PDB-2cge: Crystal structure of an Hsp90-Sba1 closed chaperone complex

ID or keywords:

Entry

Database: PDB / ID: 2cge

Title

Crystal structure of an Hsp90-Sba1 closed chaperone complex

Components

ATP-DEPENDENT MOLECULAR CHAPERONE HSP82

Keywords

CHAPERONE / CHAPERONE COMPLEX / HSP90 / HEAT SHOCK PROTEIN / CO-CHAPERONE / ATP-BINDING / HEAT SHOCK / NUCLEOTIDE-BINDING

Function / homology

Function and homology information

The NLRP3 inflammasome / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / box C/D snoRNP assembly ...
Similarity search - Function

Biological species

SACCHAROMYCES CEREVISIAE (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Ali, M.M.U. / Roe, S.M. / Prodromou, C. / Pearl, L.H.

Citation

Journal: Nature / Year: 2006
Title: Crystal Structure of an Hsp90-Nucleotide-P23/Sba1 Closed Chaperone Complex
Authors: Ali, M.M.U. / Roe, S.M. / Vaughan, C. / Meyer, P. / Panaretou, B. / Piper, P.W. / Prodromou, C. / Pearl, L.H.

History

Deposition	Mar 1, 2006	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 12, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2cge.cif.gz	490.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2cge.ent.gz	412.6 KB	Display	PDB format
PDBx/mmJSON format	2cge.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cg/2cge ftp://data.pdbj.org/pub/pdb/validation_reports/cg/2cge	HTTPS FTP

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Related structure data

Related structure data	2cg9C 1hk7S 1a4h 1ah6 1ah8 1am1 1amw 1bgq 1us7 1usu 1usv 2akp 2brc 2bre S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3hjc-1 3q6m-1 6085 3q6n-d 5hys-d 6oaa-d 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	#108 - Dec 2008 Hsp90 similarity (17) #32 - Aug 2002 Chaperones similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #166 - Oct 2013 Proteasome similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #219 - Mar 2018 Vacuolar ATPase similarity (1) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #85 - Jan 2007 Importins similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#108 - Dec 2008
Hsp90
similarity (17)
#32 - Aug 2002
Chaperones
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#166 - Oct 2013
Proteasome
similarity (1)
#196 - Apr 2016
Lead Poisoning
similarity (1)
#219 - Mar 2018
Vacuolar ATPase
similarity (1)
#203 - Nov 2016
Aminopeptidase 1 and Autophagy
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#85 - Jan 2007
Importins
similarity (1)
#24 - Dec 2001
Glycogen Phosphorylase
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)

Deposited unit

A: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82

B: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82

D: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82

141 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82

B: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82

D: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82

A: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82

B: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82

D: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82

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

Unit cell

Length a, b, c (Å)	105.555, 105.555, 289.315
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	D
1	2	A
2	2	B
3	2	D
1	3	A
2	3	B
3	3	D

NCS domain segments:

Refine code: 1

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LYS	LYS	LEU	LEU	A	A	274 - 443	2 - 171
2	1	1	LYS	LYS	LEU	LEU	B	B	274 - 443	2 - 171
3	1	1	LYS	LYS	LEU	LEU	D	C	274 - 443	2 - 171
1	1	2	ARG	ARG	GLU	GLU	A	A	444 - 529	172 - 257
2	1	2	ARG	ARG	GLU	GLU	B	B	444 - 529	172 - 257
3	1	2	ARG	ARG	GLU	GLU	D	C	444 - 529	172 - 257
1	1	3	ASP	ASP	ARG	ARG	A	A	534 - 599	262 - 327
2	1	3	ASP	ASP	ARG	ARG	B	B	534 - 599	262 - 327
3	1	3	ASP	ASP	ARG	ARG	D	C	534 - 599	262 - 327
1	2	3	LYS	LYS	ARG	ARG	A	A	610 - 670	338 - 398
2	2	3	LYS	LYS	ARG	ARG	B	B	610 - 670	338 - 398
3	2	3	LYS	LYS	ARG	ARG	D	C	610 - 670	338 - 398

NCS ensembles :

ID
1
2
3

#1: Protein	ATP-DEPENDENT MOLECULAR CHAPERONE HSP82 / HEAT SHOCK PROTEIN HSP90 HEAT-INDUCIBLE ISOFORM / 82 KDA HEAT SHOCK PROTEIN Mass: 46842.391 Da / Num. of mol.: 3 / Fragment: MIDDLE AND C-TERMINAL DOMAINS, RESIDUES 273-677 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02829

#1: Protein

ATP-DEPENDENT MOLECULAR CHAPERONE HSP82 / HEAT SHOCK PROTEIN HSP90 HEAT-INDUCIBLE ISOFORM / 82 KDA HEAT SHOCK PROTEIN

Mass: 46842.391 Da / Num. of mol.: 3 / Fragment: MIDDLE AND C-TERMINAL DOMAINS, RESIDUES 273-677
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host:

ESCHERICHIA COLI (E. coli) / References: UniProt: P02829

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.74 Å³/Da / Density % sol: 55 %
Crystal grow	pH: 7.5 / Details: pH 7.50

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9762
Detector	Type: ADSC CCD / Detector: CCD / Date: Nov 20, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 2.8→100 Å / Num. obs: 41369 / % possible obs: 100 % / Redundancy: 4.9 % / B_iso Wilson estimate: 68 Å² / R_merge(I) obs: 0.16 / Net I/σ(I): 7.7
Reflection shell	Resolution: 2.8→2.95 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.82 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HK7

1hk7

Resolution: 3→288.67 Å / Cor.coef. F_o:F_c: 0.909 / Cor.coef. F_o:F_c free: 0.896 / SU B: 51.113 / SU ML: 0.425 / Cross valid method: THROUGHOUT / ESU R Free: 0.488 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.288	1688	5 %	RANDOM
R_work	0.257	-	-	-
obs	0.258	32118	99.9 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 88.43 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.61 Å²	0 Å²	0 Å²
2-	-	-4.61 Å²	0 Å²
3-	-	-	9.23 Å²

Refinement step

Cycle: LAST / Resolution: 3→288.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9882	0	0	0	9882

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	10065
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.818	1.981	13560
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.098	5	1212
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	44.814	25.096	471
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.764	15	1965
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.219	15	51
X-RAY DIFFRACTION	r_chiral_restr	0.114	0.2	1515
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	7431
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.275	0.2	5216
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.328	0.2	7162
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.186	0.2	377
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.297	0.2	207
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.229	0.2	9
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.487	1.5	6199
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.812	2	9870
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.167	3	4292
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.916	4.5	3690
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1419	tight positional	0.07	0.05
1	2	B	1419	tight positional	0.07	0.05
1	3	D	1419	tight positional	0.07	0.05
2	1	A	707	tight positional	0.08	0.05
2	2	B	707	tight positional	0.08	0.05
2	3	D	707	tight positional	0.11	0.05
3	1	A	1007	tight positional	0.05	0.05
3	2	B	1007	tight positional	0.05	0.05
3	3	D	1007	tight positional	0.06	0.05
1	1	A	1419	tight thermal	0.15	0.5
1	2	B	1419	tight thermal	0.15	0.5
1	3	D	1419	tight thermal	0.15	0.5
2	1	A	707	tight thermal	0.19	0.5
2	2	B	707	tight thermal	0.22	0.5
2	3	D	707	tight thermal	0.37	0.5
3	1	A	1007	tight thermal	0.08	0.5
3	2	B	1007	tight thermal	0.07	0.5
3	3	D	1007	tight thermal	0.1	0.5

LS refinement shell

Resolution: 3→3.08 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.369	114
R_work	0.331	2325

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	3.0657	-1.189	0.5085	2.8433	-1.4612	2.4686	0.0382	0.0082	-0.0269	-0.2525	0.1262	-0.1432	0.2211	0.1065	-0.1645	-0.4261	-0.0106	-0.1031	-0.5003	-0.0725	-0.357	-50.085	38.8814	-13.2738
2	4.1781	-1.6325	0.2952	11.1427	0.0538	6.0554	-0.0429	-0.2622	-0.2715	0.3486	-0.1338	-0.2858	0.7589	-0.0847	0.1767	-0.288	-0.0448	-0.0898	-0.4713	0.1089	0.0057	-51.4309	15.1655	8.077
3	3.7998	-0.3632	0.2615	4.1269	-3.169	7.6363	-0.1536	-0.2536	0.2098	0.6772	0.0588	0.3195	-0.2342	-0.0032	0.0947	-0.2168	0.0263	-0.0225	0.1531	0.1894	0.4144	-55.3038	15.7538	31.2736
4	3.155	1.5501	-1.3606	2.2288	-0.9511	1.7103	-0.0198	0.1697	-0.2503	-0.0085	0.0052	-0.3985	-0.0296	0.1677	0.0147	-0.5001	0.0922	-0.0815	-0.359	-0.0119	-0.3549	-21.9885	48.4857	1.7145
5	11.648	-0.582	0.2833	9.5374	1.911	0.3967	-0.0331	0.0757	0.8658	-0.0694	0.0886	-0.5997	-0.3649	0.1724	-0.0555	-0.5039	-0.0304	-0.0553	-0.2639	0.0455	0.0023	0.1801	71.1418	5.775
6	8.9758	-0.6602	3.0735	8.6059	-0.7201	4.7376	-0.1136	-0.302	0.3828	0.3732	-0.0995	0.1135	-0.6852	0.171	0.2131	0.0118	-0.0651	-0.0435	-0.0281	-0.1324	0.3365	-2.5885	93.5478	12.1722
7	2.2342	-0.3565	1.9603	2.8589	1.1278	2.9643	0.0632	0.092	0.1	-0.2305	-0.1086	-0.2873	0.1878	0.2654	0.0454	-0.4189	0.0134	0.0542	-0.4084	0.0869	-0.2969	-34.712	66.6994	-23.2547
8	11.8628	2.2943	2.0353	7.3231	-0.8371	12.4981	0.1577	1.0284	-0.4013	-0.9456	0.1047	-0.0262	-0.3323	-0.648	-0.2624	-0.0495	0.1659	-0.0419	-0.0948	-0.0444	-0.9247	-59.5017	71.4011	-42.994
9	5.297	0.2609	4.6257	4.0095	-1.4678	5.8455	0.0246	-0.0579	0.218	-0.109	0.0208	0.2815	0.1671	-0.1872	-0.0454	-0.1052	0.0794	-0.1794	-0.1744	-0.0456	-0.104	-81.9523	76.3841	-37.592

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	273 - 443
2	X-RAY DIFFRACTION	2	A	444 - 529
3	X-RAY DIFFRACTION	3	A	534 - 670
4	X-RAY DIFFRACTION	4	B	273 - 443
5	X-RAY DIFFRACTION	5	B	444 - 529
6	X-RAY DIFFRACTION	6	B	534 - 670
7	X-RAY DIFFRACTION	7	D	273 - 443
8	X-RAY DIFFRACTION	8	D	444 - 529
9	X-RAY DIFFRACTION	9	D	534 - 670

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