PDB-5dsv: Crystal structure of human proteasome alpha7 tetradecamer

ID or keywords:

Entry

Database: PDB / ID: 5dsv

Title

Crystal structure of human proteasome alpha7 tetradecamer

Components

Proteasome subunit alpha type-3

Keywords

HYDROLASE /

Proteasome

Function / homology

Function and homology information

regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) /

Somitogenesis / proteasome core complex, alpha-subunit complex /

proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin ...

regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) /

Somitogenesis / proteasome core complex, alpha-subunit complex /

proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / proteasomal protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of AXIN / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Negative regulation of NOTCH4 signaling / G2/M Checkpoints / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / ABC-family proteins mediated transport / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / UCH proteinases / The role of GTSE1 in G2/M progression after G2 checkpoint / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling /

Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases /

synapse /

ubiquitin protein ligase binding / extracellular exosome /

nucleoplasm /

nucleus /

cytosol /

cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.75 Å

Authors

Satoh, T. / Thammaporn, R. / Seetaha, S. / Kato, K.

Funding support

Japan, 1items

Citation

Journal: Sci Rep / Year: 2015
Title: Disassembly of the self-assembled, double-ring structure of proteasome alpha 7 homo-tetradecamer by alpha 6
Authors: Ishii, K. / Noda, M. / Yagi, H. / Thammaporn, R. / Seetaha, S. / Satoh, T. / Kato, K. / Uchiyama, S.

History

Deposition	Sep 17, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Dec 2, 2015	Provider: repository / Type: Initial release
Revision 1.1	Dec 30, 2015	Group: Database references
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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	5dsv.cif.gz	648.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5dsv.ent.gz	539.2 KB	Display	PDB format
PDBx/mmJSON format	5dsv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ds/5dsv ftp://data.pdbj.org/pub/pdb/validation_reports/ds/5dsv	HTTPS FTP

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Related structure data

Related structure data	1j2pS S: Starting model for refinement
Similar structure data	6he7-d 6he5-d 1j2q-d 0210 2h6j-d 7ls6-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	#166 - Oct 2013 Proteasome similarity (10) #60 - Dec 2004 Ubiquitin similarity (17) #172 - Apr 2014 RecA and Rad51 similarity (10) #234 - Jun 2019 MDM2 and Cancer similarity (8) #80 - Aug 2006 AAA+ Proteases similarity (3) #176 - Aug 2014 Dynein similarity (3)

Deposited unit

A: Proteasome subunit alpha type-3

B: Proteasome subunit alpha type-3

C: Proteasome subunit alpha type-3

D: Proteasome subunit alpha type-3

E: Proteasome subunit alpha type-3

F: Proteasome subunit alpha type-3

G: Proteasome subunit alpha type-3

H: Proteasome subunit alpha type-3

I: Proteasome subunit alpha type-3

J: Proteasome subunit alpha type-3

K: Proteasome subunit alpha type-3

L: Proteasome subunit alpha type-3

M: Proteasome subunit alpha type-3

N: Proteasome subunit alpha type-3

399 kDa, 14 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)	132.481, 132.481, 444.563
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:
NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-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	SER	SER	LYS	LYS	A	A	2 - 244	3 - 245
2	1	SER	SER	LYS	LYS	B	B	2 - 244	3 - 245
1	2	SER	SER	GLU	GLU	A	A	2 - 245	3 - 246
2	2	SER	SER	GLU	GLU	C	C	2 - 245	3 - 246
1	3	SER	SER	GLU	GLU	A	A	2 - 245	3 - 246
2	3	SER	SER	GLU	GLU	D	D	2 - 245	3 - 246
1	4	SER	SER	LYS	LYS	A	A	2 - 244	3 - 245
2	4	SER	SER	LYS	LYS	E	E	2 - 244	3 - 245
1	5	SER	SER	GLU	GLU	A	A	2 - 245	3 - 246
2	5	SER	SER	GLU	GLU	F	F	2 - 245	3 - 246
1	6	GLY	GLY	LYS	LYS	A	A	4 - 244	5 - 245
2	6	GLY	GLY	LYS	LYS	G	G	4 - 244	5 - 245
1	7	SER	SER	LYS	LYS	A	A	2 - 244	3 - 245
2	7	SER	SER	LYS	LYS	H	H	2 - 244	3 - 245
1	8	SER	SER	LEU	LEU	A	A	2 - 243	3 - 244
2	8	SER	SER	LEU	LEU	I	I	2 - 243	3 - 244
1	9	SER	SER	GLU	GLU	A	A	2 - 245	3 - 246
2	9	SER	SER	GLU	GLU	J	J	2 - 245	3 - 246
1	10	SER	SER	LEU	LEU	A	A	2 - 243	3 - 244
2	10	SER	SER	LEU	LEU	K	K	2 - 243	3 - 244
1	11	SER	SER	LYS	LYS	A	A	2 - 244	3 - 245
2	11	SER	SER	LYS	LYS	L	L	2 - 244	3 - 245
1	12	SER	SER	LEU	LEU	A	A	2 - 243	3 - 244
2	12	SER	SER	LEU	LEU	M	M	2 - 243	3 - 244
1	13	SER	SER	GLU	GLU	A	A	2 - 245	3 - 246
2	13	SER	SER	GLU	GLU	N	N	2 - 245	3 - 246
1	14	SER	SER	GLU	GLU	B	B	1 - 245	2 - 246
2	14	SER	SER	GLU	GLU	C	C	1 - 245	2 - 246
1	15	SER	SER	LYS	LYS	B	B	2 - 244	3 - 245
2	15	SER	SER	LYS	LYS	D	D	2 - 244	3 - 245
1	16	SER	SER	GLU	GLU	B	B	1 - 245	2 - 246
2	16	SER	SER	GLU	GLU	E	E	1 - 245	2 - 246
1	17	SER	SER	LYS	LYS	B	B	2 - 244	3 - 245
2	17	SER	SER	LYS	LYS	F	F	2 - 244	3 - 245
1	18	GLY	GLY	LYS	LYS	B	B	4 - 244	5 - 245
2	18	GLY	GLY	LYS	LYS	G	G	4 - 244	5 - 245
1	19	SER	SER	LYS	LYS	B	B	1 - 244	2 - 245
2	19	SER	SER	LYS	LYS	H	H	1 - 244	2 - 245
1	20	SER	SER	LEU	LEU	B	B	1 - 243	2 - 244
2	20	SER	SER	LEU	LEU	I	I	1 - 243	2 - 244
1	21	SER	SER	GLU	GLU	B	B	1 - 245	2 - 246
2	21	SER	SER	GLU	GLU	J	J	1 - 245	2 - 246
1	22	SER	SER	LEU	LEU	B	B	1 - 243	2 - 244
2	22	SER	SER	LEU	LEU	K	K	1 - 243	2 - 244
1	23	SER	SER	GLU	GLU	B	B	1 - 245	2 - 246
2	23	SER	SER	GLU	GLU	L	L	1 - 245	2 - 246
1	24	SER	SER	LEU	LEU	B	B	1 - 243	2 - 244
2	24	SER	SER	LEU	LEU	M	M	1 - 243	2 - 244
1	25	SER	SER	LYS	LYS	B	B	2 - 244	3 - 245
2	25	SER	SER	LYS	LYS	N	N	2 - 244	3 - 245
1	26	SER	SER	GLU	GLU	C	C	2 - 245	3 - 246
2	26	SER	SER	GLU	GLU	D	D	2 - 245	3 - 246
1	27	SER	SER	GLU	GLU	C	C	1 - 245	2 - 246
2	27	SER	SER	GLU	GLU	E	E	1 - 245	2 - 246
1	28	SER	SER	GLU	GLU	C	C	2 - 245	3 - 246
2	28	SER	SER	GLU	GLU	F	F	2 - 245	3 - 246
1	29	GLY	GLY	GLU	GLU	C	C	4 - 245	5 - 246
2	29	GLY	GLY	GLU	GLU	G	G	4 - 245	5 - 246
1	30	SER	SER	LYS	LYS	C	C	1 - 244	2 - 245
2	30	SER	SER	LYS	LYS	H	H	1 - 244	2 - 245
1	31	SER	SER	LYS	LYS	C	C	1 - 244	2 - 245
2	31	SER	SER	LYS	LYS	I	I	1 - 244	2 - 245
1	32	SER	SER	GLU	GLU	C	C	1 - 245	2 - 246
2	32	SER	SER	GLU	GLU	J	J	1 - 245	2 - 246
1	33	SER	SER	LYS	LYS	C	C	1 - 244	2 - 245
2	33	SER	SER	LYS	LYS	K	K	1 - 244	2 - 245
1	34	SER	SER	GLU	GLU	C	C	1 - 245	2 - 246
2	34	SER	SER	GLU	GLU	L	L	1 - 245	2 - 246
1	35	SER	SER	LEU	LEU	C	C	1 - 243	2 - 244
2	35	SER	SER	LEU	LEU	M	M	1 - 243	2 - 244
1	36	SER	SER	GLU	GLU	C	C	2 - 245	3 - 246
2	36	SER	SER	GLU	GLU	N	N	2 - 245	3 - 246
1	37	SER	SER	LYS	LYS	D	D	2 - 244	3 - 245
2	37	SER	SER	LYS	LYS	E	E	2 - 244	3 - 245
1	38	SER	SER	GLU	GLU	D	D	2 - 245	3 - 246
2	38	SER	SER	GLU	GLU	F	F	2 - 245	3 - 246
1	39	GLY	GLY	LYS	LYS	D	D	4 - 244	5 - 245
2	39	GLY	GLY	LYS	LYS	G	G	4 - 244	5 - 245
1	40	SER	SER	LYS	LYS	D	D	2 - 244	3 - 245
2	40	SER	SER	LYS	LYS	H	H	2 - 244	3 - 245
1	41	SER	SER	LEU	LEU	D	D	2 - 243	3 - 244
2	41	SER	SER	LEU	LEU	I	I	2 - 243	3 - 244
1	42	SER	SER	GLU	GLU	D	D	2 - 245	3 - 246
2	42	SER	SER	GLU	GLU	J	J	2 - 245	3 - 246
1	43	SER	SER	LEU	LEU	D	D	2 - 243	3 - 244
2	43	SER	SER	LEU	LEU	K	K	2 - 243	3 - 244
1	44	SER	SER	LYS	LYS	D	D	2 - 244	3 - 245
2	44	SER	SER	LYS	LYS	L	L	2 - 244	3 - 245
1	45	SER	SER	LEU	LEU	D	D	2 - 243	3 - 244
2	45	SER	SER	LEU	LEU	M	M	2 - 243	3 - 244
1	46	SER	SER	GLU	GLU	D	D	2 - 245	3 - 246
2	46	SER	SER	GLU	GLU	N	N	2 - 245	3 - 246
1	47	SER	SER	LYS	LYS	E	E	2 - 244	3 - 245
2	47	SER	SER	LYS	LYS	F	F	2 - 244	3 - 245
1	48	GLY	GLY	LYS	LYS	E	E	4 - 244	5 - 245
2	48	GLY	GLY	LYS	LYS	G	G	4 - 244	5 - 245
1	49	SER	SER	LYS	LYS	E	E	1 - 244	2 - 245
2	49	SER	SER	LYS	LYS	H	H	1 - 244	2 - 245
1	50	SER	SER	LEU	LEU	E	E	1 - 243	2 - 244
2	50	SER	SER	LEU	LEU	I	I	1 - 243	2 - 244
1	51	SER	SER	GLU	GLU	E	E	1 - 245	2 - 246
2	51	SER	SER	GLU	GLU	J	J	1 - 245	2 - 246
1	52	SER	SER	LEU	LEU	E	E	1 - 243	2 - 244
2	52	SER	SER	LEU	LEU	K	K	1 - 243	2 - 244
1	53	SER	SER	GLU	GLU	E	E	1 - 245	2 - 246
2	53	SER	SER	GLU	GLU	L	L	1 - 245	2 - 246
1	54	SER	SER	LEU	LEU	E	E	1 - 243	2 - 244
2	54	SER	SER	LEU	LEU	M	M	1 - 243	2 - 244
1	55	SER	SER	LYS	LYS	E	E	2 - 244	3 - 245
2	55	SER	SER	LYS	LYS	N	N	2 - 244	3 - 245
1	56	GLY	GLY	LYS	LYS	F	F	4 - 244	5 - 245
2	56	GLY	GLY	LYS	LYS	G	G	4 - 244	5 - 245
1	57	SER	SER	LYS	LYS	F	F	2 - 244	3 - 245
2	57	SER	SER	LYS	LYS	H	H	2 - 244	3 - 245
1	58	SER	SER	LEU	LEU	F	F	2 - 243	3 - 244
2	58	SER	SER	LEU	LEU	I	I	2 - 243	3 - 244
1	59	SER	SER	GLU	GLU	F	F	2 - 245	3 - 246
2	59	SER	SER	GLU	GLU	J	J	2 - 245	3 - 246
1	60	SER	SER	LEU	LEU	F	F	2 - 243	3 - 244
2	60	SER	SER	LEU	LEU	K	K	2 - 243	3 - 244
1	61	SER	SER	LYS	LYS	F	F	2 - 244	3 - 245
2	61	SER	SER	LYS	LYS	L	L	2 - 244	3 - 245
1	62	SER	SER	LEU	LEU	F	F	2 - 243	3 - 244
2	62	SER	SER	LEU	LEU	M	M	2 - 243	3 - 244
1	63	SER	SER	GLU	GLU	F	F	2 - 245	3 - 246
2	63	SER	SER	GLU	GLU	N	N	2 - 245	3 - 246
1	64	GLY	GLY	LYS	LYS	G	G	4 - 244	5 - 245
2	64	GLY	GLY	LYS	LYS	H	H	4 - 244	5 - 245
1	65	GLY	GLY	LEU	LEU	G	G	4 - 243	5 - 244
2	65	GLY	GLY	LEU	LEU	I	I	4 - 243	5 - 244
1	66	GLY	GLY	GLU	GLU	G	G	4 - 245	5 - 246
2	66	GLY	GLY	GLU	GLU	J	J	4 - 245	5 - 246
1	67	GLY	GLY	LEU	LEU	G	G	4 - 243	5 - 244
2	67	GLY	GLY	LEU	LEU	K	K	4 - 243	5 - 244
1	68	GLY	GLY	LYS	LYS	G	G	4 - 244	5 - 245
2	68	GLY	GLY	LYS	LYS	L	L	4 - 244	5 - 245
1	69	GLY	GLY	SER	SER	G	G	4 - 242	5 - 243
2	69	GLY	GLY	SER	SER	M	M	4 - 242	5 - 243
1	70	GLY	GLY	LYS	LYS	G	G	4 - 244	5 - 245
2	70	GLY	GLY	LYS	LYS	N	N	4 - 244	5 - 245
1	71	SER	SER	LYS	LYS	H	H	1 - 244	2 - 245
2	71	SER	SER	LYS	LYS	I	I	1 - 244	2 - 245
1	72	SER	SER	LYS	LYS	H	H	1 - 244	2 - 245
2	72	SER	SER	LYS	LYS	J	J	1 - 244	2 - 245
1	73	SER	SER	LYS	LYS	H	H	1 - 244	2 - 245
2	73	SER	SER	LYS	LYS	K	K	1 - 244	2 - 245
1	74	SER	SER	LYS	LYS	H	H	1 - 244	2 - 245
2	74	SER	SER	LYS	LYS	L	L	1 - 244	2 - 245
1	75	SER	SER	LEU	LEU	H	H	1 - 243	2 - 244
2	75	SER	SER	LEU	LEU	M	M	1 - 243	2 - 244
1	76	SER	SER	LYS	LYS	H	H	2 - 244	3 - 245
2	76	SER	SER	LYS	LYS	N	N	2 - 244	3 - 245
1	77	SER	SER	LYS	LYS	I	I	1 - 244	2 - 245
2	77	SER	SER	LYS	LYS	J	J	1 - 244	2 - 245
1	78	SER	SER	LYS	LYS	I	I	1 - 244	2 - 245
2	78	SER	SER	LYS	LYS	K	K	1 - 244	2 - 245
1	79	SER	SER	LEU	LEU	I	I	1 - 243	2 - 244
2	79	SER	SER	LEU	LEU	L	L	1 - 243	2 - 244
1	80	SER	SER	LEU	LEU	I	I	1 - 243	2 - 244
2	80	SER	SER	LEU	LEU	M	M	1 - 243	2 - 244
1	81	SER	SER	LEU	LEU	I	I	2 - 243	3 - 244
2	81	SER	SER	LEU	LEU	N	N	2 - 243	3 - 244
1	82	SER	SER	LYS	LYS	J	J	1 - 244	2 - 245
2	82	SER	SER	LYS	LYS	K	K	1 - 244	2 - 245
1	83	SER	SER	GLU	GLU	J	J	1 - 245	2 - 246
2	83	SER	SER	GLU	GLU	L	L	1 - 245	2 - 246
1	84	SER	SER	LEU	LEU	J	J	1 - 243	2 - 244
2	84	SER	SER	LEU	LEU	M	M	1 - 243	2 - 244
1	85	SER	SER	GLU	GLU	J	J	2 - 245	3 - 246
2	85	SER	SER	GLU	GLU	N	N	2 - 245	3 - 246
1	86	SER	SER	LEU	LEU	K	K	1 - 243	2 - 244
2	86	SER	SER	LEU	LEU	L	L	1 - 243	2 - 244
1	87	SER	SER	LEU	LEU	K	K	1 - 243	2 - 244
2	87	SER	SER	LEU	LEU	M	M	1 - 243	2 - 244
1	88	SER	SER	LEU	LEU	K	K	2 - 243	3 - 244
2	88	SER	SER	LEU	LEU	N	N	2 - 243	3 - 244
1	89	SER	SER	LEU	LEU	L	L	1 - 243	2 - 244
2	89	SER	SER	LEU	LEU	M	M	1 - 243	2 - 244
1	90	SER	SER	LYS	LYS	L	L	2 - 244	3 - 245
2	90	SER	SER	LYS	LYS	N	N	2 - 244	3 - 245
1	91	SER	SER	LEU	LEU	M	M	2 - 243	3 - 244
2	91	SER	SER	LEU	LEU	N	N	2 - 243	3 - 244

NCS ensembles :

#1: Protein	Proteasome subunit alpha type-3 / / proteasome alpha7 subunit / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 ...proteasome alpha7 subunit / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8 Mass: 28469.252 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA3, HC8, PSC8 / Plasmid: pRSF-Duet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P25788, proteasome endopeptidase complex

#1: Protein

Proteasome subunit alpha type-3 /

/ proteasome alpha7 subunit / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 ...

Mass: 28469.252 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: PSMA3, HC8, PSC8 / Plasmid: pRSF-Duet1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P25788,

proteasome endopeptidase complex

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.74 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 24% PEG400, 100 mM Tris-HCl (pH 7.5), 0.2 M magnesium chloride

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Data collection

Diffraction	Mean temperature: 95 K
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.75→50 Å / Num. all: 41746 / Num. obs: 40504 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / R_merge(I) obs: 0.081 / Net I/σ(I): 16.3
Reflection shell	Resolution: 3.75→3.81 Å / Redundancy: 5 % / R_merge(I) obs: 0.497 / Mean I/σ(I) obs: 2.5 / % possible all: 98.5

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0069	refinement
SCALEPACK		data reduction
DENZO		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1J2P

1j2p

Resolution: 3.75→20 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.903 / SU B: 52.338 / SU ML: 0.719 / Cross valid method: THROUGHOUT / ESU R Free: 0.935 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29107	2039	5.1 %	RANDOM
R_work	0.20945	-	-	-
obs	0.21349	38252	96.53 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 152.993 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.99 Å²	0 Å²	0 Å²
2-	-	4.99 Å²	0 Å²
3-	-	-	-9.99 Å²

Refinement step

Cycle: 1 / Resolution: 3.75→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26493	0	0	0	26493

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	26988
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	25767
X-RAY DIFFRACTION	r_angle_refined_deg	1.225	1.958	36343
X-RAY DIFFRACTION	r_angle_other_deg	0.935	3	59301
X-RAY DIFFRACTION	r_dihedral_angle_1_deg
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.055	0.2	3960
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	30480
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	6158
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	13.594	14.687	13549
X-RAY DIFFRACTION	r_mcbond_other	13.592	14.687	13548
X-RAY DIFFRACTION	r_mcangle_it	20.891	21.981	16903
X-RAY DIFFRACTION	r_mcangle_other	20.892	21.981	16904
X-RAY DIFFRACTION	r_scbond_it	13.746	15.832	13438
X-RAY DIFFRACTION	r_scbond_other	13.746	15.832	13436
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	21.485	23.325	19439
X-RAY DIFFRACTION	r_long_range_B_refined	28.355		21569
X-RAY DIFFRACTION	r_long_range_B_other	28.356		21570
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	15054	0.02
1	2	B	15054	0.02
2	1	A	14131	0.03
2	2	C	14131	0.03
3	1	A	15073	0.02
3	2	D	15073	0.02
4	1	A	15031	0.02
4	2	E	15031	0.02
5	1	A	15128	0.01
5	2	F	15128	0.01
6	1	A	14871	0.02
6	2	G	14871	0.02
7	1	A	14678	0.03
7	2	H	14678	0.03
8	1	A	14934	0.02
8	2	I	14934	0.02
9	1	A	14674	0.02
9	2	J	14674	0.02
10	1	A	14953	0.03
10	2	K	14953	0.03
11	1	A	15018	0.02
11	2	L	15018	0.02
12	1	A	14477	0.02
12	2	M	14477	0.02
13	1	A	15120	0.02
13	2	N	15120	0.02
14	1	B	14205	0.03
14	2	C	14205	0.03
15	1	B	15013	0.02
15	2	D	15013	0.02
16	1	B	15136	0.02
16	2	E	15136	0.02
17	1	B	15071	0.02
17	2	F	15071	0.02
18	1	B	14877	0.02
18	2	G	14877	0.02
19	1	B	14750	0.02
19	2	H	14750	0.02
20	1	B	14998	0.02
20	2	I	14998	0.02
21	1	B	14745	0
21	2	J	14745	0
22	1	B	15025	0.03
22	2	K	15025	0.03
23	1	B	15129	0.02
23	2	L	15129	0.02
24	1	B	14542	0.02
24	2	M	14542	0.02
25	1	B	15066	0.02
25	2	N	15066	0.02
26	1	C	14185	0.02
26	2	D	14185	0.02
27	1	C	14185	0.03
27	2	E	14185	0.03
28	1	C	14148	0.03
28	2	F	14148	0.03
29	1	C	14065	0.02
29	2	G	14065	0.02
30	1	C	14186	0.02
30	2	H	14186	0.02
31	1	C	14214	0.02
31	2	I	14214	0.02
32	1	C	14242	0.03
32	2	J	14242	0.03
33	1	C	14174	0.02
33	2	K	14174	0.02
34	1	C	14253	0.02
34	2	L	14253	0.02
35	1	C	13752	0.02
35	2	M	13752	0.02
36	1	C	14148	0.03
36	2	N	14148	0.03
37	1	D	14996	0.02
37	2	E	14996	0.02
38	1	D	15086	0.01
38	2	F	15086	0.01
39	1	D	14919	0.01
39	2	G	14919	0.01
40	1	D	14643	0.03
40	2	H	14643	0.03
41	1	D	14983	0.01
41	2	I	14983	0.01
42	1	D	14638	0.01
42	2	J	14638	0.01
43	1	D	14921	0.03
43	2	K	14921	0.03
44	1	D	15061	0.01
44	2	L	15061	0.01
45	1	D	14524	0.01
45	2	M	14524	0.01
46	1	D	15086	0.02
46	2	N	15086	0.02
47	1	E	15045	0.02
47	2	F	15045	0.02
48	1	E	14871	0.02
48	2	G	14871	0.02
49	1	E	14731	0.03
49	2	H	14731	0.03
50	1	E	14989	0.02
50	2	I	14989	0.02
51	1	E	14725	0.02
51	2	J	14725	0.02
52	1	E	15006	0.03
52	2	K	15006	0.03
53	1	E	15111	0.02
53	2	L	15111	0.02
54	1	E	14529	0.03
54	2	M	14529	0.03
55	1	E	15048	0.02
55	2	N	15048	0.02
56	1	F	14887	0.01
56	2	G	14887	0.01
57	1	F	14693	0.02
57	2	H	14693	0.02
58	1	F	14948	0.01
58	2	I	14948	0.01
59	1	F	14689	0
59	2	J	14689	0
60	1	F	14972	0.02
60	2	K	14972	0.02
61	1	F	15037	0.01
61	2	L	15037	0.01
62	1	F	14494	0.02
62	2	M	14494	0.02
63	1	F	15136	0.01
63	2	N	15136	0.01
64	1	G	14536	0.03
64	2	H	14536	0.03
65	1	G	14848	0.01
65	2	I	14848	0.01
66	1	G	14527	0.01
66	2	J	14527	0.01
67	1	G	14788	0.02
67	2	K	14788	0.02
68	1	G	14931	0.01
68	2	L	14931	0.01
69	1	G	14312	0.02
69	2	M	14312	0.02
70	1	G	14889	0.01
70	2	N	14889	0.01
71	1	H	14715	0.03
71	2	I	14715	0.03
72	1	H	14687	0.02
72	2	J	14687	0.02
73	1	H	14775	0.01
73	2	K	14775	0.01
74	1	H	14718	0.03
74	2	L	14718	0.03
75	1	H	14225	0.03
75	2	M	14225	0.03
76	1	H	14692	0.02
76	2	N	14692	0.02
77	1	I	14670	0.01
77	2	J	14670	0.01
78	1	I	15075	0.02
78	2	K	15075	0.02
79	1	I	15054	0
79	2	L	15054	0
80	1	I	14600	0.01
80	2	M	14600	0.01
81	1	I	14951	0.01
81	2	N	14951	0.01
82	1	J	14690	0.02
82	2	K	14690	0.02
83	1	J	14710	0.01
83	2	L	14710	0.01
84	1	J	14206	0.02
84	2	M	14206	0.02
85	1	J	14687	0.01
85	2	N	14687	0.01
86	1	K	14994	0.02
86	2	L	14994	0.02
87	1	K	14537	0.03
87	2	M	14537	0.03
88	1	K	14973	0.02
88	2	N	14973	0.02
89	1	L	14603	0.01
89	2	M	14603	0.01
90	1	L	15032	0.01
90	2	N	15032	0.01
91	1	M	14494	0.02
91	2	N	14494	0.02

LS refinement shell

Resolution: 3.75→3.844 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.405	127	-
R_work	0.332	2737	-
obs	-	-	98.59 %

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