9C87

Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Poised to Unfold a Linear-Degron DHFR-ssrA Substrate Bound with MTX

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, B, C, D, E... (A, B, C, D, E...)	ATP-dependent Clp protease ATP-binding subunit ClpX	polymer	389	42412.9	6	UniProt (P0A6H1) Pfam (PF07724) Pfam (PF10431)	Escherichia coli	ATP-dependent unfoldase ClpX
2	G (S)	Dihydrofolate reductase	polymer	210	23777.6	1	UniProt (A0A4C7B7M9) Pfam (PF00186) UniProt (by SIFTS) (P0ABQ4)	Escherichia coli
3	H, I, J, K, L... (h, i, j, k, l...)	ATP-dependent Clp protease proteolytic subunit	polymer	207	23468.9	14	UniProt (P0A6G7) Pfam (PF00574)	Escherichia coli	Caseinolytic protease,Endopeptidase Clp,Heat shock protein F21.5,Protease Ti
4	V, X, Z (A, B, C)	ADENOSINE-5'-TRIPHOSPHATE	non-polymer		507.2	3	Chemie (ATP)
5	AA, CA, W, Y (C, D, A, B)	MAGNESIUM ION	non-polymer		24.3	4	Chemie (MG)
6	BA, DA, EA (D, E, F)	ADENOSINE-5'-DIPHOSPHATE	non-polymer		427.2	3	Chemie (ADP)
7	FA (S)	METHOTREXATE	non-polymer		454.4	1	Chemie (MTX)

Sequence modifications

A, B, C, D, E, F: 62 - 435 (UniProt: P0A6H1)

PDB	External Database	Details
Met 37	-	initiating methionine
Gly 38	-	expression tag
Ser 39	-	expression tag
Ser 40	-	expression tag
His 41	-	expression tag
His 42	-	expression tag
His 43	-	expression tag
His 44	-	expression tag
His 45	-	expression tag
His 46	-	expression tag
Asp 47	-	expression tag
Tyr 48	-	expression tag
Asp 49	-	expression tag
Ile 50	-	expression tag
Pro 51	-	expression tag
Thr 52	-	expression tag
Thr 53	-	expression tag
Glu 54	-	expression tag
Asn 55	-	expression tag
Leu 56	-	expression tag
Tyr 57	-	expression tag
Phe 58	-	expression tag
Gln 59	-	expression tag
Gly 60	-	expression tag
Ser 61	-	expression tag
Ser 169	Cys 169	conflict
Glu 408	Lys 408	conflict
Gly 436	-	expression tag

S: 2 - 159 (UniProt: A0A4C7B7M9)

PDB	External Database	Details
Met -12	-	initiating methionine
His -11	-	expression tag
His -10	-	expression tag
His -9	-	expression tag
His -8	-	expression tag
His -7	-	expression tag
His -6	-	expression tag
Glu -5	-	expression tag
Asn -4	-	expression tag
Leu -3	-	expression tag
Tyr -2	-	expression tag
Phe -1	-	expression tag
Gln 0	-	expression tag
Gly 1	-	expression tag
Asp 37	Asn 74	conflict
Gly 160	-	expression tag
Ser 161	-	expression tag
His 162	-	expression tag
Leu 163	-	expression tag
Gly 164	-	expression tag
Leu 165	-	expression tag
Ile 166	-	expression tag
Glu 167	-	expression tag
Val 168	-	expression tag
Glu 169	-	expression tag
Lys 170	-	expression tag
Pro 171	-	expression tag
Leu 172	-	expression tag
Tyr 173	-	expression tag
Cys 174	-	expression tag
Gly 175	-	expression tag
Ser 176	-	expression tag
Gly 177	-	expression tag
Ser 178	-	expression tag
Trp 179	-	expression tag
Ser 180	-	expression tag
His 181	-	expression tag
Pro 182	-	expression tag
Gln 183	-	expression tag
Phe 184	-	expression tag
Glu 185	-	expression tag
Lys 186	-	expression tag
Ala 187	-	expression tag
Ala 188	-	expression tag
Asn 189	-	expression tag
Asp 190	-	expression tag
Glu 191	-	expression tag
Asn 192	-	expression tag
Tyr 193	-	expression tag
Ala 194	-	expression tag
Leu 195	-	expression tag
Ala 196	-	expression tag
Ala 197	-	expression tag

h, i, j, k, l, m, n, p, q, r, s, t, u, v: 2 - 193 (UniProt: P0A6G7)

PDB	External Database	Details
Glu 194	-	expression tag
Asn 195	-	expression tag
Leu 196	-	expression tag
Tyr 197	-	expression tag
Phe 198	-	expression tag
Gln 199	-	expression tag
Ser 200	-	expression tag
Leu 201	-	expression tag
Glu 202	-	expression tag
His 203	-	expression tag
His 204	-	expression tag
His 205	-	expression tag
His 206	-	expression tag
His 207	-	expression tag
His 208	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	21
	Total formula weight	606818.9
Non-Polymers*	Number of molecules	11
	Total formula weight	3354.8
All*	Total formula weight	610173.7

*Water molecules are not included.