dihedral_angle_d	13.7177	2072

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 (%)
1.55-1.57	0.381	13	0.3291	296	X-RAY DIFFRACTION	8.23
1.57-1.59	0.2908	20	0.293	506	X-RAY DIFFRACTION	13.86
1.59-1.61	0.334	41	0.2964	667	X-RAY DIFFRACTION	18.79
1.61-1.63	0.3305	51	0.2959	900	X-RAY DIFFRACTION	25.16
1.63-1.65	0.3035	56	0.2799	1175	X-RAY DIFFRACTION	32.45
1.66-1.68	0.3163	77	0.2841	1417	X-RAY DIFFRACTION	39.48
1.68-1.71	0.2773	74	0.2745	1699	X-RAY DIFFRACTION	46.54
1.71-1.73	0.3229	120	0.2699	2012	X-RAY DIFFRACTION	56.67
1.73-1.76	0.2546	165	0.2524	2417	X-RAY DIFFRACTION	67.86
1.76-1.8	0.2954	146	0.2486	2644	X-RAY DIFFRACTION	74.34
1.8-1.83	0.2465	147	0.2423	3002	X-RAY DIFFRACTION	82.11
1.83-1.87	0.2715	135	0.226	3126	X-RAY DIFFRACTION	85.97
1.87-1.91	0.2814	160	0.2288	3180	X-RAY DIFFRACTION	88.85
1.91-1.95	0.2676	92	0.226	1812	X-RAY DIFFRACTION	49.62
1.95-2	0.2259	201	0.2141	3469	X-RAY DIFFRACTION	97.22
2-2.06	0.2459	215	0.1989	3525	X-RAY DIFFRACTION	98.32
2.06-2.12	0.2146	194	0.1815	3573	X-RAY DIFFRACTION	99.5
2.12-2.18	0.2393	221	0.1726	3569	X-RAY DIFFRACTION	99.76
2.18-2.26	0.2124	193	0.18	3599	X-RAY DIFFRACTION	99.68
2.26-2.35	0.2274	176	0.1761	3616	X-RAY DIFFRACTION	99.79
2.35-2.46	0.2488	191	0.1742	3603	X-RAY DIFFRACTION	99.87
2.46-2.59	0.2168	192	0.1702	3622	X-RAY DIFFRACTION	99.69
2.59-2.75	0.21	194	0.1773	3565	X-RAY DIFFRACTION	99.55
2.75-2.96	0.1987	179	0.1707	3622	X-RAY DIFFRACTION	99.71
2.96-3.26	0.2025	193	0.1625	3634	X-RAY DIFFRACTION	99.74
3.26-3.73	0.1862	173	0.1445	3627	X-RAY DIFFRACTION	99.22
3.73-4.7	0.1552	181	0.1308	3601	X-RAY DIFFRACTION	98.88
4.7-35.95	0.193	186	0.1622	3628	X-RAY DIFFRACTION	97.92

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	4.89305782463	-0.118869960734	0.200108274373	4.83204252044	-0.249582471368	3.59881327356	-0.0316936202859	-0.144837391014	0.0578325430221	0.259138751156	0.00937283014076	-0.261358845923	0.278538857318	0.126943629132	0.0450855540936	0.121018177392	0.0169679099445	-0.0355901451623	0.143581028731	0.00122118613234	0.0953598810028	22.819336082	-13.5383101141	15.2703787629
2	6.33771626707	1.48216808094	-0.971681087772	6.32674012182	0.497053682483	3.37787146334	0.000521991841524	0.369913355113	0.249137712412	-0.106264334604	-0.0525273366408	-0.407750379705	0.0759970616822	0.510199745893	0.0155993315688	0.0868663516185	0.0225682779457	0.00984848812593	0.201369681696	0.0289703404445	0.0699967281024	29.3614769246	-14.8941827948	7.50594909029
3	2.2108236319	0.319019183363	0.982346802105	4.08643772409	-0.50044968292	3.32242284967	-0.0700685904611	0.189446400605	0.00559647742943	0.0460760313194	-0.0960862529327	-0.01671953352	0.242467547055	-0.0246933715401	0.0908307200656	0.0882376059895	0.0101802344071	-0.00287050293007	0.137063438638	0.0451594122523	0.044311068747	17.435079183	-16.1026882293	7.94675798872
4	2.31175386668	0.434870915246	0.262935314288	5.90812163497	-1.68862461556	4.69499330678	0.0770349839045	0.440949576682	0.199545219042	-0.250565421355	-0.134902329049	-0.550617920047	-0.260463510664	0.217073988587	0.135614993689	0.148645998379	0.0210563163324	0.00170447708284	0.232855068652	0.146681641974	0.228245908372	13.3465944081	-2.05718810577	-8.3511269064
5	4.52038547948	-0.460138391277	3.55061625009	6.55180601028	2.5426258174	4.08543624278	0.135416353868	0.976379244201	0.294662571507	-1.68223018754	-0.229538956881	0.532464474504	0.161239158047	0.0972360955242	0.098681292832	0.348248785153	0.00373354965808	-0.154215578867	0.654452805902	0.0766595394923	0.191367863868	5.30872605731	-5.23079382636	-20.8424656481
6	4.76700839882	-2.40038984933	-0.839690098539	5.52070799856	-0.193746730895	4.82263294925	-0.0379801678703	0.529487857124	-0.409357527419	-0.417879703612	-0.11762171272	-0.183396285152	0.431497189084	-0.134400419885	0.134686919844	0.204858595318	-0.0549226987696	0.0044760291322	0.241728348296	0.0249977378814	0.0909485092993	9.34706200687	-12.7627402053	-9.97533207612
7	1.27690708587	-1.50749101084	-1.23190149818	4.16160504981	-0.0856701545072	2.20958899014	0.12824282307	0.533055796331	-0.263652882398	-0.707792616631	-0.147769391415	0.711040348004	0.198444061966	-0.663254552309	-0.435817526974	0.220524465857	-0.0251053190901	-0.214579526118	0.654563579227	0.16566005494	0.25494900239	-1.69565168673	-6.43842552341	-10.652660424
8	1.54829775333	-0.388923876467	-0.114017671539	0.804569575317	0.336475456392	0.143331750898	0.11908764535	0.507872070493	0.360488035274	-0.814770291035	-0.0752702726039	0.44200193748	-0.0244590060999	-0.288889972334	0.181555788739	0.290055435417	0.0615960110452	-0.142713687214	0.601688837694	0.294788654605	0.345402643445	1.44782536147	0.722612881032	-14.7009028893
9	1.28968818712	0.034687518936	0.0413516043953	7.25871507386	-4.89242033092	5.28153516703	0.0147432173028	0.438332749849	-0.0152893679153	-0.311105581362	0.141595507239	0.227798545657	0.193283180669	-0.344451955281	-0.146415244397	0.0914004551203	-0.0199115268824	0.00273802374293	0.180138521566	0.0368569399414	0.0897539416233	7.30164723396	-11.369214815	-1.3573559473
10	0.475107776763	0.249086001927	0.536174512839	4.06156489411	0.351780809894	0.859830762463	0.127759714055	0.377675971796	0.84932105247	-0.562657784084	0.147722588414	1.33125518433	-0.779887447473	-0.499813543164	-0.194036004301	0.441547083036	0.125062362529	0.0893234447864	0.315425985146	0.217070943975	0.592379619193	-5.1601675994	9.29060185066	-0.434118282275
11	1.17597034257	-0.0484386486002	-0.198299392952	0.93943436298	-0.290441875587	0.41365100925	0.0965653856474	0.0529099414466	0.248791724486	0.198147761505	0.146875737817	0.316752941749	-0.471995920429	-0.238621263475	0.0610842813787	0.571923762576	0.213142237358	0.30295237115	0.116217713409	0.325303132017	0.630544005532	-4.95071507343	10.9939905651	8.64790889268
12	4.94148087057	0.869741380567	-5.62594341885	2.87395947963	-1.20951232264	7.32761314084	0.897029682064	-0.0523652065606	0.985870010026	0.438390599494	0.0918155967364	0.108761398298	-1.26740938135	-0.238604112247	-0.834173748665	0.33418787681	0.0119901837584	0.100348305982	0.166142618872	0.062799985537	0.271415211831	-0.725389137777	4.40290631457	11.1194129068
13	1.71494335848	-1.82089762189	-0.990728449226	8.06264879914	-0.2718763616	6.98549064589	0.377298932903	-0.287670993878	0.70185575032	0.611697161656	0.210107227588	-0.663643731667	-1.06352862302	0.455276599146	-0.424488215675	0.391152833052	-0.082509978946	0.0847308199625	0.296456642516	0.0157932390775	0.311415660055	7.51151303314	8.51628022304	2.79837809798
14	6.0849100182	1.61672323589	1.53955361024	7.38125265159	1.62668574148	2.07867620027	0.0936750591473	0.970638610262	0.948279749624	-1.05009344589	0.166790252212	0.348856012731	-1.27131916808	-0.0921279837638	0.0426126046885	0.654956624577	-0.00284362059902	0.160965346794	0.404201031816	0.277454094645	0.427421934715	3.02373720883	12.3695839724	-5.23901763545
15	2.55590225495	-0.387678587794	1.3206711212	4.43475071786	-3.02709504884	2.80034058761	0.172996156136	0.132342293357	0.160207378107	0.0529985405711	-0.411878129514	-0.282514543495	-0.0824644755513	0.856441277289	0.242893139816	0.115280236207	0.0189492013656	0.0158432239554	0.175439738853	0.0825801550663	0.216651210438	1.23249909348	-0.620932142203	9.38288396444
16	4.95026485998	0.230308283711	0.168447492516	4.29883590358	-0.444970356701	3.78259508436	0.0854645564568	0.164744551318	0.141904566253	-0.0145485922832	0.038119579888	0.20501718021	0.194632603205	-0.471100069211	-0.110398935583	0.0584804358423	-0.052131794557	-0.00654515640496	0.103581970823	0.00564557329277	0.155897096924	-13.7804397132	-15.9341923364	19.471217711
17	4.11094478803	0.22415617149	1.10645253935	4.92356345999	-2.68411504592	2.31602287882	-0.173027374433	0.335413090516	-0.155278937513	-0.557360388177	-0.0601859044871	-0.0818643988981	0.603327002618	0.0924019909286	0.260054342729	0.152474984609	-0.0660392788409	0.0156254225642	0.133441579343	-0.0253765117178	0.112236051432	-10.0918866582	-19.4732185995	15.8237553721
18	2.05859784085	-0.860249260175	-0.895636275475	1.56011274448	-0.910420589997	3.13277081787	-0.0819839150443	0.546484155399	-0.13735793062	-0.237194131029	-0.0831476949591	0.0982452731869	0.349902200429	-0.190319872344	0.170936679947	0.106972988429	-0.0477684130331	-0.00358537892763	0.18797261504	-0.0200454749658	0.0859957749571	-2.07140404831	-13.1633637423	10.3706134058
19	9.06433435913	-6.40649048944	-2.19995692287	8.07178635614	2.46623641191	3.61311040749	0.0441291095613	-0.263968000633	0.499938645044	0.13215054568	0.0827080357865	0.0629354916254	-0.223317184212	-0.0376107622084	-0.132982766433	0.132122009778	-0.0452515842711	0.0385791196073	0.112895387384	0.0130883154539	0.137301145351	-3.36376062314	-6.75504053908	20.0891171771
20	1.97997716366	-0.337177386468	-3.43700750662	0.187965706015	1.11389943542	7.9819595609	-0.103565275292	-0.384690121851	0.132179561419	0.0184014478192	0.0399888281712	0.00469877078175	0.137633255737	0.527179901858	0.0375160452973	0.119352642205	-0.0227745202486	-0.0254913436411	0.163039952173	-0.00614517094123	0.0925742941447	3.50529726898	-15.5421706027	22.2722269886
21	3.91692771477	-0.597442668597	-0.704439567393	1.98846596716	-1.25844755599	1.77578400952	-0.0018788309548	0.111316961796	-0.148970164208	-0.048027943873	-0.0615736674588	0.057380911037	0.387717459837	-0.0394947990569	0.0679840479413	0.105760839665	-0.0422718751252	-0.025791783752	0.0989591875495	-0.0118884569051	0.0739328083772	-5.94109730039	-18.4318960059	20.7925355186
22	1.77892811654	-0.176798311427	-0.533901222924	0.71122716282	0.0409901177801	2.77486389904	0.0444431876925	0.13415677517	0.30684513008	0.0770051767538	-0.0140389223216	-0.135125766645	-0.134709791832	0.109411105477	-0.0620270235654	0.071539582834	-0.00312549107634	-0.0231836098455	0.0735445685574	0.0348881127279	0.144626113306	1.34724203105	-6.46703355764	13.6255686365
23	6.43869683161	0.424099224601	-1.84444145251	2.47288468826	-0.137438792425	4.84387920398	-0.0284860737805	0.216242735677	0.515855673253	-0.0712584895445	0.171051070308	0.235918475915	-0.1895774594	-0.195142910338	-0.0895996746052	0.0772482856721	-0.00592493193274	-0.0111784870751	0.102123829798	0.0360266388291	0.109312453109	-3.25934861503	-6.70154381373	8.95814847505
24	8.68136836706	-0.697301763957	0.0865327860595	7.39864119589	-1.04628315529	1.95078157689	0.122228631498	-0.47762216932	0.24685980207	0.614246211136	0.10549884162	0.639375927698	-0.233468782591	-0.731829795359	-0.252658537902	0.124719578686	-0.0197430649577	0.0517122718816	0.182954971335	-0.0168234855877	0.195429678692	-16.2439291064	-11.2656055035	26.1858554511
25	3.7842843632	-4.22854575825	0.212626257122	7.49885584783	-2.08508887659	4.26167308053	-0.0142491402178	0.243360554397	-0.371653417938	-0.31666016349	-0.00626148390127	-0.454069385644	0.536932125342	0.133960173758	0.00123194146343	0.265191286101	0.00161159548764	0.0146457724756	0.118856356862	-0.0651559287148	0.287412430676	8.40010751854	-21.4140871813	38.60610621
26	3.39306626165	0.678772807767	1.99568536851	2.33207514257	-2.95764869417	6.72118089335	-0.1566070107	0.0637158178658	-0.365252413412	0.0313537654447	0.0605533054567	0.397268743724	0.0310395399089	-0.229816659399	0.0231766078297	0.111923492436	-0.00331368452875	0.0414972236073	0.0989086273889	0.000580828394159	0.203425089305	-0.0804283624032	-17.9883621958	44.5675007603
27	0.630883505183	1.14003021028	0.453523689026	2.19637509159	0.976055952433	0.480715087684	-0.0514949353814	-0.361140695998	-0.58062448056	0.435433677338	0.070845946361	0.165381451895	0.337244718363	0.0311045874939	-0.032465515225	0.25789111926	0.0382763548049	0.0129417314332	0.11637049038	0.0628144169748	0.216900225599	7.46359045434	-17.0100771736	50.691849279
28	3.84543785008	-0.17241137716	0.857347803398	5.57846432994	-0.662046397748	4.62503496563	-0.10362475285	0.235601564274	-0.250725068153	-0.222933344355	-0.0879306252503	-0.210847630117	0.148545380278	0.249179976014	0.123414515955	0.101265293412	0.0160615786279	0.0163135976915	0.0642464525471	-0.00979625667197	0.112206236577	9.79360561147	-12.8019811126	42.4983313871
29	5.16785661909	-0.797577802866	-3.73290545864	3.77994666865	1.59977106652	8.85446571368	-0.106398096613	-0.29101015675	-0.553208271636	0.338733635046	0.0820829300895	0.592632055699	0.158386223696	-0.28749322422	0.0133593628244	0.143647613788	0.0430996134622	0.0387429253138	0.12290046374	0.0863248456528	0.241837037472	-3.81994781897	1.61401640382	55.7879612423
30	3.96036656869	2.95786261963	3.76165909238	8.62816449827	4.99972204101	5.1163312345	0.220550874345	-1.50502226118	0.87729905073	1.34548729722	0.0119087030279	0.664165193777	-0.487614634591	-0.0264596653478	-0.106998765152	0.641283671781	0.0347646663121	0.113990553998	0.318217380123	-0.0721230149185	0.228683580877	0.371283387232	11.0488036137	67.073076809
31	4.62154578334	0.775834726906	-2.20565991506	4.47932449343	-2.44219853862	6.78315902351	0.00375100268841	-0.55562010308	-0.310948259265	0.461841012705	-0.0068207539449	-0.0830352791619	-0.057452540189	0.22287786736	0.00203085085752	0.155221668109	0.010450998187	-0.025298707366	0.1600690364	0.0187268015116	0.0946269617768	6.876689149	1.03164896186	59.8291328042
32	4.99050438587	0.490176323134	-0.787941926861	4.66238068455	-0.822190957979	2.8393533126	0.191384647331	-0.569104118608	0.386081868973	1.0022289282	0.105471208412	0.165028714678	-0.564421048009	-0.0564305304341	-0.239143613516	0.432330682111	0.0175124353336	0.0531512532469	0.109524391978	0.00459326773465	0.189293799125	2.04477136048	13.7698459366	57.5474811406
33	9.15414567738	-5.23386212036	-1.65969452661	5.45206335715	0.76918050781	3.08485861936	0.00160379060383	-0.203259224619	0.0056883852237	0.289628210774	0.082214773598	-0.272402822732	0.053660874999	0.119697176998	-0.0566506637294	0.103314435568	-0.00588165452589	-0.0329052915043	0.0601218478502	0.00338790496355	0.0946859867405	8.47329698309	0.80248990795	51.141466915
34	5.60743672313	-3.03131347642	1.20326466065	5.2400162465	-0.772402825173	3.16204699022	-0.0251948454177	0.177538545607	0.587168693267	0.0490892560035	-0.037430603652	-0.0948470477788	-0.339053216466	-0.398273294639	0.0445130350353	0.161373655107	0.0412505213801	0.0477142878418	0.134209556156	0.0264386482398	0.0966571507958	-3.11324164111	20.094290562	41.6625296426
35	6.76134001219	-0.0258807247825	-2.26118856652	8.78937141523	-2.37996732943	7.21095401995	0.360789751216	0.568634738102	0.391601134944	-0.507393267133	-0.480818821078	-0.48469632404	-0.878478422686	-0.439234250536	0.13277407559	0.28471252569	0.115203043924	0.0220668055788	0.228032636695	0.0525089943193	0.179028519174	-2.4525142343	17.7995564119	32.9137802337
36	5.91995413677	-2.2840147363	-4.19233424693	1.017683674	1.69422568091	3.11882299521	0.236949133818	0.853229532175	0.170763812841	-0.330187290774	-0.0889158623228	0.129394386937	0.109981550494	-0.500239074327	-0.040479151434	0.180684656531	0.0141906606414	0.00543337791997	0.193028792165	-0.00547971109321	0.0963883943636	1.38511652457	10.5744730569	33.4836961446
37	6.7316055437	-3.89695571508	4.5816304212	4.43294803672	-3.10207497136	3.79822087549	0.365736548056	0.519684860515	-1.05648333214	-0.48125467705	0.117542058986	0.647903312654	0.781443213286	-0.694860110461	-0.371800156479	0.20410253987	-0.0466463281847	-0.0103235588507	0.310296802553	-0.0179886754478	0.246470905034	-7.84408256237	7.71023137464	41.143489472
38	4.12787555294	-0.543800578109	-0.597757785831	8.65728354927	1.31091518345	2.34159835009	-0.012843425635	-0.135792383718	-0.00670235316503	0.600938963729	-0.104264470393	0.640612480432	-0.0460897462401	-0.623165466099	0.178444259676	0.161541494692	0.0408161693401	0.0718309793869	0.224965449382	-0.0222682283156	0.191601582179	-9.95233939371	15.9244641566	46.9076638079
39	6.47038045165	-3.99491455513	-5.46290665904	3.37376539819	5.0220028135	8.04815883001	-0.17473165723	0.223878010681	-0.110386955878	0.201155105378	-0.00670000150429	0.140786457934	0.360467358593	-0.176629091018	0.153728619321	0.139174051558	0.00534441464475	0.00293715335127	0.0823015698337	0.0378215059178	0.0738836798729	4.26536890739	7.72408511496	37.0930972526
40	2.43445913264	-0.566218551362	-1.03655602181	2.63067543506	1.2696484926	2.51074569123	0.218823286575	-0.304732775987	0.597659116436	-0.0419584123521	0.0462397498579	-0.0779355494638	-0.574259250342	0.518583714694	-0.35347468501	0.291903281623	-0.116925658212	0.151206172218	0.234925195336	-0.144236170404	0.427966075917	26.5536730939	10.6415230069	28.6515692382
41	5.14255713844	-1.32174382198	-0.554988278322	4.1546968652	1.05628520745	1.30631243818	-0.0943546768601	-0.671185030721	0.371713765626	0.246607307432	0.343228942967	-0.187985752016	-0.115107248219	0.281230023384	-0.199118536598	0.132927557397	-0.0972643347924	0.048232982994	0.25445903656	-0.133055053795	0.276086158025	27.6334225791	6.53189934477	34.089946244
42	2.28530235961	0.232138652546	-1.53168898985	3.47400256855	-1.31532206224	3.72120985809	0.0964968859145	-0.034848291902	0.233375410476	0.0179604284634	0.0553065446963	-0.133364277757	-0.173522254707	0.035422267288	-0.0244162817547	0.0828505883139	0.000479747703002	0.0213423506401	0.0479606822946	9.18963920589E-5	0.105537285053	15.7024464961	2.48166191296	34.3806401059
43	3.15649163089	0.389214370139	2.82508491494	4.98818446912	1.23902976562	7.80998886139	0.188056673701	-0.727639100123	0.0044992537633	0.380800772662	-0.0891880365929	-0.266069423563	0.459419548628	-0.170844387505	-0.0821246492964	0.103954352003	-0.0152241464256	-0.00342897657046	0.214951502321	-0.00803911095533	0.147590885861	23.0704200126	-1.13341433008	31.9729631684
44	1.67172297075	0.26102583531	-2.18340247163	1.55605846254	0.0381489620738	2.92402627622	0.29785131549	-0.0672572153637	0.387342404311	-0.170599247887	0.162858050133	-0.138304213291	-0.273843909708	0.202092003997	-0.360185619147	0.127482262438	-0.0113609193749	0.0254692922124	0.0920706764314	-0.00978380581965	0.168060934968	21.1141578757	5.3472655193	28.6801330789
45	4.66429755726	-2.36864367779	-3.7052676343	1.57185311255	1.82089820278	3.13197884861	-0.417127449889	-0.0976857854806	0.60746682807	-0.104974785255	-0.162326336319	0.0900505152577	-0.304578775591	-0.882720528463	0.316947277253	0.158618699551	0.0152279190261	-0.0720358764423	0.208041638067	-0.0483170311146	0.295604263277	1.98227557469	-2.52342350374	34.4538603271
46	4.80008588056	1.08236779521	-4.36042761909	1.84088698596	-1.10833154964	4.01300148635	0.316880253118	0.20188459939	0.532885886525	-0.226879232521	0.150636087044	-0.222463248409	-0.359185619449	-0.0498306269086	-0.33375191496	0.227848906185	0.00814320236889	0.0506162326878	0.0810830616002	0.0154347819869	0.166243321082	15.723783477	9.55082610182	32.1911328069

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 22 )	A	A	1 - 22	1 - 22
2	2	chain 'A' and (resid 23 through 44 )	A	A	23 - 44	23 - 44
3	3	chain 'A' and (resid 45 through 71 )	A	A	45 - 71	45 - 71
4	4	chain 'B' and (resid 1 through 16 )	B	E	1 - 16	1 - 16
5	5	chain 'B' and (resid 17 through 22 )	B	E	17 - 22	17 - 22
6	6	chain 'B' and (resid 23 through 44 )	B	E	23 - 44	23 - 44
7	7	chain 'B' and (resid 45 through 56 )	B	E	45 - 56	45 - 56
8	8	chain 'B' and (resid 57 through 65 )	B	E	57 - 65	57 - 65
9	9	chain 'B' and (resid 66 through 76 )	B	E	66 - 76	66 - 76
10	10	chain 'C' and (resid 1 through 22 )	C	G	1 - 22	1 - 22
11	11	chain 'C' and (resid 23 through 34 )	C	G	23 - 34	23 - 34
12	12	chain 'C' and (resid 35 through 44 )	C	G	35 - 44	35 - 44
13	13	chain 'C' and (resid 45 through 56 )	C	G	45 - 56	45 - 56
14	14	chain 'C' and (resid 57 through 65 )	C	G	57 - 65	57 - 65
15	15	chain 'C' and (resid 66 through 76 )	C	G	66 - 76	66 - 76
16	16	chain 'D' and (resid 4 through 19 )	D	K	4 - 19	1 - 16
17	17	chain 'D' and (resid 20 through 26 )	D	K	20 - 26	17 - 23
18	18	chain 'D' and (resid 27 through 41 )	D	K	27 - 41	24 - 38
19	19	chain 'D' and (resid 42 through 54 )	D	K	42 - 54	39 - 51
20	20	chain 'D' and (resid 55 through 68 )	D	K	55 - 68	52 - 65
21	21	chain 'D' and (resid 69 through 90 )	D	K	69 - 90	66 - 87
22	22	chain 'D' and (resid 91 through 106 )	D	K	91 - 106	88 - 103
23	23	chain 'D' and (resid 107 through 115 )	D	K	107 - 115	104 - 112
24	24	chain 'D' and (resid 116 through 122 )	D	K	116 - 122	113 - 119
25	25	chain 'E' and (resid 1 through 16 )	E	N	1 - 16	1 - 16
26	26	chain 'E' and (resid 17 through 34 )	E	N	17 - 34	17 - 34
27	27	chain 'E' and (resid 35 through 56 )	E	N	35 - 56	35 - 56
28	28	chain 'E' and (resid 57 through 71 )	E	N	57 - 71	57 - 71
29	29	chain 'F' and (resid 1 through 16 )	F	Q	1 - 16	1 - 16
30	30	chain 'F' and (resid 17 through 22 )	F	Q	17 - 22	17 - 22
31	31	chain 'F' and (resid 23 through 44 )	F	Q	23 - 44	23 - 44
32	32	chain 'F' and (resid 45 through 65 )	F	Q	45 - 65	45 - 65
33	33	chain 'F' and (resid 66 through 76 )	F	Q	66 - 76	66 - 76
34	34	chain 'G' and (resid 1 through 22 )	G	T	1 - 22	1 - 22
35	35	chain 'G' and (resid 23 through 34 )	G	T	23 - 34	23 - 34
36	36	chain 'G' and (resid 35 through 44 )	G	T	35 - 44	35 - 44
37	37	chain 'G' and (resid 45 through 56 )	G	T	45 - 56	45 - 56
38	38	chain 'G' and (resid 57 through 65 )	G	T	57 - 65	57 - 65
39	39	chain 'G' and (resid 66 through 76 )	G	T	66 - 76	66 - 76
40	40	chain 'H' and (resid 5 through 19 )	H	X	5 - 19	1 - 15
41	41	chain 'H' and (resid 20 through 26 )	H	X	20 - 26	16 - 22
42	42	chain 'H' and (resid 27 through 61 )	H	X	27 - 61	23 - 57
43	43	chain 'H' and (resid 62 through 76 )	H	X	62 - 76	58 - 72
44	44	chain 'H' and (resid 77 through 100 )	H	X	77 - 100	73 - 96
45	45	chain 'H' and (resid 101 through 106 )	H	X	101 - 106	97 - 102
46	46	chain 'H' and (resid 107 through 122 )	H	X	107 - 122	103 - 118

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Polyubiquitin- ... , 2 types, 6 molecules AEBCFG

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-Polyubiquitin- ... , 2 types, 6 molecules AEBCFG

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-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

-
Polyubiquitin- ... , 2 types, 6 molecules AEBCFG

-
Protein , 1 types, 2 molecules DH

-
Non-polymers , 5 types, 740 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

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Yorodumi