PDB-4pj1: Crystal structure of the human mitochondrial chaperonin symmetric...

ID or keywords:

Entry

Database: PDB / ID: 4pj1

Title

Crystal structure of the human mitochondrial chaperonin symmetrical 'football' complex

Components

10 kDa heat shock protein, mitochondrial
60 kDa heat shock protein, mitochondrial

Keywords

CHAPERONE / Human / Mitochondrial / Chaperonin / Complex / Symmetric

Function / homology

Function and homology information

coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / apolipoprotein A-I binding / lipopolysaccharide receptor complex / protein import into mitochondrial intermembrane space / high-density lipoprotein particle binding / migrasome / cysteine-type endopeptidase activator activity ...coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / apolipoprotein A-I binding / lipopolysaccharide receptor complex / protein import into mitochondrial intermembrane space / high-density lipoprotein particle binding / migrasome / cysteine-type endopeptidase activator activity / positive regulation of T cell mediated immune response to tumor cell / chaperonin ATPase / Mitochondrial protein import / positive regulation of macrophage activation / negative regulation of execution phase of apoptosis / cellular response to interleukin-7 / MyD88-dependent toll-like receptor signaling pathway / biological process involved in interaction with symbiont / 'de novo' protein folding / sperm plasma membrane / apoptotic mitochondrial changes / B cell activation / : / B cell proliferation / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / DNA replication origin binding / apolipoprotein binding / RHOG GTPase cycle / positive regulation of execution phase of apoptosis / response to unfolded protein / Mitochondrial unfolded protein response (UPRmt) / isomerase activity / chaperone-mediated protein complex assembly / sperm midpiece / clathrin-coated pit / positive regulation of interleukin-12 production / protein folding chaperone / Mitochondrial protein degradation / intrinsic apoptotic signaling pathway / response to cold / secretory granule / T cell activation / protein maturation / ATP-dependent protein folding chaperone / lipopolysaccharide binding / positive regulation of T cell activation / positive regulation of interleukin-6 production / positive regulation of type II interferon production / osteoblast differentiation / p53 binding / unfolded protein binding / protein folding / single-stranded DNA binding / double-stranded RNA binding / protein-folding chaperone binding / protein refolding / early endosome / mitochondrial inner membrane / protein stabilization / mitochondrial matrix / ubiquitin protein ligase binding / negative regulation of apoptotic process / enzyme binding / cell surface / protein-containing complex / ATP hydrolysis activity / mitochondrion / extracellular space / RNA binding / extracellular exosome / ATP binding / metal ion binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.15 Å

Authors

Frolow, F. / Azem, A. / Nisemblat, S.

Funding support

Israel, 2items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Crystal structure of the human mitochondrial chaperonin symmetrical football complex.
Authors: Nisemblat, S. / Yaniv, O. / Parnas, A. / Frolow, F. / Azem, A.

History

Deposition	May 10, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 29, 2015	Provider: repository / Type: Initial release
Revision 1.1	May 13, 2015	Group: Derived calculations
Revision 1.2	May 20, 2015	Group: Database references
Revision 1.3	Nov 22, 2017	Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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	4pj1.cif.gz	1.6 MB	Display	PDBx/mmCIF format
PDB format	pdb4pj1.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	4pj1.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4pj1_validation.pdf.gz	4 MB	Display	wwPDB validaton report
Full document	4pj1_full_validation.pdf.gz	4.2 MB	Display
Data in XML	4pj1_validation.xml.gz	290.6 KB	Display
Data in CIF	4pj1_validation.cif.gz	389.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pj/4pj1 ftp://data.pdbj.org/pub/pdb/validation_reports/pj/4pj1	HTTPS FTP

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Related structure data

Related structure data	1aonS S: Starting model for refinement
Similar structure data	5opx-d 4pkn-d 6mrc-d 4pko-d 5lox-d 6ht7-d 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	#32 - Aug 2002 Chaperones similarity (17) #13 - Jan 2001 Alcohol Dehydrogenase similarity (1) #35 - Nov 2002 Ferritin and Transferrin similarity (1)

Deposited unit

A: 60 kDa heat shock protein, mitochondrial

B: 60 kDa heat shock protein, mitochondrial

C: 60 kDa heat shock protein, mitochondrial

D: 60 kDa heat shock protein, mitochondrial

E: 60 kDa heat shock protein, mitochondrial

F: 60 kDa heat shock protein, mitochondrial

G: 60 kDa heat shock protein, mitochondrial

H: 60 kDa heat shock protein, mitochondrial

I: 60 kDa heat shock protein, mitochondrial

J: 60 kDa heat shock protein, mitochondrial

K: 60 kDa heat shock protein, mitochondrial

L: 60 kDa heat shock protein, mitochondrial

M: 60 kDa heat shock protein, mitochondrial

N: 60 kDa heat shock protein, mitochondrial

O: 10 kDa heat shock protein, mitochondrial

P: 10 kDa heat shock protein, mitochondrial

Q: 10 kDa heat shock protein, mitochondrial

R: 10 kDa heat shock protein, mitochondrial

S: 10 kDa heat shock protein, mitochondrial

T: 10 kDa heat shock protein, mitochondrial

U: 10 kDa heat shock protein, mitochondrial

V: 10 kDa heat shock protein, mitochondrial

W: 10 kDa heat shock protein, mitochondrial

X: 10 kDa heat shock protein, mitochondrial

Y: 10 kDa heat shock protein, mitochondrial

Z: 10 kDa heat shock protein, mitochondrial

1: 10 kDa heat shock protein, mitochondrial

2: 10 kDa heat shock protein, mitochondrial

hetero molecules

1.02 MDa, 28 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	199.100, 199.100, 627.390
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASP	ASP	chain 1 and segid Z	1	AA	3 - 102	3 - 102
2	1	ASP	ASP	chain 2 and segid 1	2	BA	3 - 102	3 - 102
3	1	ASP	ASP	chain O and segid O	O	O	3 - 102	3 - 102
4	1	ASP	ASP	chain P and segid P	P	P	3 - 102	3 - 102
5	1	ASP	ASP	chain Q and segid Q	Q	Q	3 - 102	3 - 102
6	1	ASP	ASP	chain R and segid R	R	R	3 - 102	3 - 102
7	1	ASP	ASP	chain S and segid S	S	S	3 - 102	3 - 102
8	1	ASP	ASP	chain T and segid T	T	T	3 - 102	3 - 102
9	1	ASP	ASP	chain U and segid U	U	U	3 - 102	3 - 102
10	1	ASP	ASP	chain V and segid 2	V	V	3 - 102	3 - 102
11	1	ASP	ASP	chain W and segid V	W	W	3 - 102	3 - 102
12	1	ASP	ASP	chain X and segid W	X	X	3 - 102	3 - 102
13	1	ASP	ASP	chain Y and segid X	Y	Y	3 - 102	3 - 102
14	1	ASP	ASP	chain Z and segid Y	Z	Z	3 - 102	3 - 102
1	2	PRO	PRO	chain A and segid	A	A	1 - 526	27 - 552
2	2	PRO	PRO	chain B and segid	B	B	1 - 526	27 - 552
3	2	PRO	PRO	chain C and segid	C	C	1 - 526	27 - 552
4	2	PRO	PRO	chain D and segid	D	D	1 - 526	27 - 552
5	2	PRO	PRO	chain E and segid	E	E	1 - 526	27 - 552
6	2	PRO	PRO	chain F and segid	F	F	1 - 526	27 - 552
7	2	PRO	PRO	chain G and segid	G	G	1 - 526	27 - 552
8	2	PRO	PRO	chain H and segid	H	H	1 - 526	27 - 552
9	2	PRO	PRO	chain I and segid	I	I	1 - 526	27 - 552
10	2	PRO	PRO	chain J and segid	J	J	1 - 526	27 - 552
11	2	PRO	PRO	chain K and segid	K	K	1 - 526	27 - 552
12	2	PRO	PRO	chain L and segid	L	L	1 - 526	27 - 552
13	2	PRO	PRO	chain M and segid	M	M	1 - 526	27 - 552
14	2	PRO	PRO	chain N and segid	N	N	1 - 526	27 - 552

NCS ensembles :

ID
1
2

#1: Protein	60 kDa heat shock protein, mitochondrial / 60 kDa chaperonin / Chaperonin 60 / CPN60 / Heat shock protein 60 / Hsp60 / HuCHA60 / Mitochondrial ...60 kDa chaperonin / Chaperonin 60 / CPN60 / Heat shock protein 60 / Hsp60 / HuCHA60 / Mitochondrial matrix protein P1 / P60 lymphocyte protein Mass: 59859.465 Da / Num. of mol.: 14 / Fragment: UNP residues 27-550 / Mutation: E321K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPD1, HSP60 / Plasmid: PET-21d Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others) References: UniProt: P10809
#2: Protein	10 kDa heat shock protein, mitochondrial / Hsp10 / 10 kDa chaperonin / Chaperonin 10 / CPN10 / Early-pregnancy factor / EPF Mass: 12335.250 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPE1 / Plasmid: PET-24d Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others) References: UniProt: P61604
#3: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.29 Å³/Da / Density % sol: 62.56 %
Crystal grow	Temperature: 303 K / Method: vapor diffusion, hanging drop Details: Protein concentration: mHsp60, 9.5 mg/ml ; mHsp10, 1.6 mg/ml; Composition of protein solution: 50 mM Tris-HCl pH 7.7, 300 mM NaCl, 5% glycerol, 15 mM MgCl2, 0.5 mM KCl,1 mM ATP; Composition ...Details: Protein concentration: mHsp60, 9.5 mg/ml ; mHsp10, 1.6 mg/ml; Composition of protein solution: 50 mM Tris-HCl pH 7.7, 300 mM NaCl, 5% glycerol, 15 mM MgCl2, 0.5 mM KCl,1 mM ATP; Composition of reservoir solution: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dehydrate,30-35%(v/v) PEG 400 Volume and ratio of drop:5 micro l (1:1) PH range: 7.7 / Temp details: 303 for 3 days, then moved to 293

Crystal

Density Matthews: 3.29 Å³/Da / Density % sol: 62.56 %

Crystal grow

Temperature: 303 K / Method: vapor diffusion, hanging drop
Details: Protein concentration: mHsp60, 9.5 mg/ml ; mHsp10, 1.6 mg/ml; Composition of protein solution: 50 mM Tris-HCl pH 7.7, 300 mM NaCl, 5% glycerol, 15 mM MgCl2, 0.5 mM KCl,1 mM ATP; Composition ...
PH range: 7.7 / Temp details: 303 for 3 days, then moved to 293

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID29 / Wavelength: 0.9537 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2013

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9537 Å / Relative weight: 1

Reflection

Redundancy: 6.2 % / Number: 1351770 / R_merge(I) obs: 0.136 / D res high: 3.15 Å / D res low: 49.78 Å / Num. obs: 217130 / % possible obs: 99.8

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	ID	R_merge(I) obs	Redundancy
3.15	3.26	1	1.491	4.1
12.2	49.78	1	0.034	5.9

Reflection

Resolution: 3.15→49.78 Å / Num. obs: 217130 / % possible obs: 99.8 % / Redundancy: 6.2 % / R_merge(I) obs: 0.136 / R_pim(I) all: 0.058 / Net I/σ(I): 9 / Num. measured all: 1351770

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_pim(I) all	% possible all
3.15-3.26	4.1	1.491	0.7	85114	20886	0.793	99.1
12.2-49.78	5.9	0.034	30.6	24461	4126	0.015	98.5

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS	0.2.14	data reduction
PDB_EXTRACT	3.14	data extraction
MOLREP		phasing
PHENIX	(phenix.refine: 1.9_1692)	refinement
XSCALE		data scaling
Aimless		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1AON

1aon

Resolution: 3.15→49.775 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.73 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2704	10844	5.02 %	RANDOM
R_work	0.2407	204970	-	-
obs	0.2422	215814	99.28 %	-

Solvent computation

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

Displacement parameters

B_iso max: 387.11 Å² / B_iso mean: 121.1628 Å² / B_iso min: 53.11 Å²

Refinement step

Cycle: final / Resolution: 3.15→49.775 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	65571	0	392	0	65963
B_iso mean	-	-	86.93	-	-
Num. residues	-	-	-	-	8783

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	66580
X-RAY DIFFRACTION	f_angle_d	1.109	89824
X-RAY DIFFRACTION	f_chiral_restr	0.041	10846
X-RAY DIFFRACTION	f_plane_restr	0.004	11487
X-RAY DIFFRACTION	f_dihedral_angle_d	18.178	25306

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	1	6702	X-RAY DIFFRACTION	18.114	TORSIONAL
1	2	2	6702	X-RAY DIFFRACTION	18.114	TORSIONAL
1	3	O	6702	X-RAY DIFFRACTION	18.114	TORSIONAL
1	4	P	6702	X-RAY DIFFRACTION	18.114	TORSIONAL
1	5	Q	6702	X-RAY DIFFRACTION	18.114	TORSIONAL
1	6	R	6702	X-RAY DIFFRACTION	18.114	TORSIONAL
1	7	S	6702	X-RAY DIFFRACTION	18.114	TORSIONAL
1	8	T	6702	X-RAY DIFFRACTION	18.114	TORSIONAL
1	9	U	6702	X-RAY DIFFRACTION	18.114	TORSIONAL
1	10	V	6702	X-RAY DIFFRACTION	18.114	TORSIONAL
1	11	W	6702	X-RAY DIFFRACTION	18.114	TORSIONAL
1	12	X	6702	X-RAY DIFFRACTION	18.114	TORSIONAL
1	13	Y	6702	X-RAY DIFFRACTION	18.114	TORSIONAL
1	14	Z	6702	X-RAY DIFFRACTION	18.114	TORSIONAL
2	1	A	34907	X-RAY DIFFRACTION	18.114	TORSIONAL
2	2	B	34907	X-RAY DIFFRACTION	18.114	TORSIONAL
2	3	C	34907	X-RAY DIFFRACTION	18.114	TORSIONAL
2	4	D	34907	X-RAY DIFFRACTION	18.114	TORSIONAL
2	5	E	34907	X-RAY DIFFRACTION	18.114	TORSIONAL
2	6	F	34907	X-RAY DIFFRACTION	18.114	TORSIONAL
2	7	G	34907	X-RAY DIFFRACTION	18.114	TORSIONAL
2	8	H	34907	X-RAY DIFFRACTION	18.114	TORSIONAL
2	9	I	34907	X-RAY DIFFRACTION	18.114	TORSIONAL
2	10	J	34907	X-RAY DIFFRACTION	18.114	TORSIONAL
2	11	K	34907	X-RAY DIFFRACTION	18.114	TORSIONAL
2	12	L	34907	X-RAY DIFFRACTION	18.114	TORSIONAL
2	13	M	34907	X-RAY DIFFRACTION	18.114	TORSIONAL
2	14	N	34907	X-RAY DIFFRACTION	18.114	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.15-3.1858	0.4271	392	0.405	6214	6606	93
3.1858-3.2232	0.3828	334	0.3874	6510	6844	96
3.2232-3.2626	0.3999	362	0.3887	6605	6967	97
3.2626-3.3038	0.4023	372	0.3867	6637	7009	98
3.3038-3.3473	0.381	364	0.3784	6728	7092	99
3.3473-3.3931	0.3916	342	0.3623	6839	7181	100
3.3931-3.4416	0.3804	368	0.3495	6777	7145	100
3.4416-3.493	0.3666	340	0.3356	6805	7145	100
3.493-3.5475	0.3647	351	0.3233	6776	7127	100
3.5475-3.6057	0.3086	365	0.3087	6826	7191	100
3.6057-3.6678	0.3557	370	0.308	6786	7156	100
3.6678-3.7345	0.3201	341	0.2981	6851	7192	100
3.7345-3.8063	0.3313	345	0.29	6829	7174	100
3.8063-3.884	0.2856	363	0.2708	6803	7166	100
3.884-3.9684	0.319	424	0.2725	6775	7199	100
3.9684-4.0607	0.2924	355	0.2502	6857	7212	100
4.0607-4.1622	0.2921	323	0.2464	6844	7167	100
4.1622-4.2746	0.2827	355	0.2423	6858	7213	100
4.2746-4.4004	0.2854	354	0.224	6854	7208	100
4.4004-4.5423	0.2399	357	0.2222	6889	7246	100
4.5423-4.7045	0.2562	336	0.2196	6865	7201	100
4.7045-4.8927	0.2435	361	0.2165	6868	7229	100
4.8927-5.1152	0.2389	353	0.2141	6932	7285	100
5.1152-5.3846	0.2587	379	0.2137	6888	7267	100
5.3846-5.7215	0.2867	343	0.236	6953	7296	100
5.7215-6.1625	0.2743	337	0.2384	6970	7307	100
6.1625-6.7813	0.2821	398	0.2367	6946	7344	100
6.7813-7.7594	0.2418	371	0.2058	7031	7402	100
7.7594-9.7639	0.1648	384	0.1509	7071	7455	99
9.7639-49.7812	0.2061	405	0.1958	7383	7788	99

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