PDB-7odb: Crystal structure of bovine Hsc70(aa1-554)E213A/D214A in complex ...

ID or keywords:

Entry

Database: PDB / ID: 7odb

Title

Crystal structure of bovine Hsc70(aa1-554)E213A/D214A in complex with triazine-derivative

Components

Heat shock cognate 71 kDa protein

Keywords

CHAPERONE

Function / homology

Function and homology information

Regulation of HSF1-mediated heat shock response / Attenuation phase / HSF1-dependent transactivation / Protein methylation / GABA synthesis, release, reuptake and degradation / PKR-mediated signaling / mRNA Splicing - Major Pathway / synaptic vesicle uncoating / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein targeting to lysosome involved in chaperone-mediated autophagy ...
Similarity search - Function

Biological species

Bos taurus (domestic cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.662 Å

Authors

Zehe, M. / Grimm, C. / Sotriffer, C.

Citation

Journal: Acs Chem.Biol. / Year: 2024
Title: Combined In-Solution Fragment Screening and Crystallographic Binding-Mode Analysis with a Two-Domain Hsp70 Construct.
Authors: Zehe, M. / Kehrein, J. / Schollmayer, C. / Plank, C. / Kovacs, H. / Merino Asumendi, E. / Holzgrabe, U. / Grimm, C. / Sotriffer, C.

History

Deposition	Apr 29, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 1, 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	Feb 14, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7odb.cif.gz	264.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7odb.ent.gz	187.4 KB	Display	PDB format
PDBx/mmJSON format	7odb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7odb_validation.pdf.gz	784.3 KB	Display	wwPDB validaton report
Full document	7odb_full_validation.pdf.gz	787.2 KB	Display
Data in XML	7odb_validation.xml.gz	25.1 KB	Display
Data in CIF	7odb_validation.cif.gz	37.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/od/7odb ftp://data.pdbj.org/pub/pdb/validation_reports/od/7odb	HTTPS FTP

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Related structure data

Related structure data	6h54C 7o6rC 7oddC 7odiC 7plkC 4fl9S C: citing same article (ref.) S: Starting model for refinement
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	#32 - Aug 2002 Chaperones similarity (9)

Deposited unit

A: Heat shock cognate 71 kDa protein

hetero molecules

61.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	65.611, 50.221, 86.679
Angle α, β, γ (deg.)	90.000, 100.014, 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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Protein , 1 types, 1 molecules A

#1: Protein	Heat shock cognate 71 kDa protein / Heat shock 70 kDa protein 8 Mass: 60978.867 Da / Num. of mol.: 1 / Mutation: E213A, D214A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: HSPA8, HSC70 / Production host: Escherichia coli (E. coli) / References: UniProt: P19120

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Non-polymers , 5 types, 449 molecules

#2: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-V8Q / 6-methyl-5-sulfanylidene-2H-1,2,4-triazin-3-one / 6-Methyl-5-thioxo-4,5-dihydro-1,2,4-triazin-3(2H)-one / 1383425 Mass: 143.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₅N₃OS / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 2.31 Å³/Da / Density % sol: 46.67 %
Crystal grow	Temperature: 291 K / Method: microbatch / pH: 7.5 Details: PEG 8000, TMAO. potassium chloride, HEPES-NaOH, glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.66→85.4 Å / Num. obs: 64069 / % possible obs: 97.5 % / Redundancy: 4.9 % / B_iso Wilson estimate: 26.61 Å² / CC_1/2: 0.999 / R_rim(I) all: 0.06 / Net I/σ(I): 14.33
Reflection shell	Resolution: 1.66→1.76 Å / Mean I/σ(I) obs: 1.17 / Num. unique obs: 8985 / CC_1/2: 0.686

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Processing

Software

Name	Version	Classification
MxCuBE		data collection
Coot		model building
PHENIX	1.14_3260	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4FL9

4fl9

Resolution: 1.662→64.61 Å / SU ML: 0.2345 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3356 / Stereochemistry target values: CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2079	3110	4.86 %
R_work	0.1996	60918	-
obs	0.2	64028	97.46 %

Solvent computation

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

Displacement parameters

B_iso mean: 34.22 Å²

Refinement step

Cycle: LAST / Resolution: 1.662→64.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4139	0	44	442	4625

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0121	4290
X-RAY DIFFRACTION	f_angle_d	1.5673	5797
X-RAY DIFFRACTION	f_chiral_restr	0.1103	659
X-RAY DIFFRACTION	f_plane_restr	0.0078	759
X-RAY DIFFRACTION	f_dihedral_angle_d	21.5124	1621

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 (%)
1.662-1.69	0.4081	79	0.4102	1499	X-RAY DIFFRACTION	53.26
1.69-1.72	0.3274	167	0.3507	2601	X-RAY DIFFRACTION	93.99
1.72-1.75	0.3417	141	0.3129	2799	X-RAY DIFFRACTION	99.22
1.75-1.78	0.3803	142	0.3078	2837	X-RAY DIFFRACTION	99.77
1.78-1.81	0.2867	128	0.285	2820	X-RAY DIFFRACTION	99.97
1.81-1.85	0.3014	126	0.2855	2862	X-RAY DIFFRACTION	99.73
1.85-1.89	0.2538	142	0.2666	2811	X-RAY DIFFRACTION	99.86
1.89-1.93	0.3104	131	0.2537	2878	X-RAY DIFFRACTION	99.87
1.93-1.98	0.2516	134	0.2409	2776	X-RAY DIFFRACTION	99.69
1.98-2.03	0.2531	134	0.233	2827	X-RAY DIFFRACTION	99.83
2.03-2.09	0.2485	157	0.2269	2844	X-RAY DIFFRACTION	99.9
2.09-2.16	0.2437	138	0.2223	2801	X-RAY DIFFRACTION	99.83
2.16-2.24	0.223	142	0.2125	2833	X-RAY DIFFRACTION	100
2.24-2.33	0.2335	136	0.2104	2844	X-RAY DIFFRACTION	99.9
2.33-2.44	0.2212	151	0.2104	2847	X-RAY DIFFRACTION	99.9
2.44-2.56	0.2372	150	0.2086	2824	X-RAY DIFFRACTION	99.97
2.56-2.72	0.2152	131	0.2081	2859	X-RAY DIFFRACTION	99.9
2.72-2.93	0.2105	148	0.1986	2858	X-RAY DIFFRACTION	99.9
2.93-3.23	0.1705	165	0.1849	2819	X-RAY DIFFRACTION	99.93
3.23-3.7	0.1601	165	0.1677	2856	X-RAY DIFFRACTION	99.93
3.7-4.66	0.1673	133	0.1546	2894	X-RAY DIFFRACTION	99.87
4.66-64.61	0.1925	170	0.1778	2929	X-RAY DIFFRACTION	99.49

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	2.02487085433	-0.653092619126	0.524296768212	5.13880555595	-0.286524132206	2.81868877866	0.0663233354326	-0.176449292343	-0.193791544166	0.127768514401	0.0204269730394	-0.0752868753821	0.282768949762	0.0426283553666	-0.0573996334921	0.150385541876	-0.025890422309	0.00934905608355	0.153429684384	0.0224359080503	0.188974702365	-12.790907979	-20.9768954833	-7.61124443172
2	1.42014198177	0.353492679372	0.10631936574	1.25144472835	-0.188101953287	2.14312394416	0.00937108414969	-0.087360234706	0.049415767035	-0.0326421140121	0.0199259546611	0.187629802647	0.018922751267	-0.208072503247	-0.0371481606092	0.117321120082	-0.0331000095437	-0.00155419705613	0.143082231466	-0.0120828492576	0.185893453529	-21.1667218497	-10.3465113119	-13.6151692453
3	2.29827912824	-1.25068289459	1.05497015042	3.36497046414	-1.57400791109	2.53373030235	0.14338140067	-0.10452828079	-0.0533007090422	0.0544085153939	-0.228018399304	-0.187988030508	0.189387086095	0.400297369062	0.113695126521	0.2324133877	-0.0387964296551	0.0175105407654	0.332954626659	0.0384495828066	0.186038194164	12.1094431187	-16.1991687703	-19.0575112038
4	2.34791041192	-0.245343621039	-0.544713138796	0.852978505554	-0.041541432083	1.68604325711	0.0273824691036	0.237602707133	0.307151399323	-0.184290080909	0.0341289640998	0.0525582218854	-0.170965648084	0.0222008519551	-0.0645069133647	0.257761742807	-0.0329581035972	-0.00967444420545	0.184034930477	0.0244545201413	0.250518073284	-12.1567595424	-2.23990657613	-25.9432322058
5	5.7339185729	4.74060725201	3.07184388847	2.31879412145	3.60133599738	6.68038722132	-0.022672542583	-0.103652006398	0.210071692567	-0.216787292066	0.0321106955676	-0.0562332089532	-0.684789080099	0.369252119643	-0.0120697109889	0.240370607159	-0.0425760306746	-0.00250931924969	0.265653904953	0.0367617908173	0.249891793897	-40.1534407703	-0.202901402109	-34.7971039462
6	5.68689739093	1.51396861052	0.11335298788	2.58120750652	5.97315642079	2.61540511471	-0.225599655126	0.569696144828	0.226413259469	-0.916002696537	0.118406113428	0.209469756729	-0.331611351628	0.30425405389	0.0113160896874	0.434523804242	-0.0301235275869	-0.0432307639399	0.342923775616	0.107266434776	0.23796779083	-47.7541838677	-4.11235762596	-48.8317076287
7	8.08751966993	-3.8352912171	6.5197455095	2.02768340244	-3.32971597151	2.25431648211	0.331201760756	0.127438101438	-0.188746153666	0.0271094338707	-0.0850512693381	0.0541994618597	0.193101180304	0.209056513286	-0.22996368624	0.242623824731	-0.0246031784604	0.0156672132408	0.294741942764	0.00560409162994	0.245051305168	-45.7238430945	-8.02910799074	-34.6777378531
8	5.37126117582	-3.24589814543	7.11995150821	5.04000902201	-3.65938308917	2.08911516488	0.324056236131	0.0329191260816	0.0621111368622	-0.412007615584	-0.330466207733	0.171795860414	0.62323726782	0.0976511584753	-0.0277619212221	0.17389693667	0.0231938676885	0.0513182941964	0.286709426221	0.0124102317632	0.171646982883	-54.4567534927	-3.55464580603	-37.9381169441
9	3.72971593755	1.99562135938	3.39894286988	8.24704863474	7.18262044372	2.47552786898	0.431723016683	0.307699171599	0.0630952840082	-0.345569764864	-0.406292693221	-0.0438900761585	-0.169618591908	-0.230484293532	0.0671990772835	0.434193104266	0.040021231051	0.0521628866796	0.336157547277	0.0614962250351	0.223609149391	-49.8392385389	-1.67930053108	-50.4510038783
10	4.67366233619	-0.990343354852	1.0999080324	1.63921959435	-0.144016756445	8.47587692267	-0.118467247618	-0.365463964124	0.339425489599	0.311588525076	0.108786162993	0.0775007036154	-0.596488950414	-0.142637117645	0.0403517771552	0.346274130537	0.0164253097547	0.0495157573135	0.188459815923	0.0210158962221	0.267189045486	-52.3950489055	6.13785855915	-41.7772571858
11	4.1727164103	-0.856645490766	6.21031254257	2.15471363059	-1.58667263419	9.27809184619	-0.654943077026	-0.96746357379	0.18439002082	0.198060056452	-0.333960065233	0.815641400192	-1.92469681314	-1.81620315845	0.814415633748	0.716105660847	0.25687292395	0.0391742621076	1.04771882252	-0.127996663059	0.521108593009	-47.5866511206	3.88987250673	-21.8776506318
12	6.67657656151	-6.48440594166	-4.88826244946	2.11406253379	1.98405249597	2.0547657086	-0.115472893878	-0.685377356525	-0.246333336547	1.2475429983	0.338005278292	-0.61512838336	0.568873514992	-0.164833131378	-0.203232303129	0.367472437917	-0.0067728459007	-0.0312172067556	0.398840499261	0.0523695811535	0.362111492895	-35.9325044767	-6.7056862278	-21.7325117392
13	2.05566958603	-0.132614316813	0.38640349626	2.04033835167	2.96298264407	2.01607040538	0.35076739754	0.99783607344	-1.0919466911	-2.44252408083	-0.315062781288	-0.998287919619	0.860089159337	0.303501266138	-0.0846049878753	0.996678933051	0.204002829427	0.210885236086	0.468020620463	-0.104511121741	0.777600145538	-33.8466737233	-15.8086251208	-36.2211951892
14	1.50703787146	-1.77121198722	1.4736467153	6.48242707681	-4.862566582	2.1347197645	0.00431135384076	0.434032564886	-0.36174047157	-0.678636541457	-0.400605805202	-0.546901822851	0.508404936273	0.266523410719	0.502860766587	0.365563640736	-0.0450422162161	0.0594215671694	0.359873645095	-0.0590999665803	0.274083036095	-48.7871462259	-13.5137042999	-43.0738701523

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 109 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 110 through 229 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 230 through 306 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 307 through 382 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 395 through 421 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 422 through 436 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 437 through 453 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 454 through 462 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 463 through 480 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 481 through 503 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 504 through 511 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 512 through 524 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 525 through 535 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 536 through 551 )

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