9QRU

Cryo-EM structure of the MMM ubiquitin ligase complex with nanobody 270 (Composite map)

This is a non-PDB format compatible entry.

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (D)	Isoform 4 of E3 ubiquitin-protein ligase MGRN1	polymer	539	59455.0	1	UniProt (O60291) Pfam (PF26192) Pfam (PF13920)	Homo sapiens (human)	Mahogunin RING finger protein 1,RING finger protein 156,RING-type E3 ubiquitin transferase MGRN1
2	B (A)	Modulator of smoothened protein	polymer	211	22594.2	1	UniProt (Q8NHV5) Pfam (PF18800)	Homo sapiens (human)	Attenuator of hedgehog
3	C (B)	Isoform 2 of Multiple epidermal growth factor-like domains protein 8	polymer	477	50353.0	1	UniProt (Q7Z7M0)	Homo sapiens (human)	Multiple EGF-like domains protein 8,Epidermal growth factor-like protein 4,EGF-like protein 4
4	D (C)	Nanobody 270	polymer	129	14378.9	1		Lama glama
5	E, F (D)	ZINC ION	non-polymer		65.4	2	Chemie (ZN) PubChem (32051)
6	G (A)	PALMITIC ACID	non-polymer		256.4	1	Chemie (PLM) PubChem (985)	Homo sapiens (human)	Attenuator of hedgehog
7	H (B)	(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-16-methoxy-5',7,9,13-tetramethyl-spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]	non-polymer		428.6	1	Chemie (A1JAX)
8	I, J, K (A, B, C)	water	water		18.0	26	Chemie (HOH)

Sequence modifications

D: 1 - 530 (UniProt: O60291)

PDB	External Database	Details
Glu 317	Arg 317	engineered mutation
Gly 531	-	expression tag
Thr 532	-	expression tag
Lys 533	-	expression tag
His 534	-	expression tag
His 535	-	expression tag
His 536	-	expression tag
His 537	-	expression tag
His 538	-	expression tag
His 539	-	expression tag

A: 1 - 167 (UniProt: Q8NHV5)

PDB	External Database	Details
Gly 168	-	linker
Thr 169	-	linker
Leu 170	-	expression tag
Glu 171	-	expression tag
Val 172	-	expression tag
Leu 173	-	expression tag
Phe 174	-	expression tag
Gln 175	-	expression tag
Gly 176	-	expression tag
Pro 177	-	expression tag
Gly 178	-	linker
Gly 179	-	linker
Ser 180	-	linker
Gly 181	-	linker
Ser 182	-	expression tag
Ala 183	-	expression tag
Trp 184	-	expression tag
Ser 185	-	expression tag
His 186	-	expression tag
Pro 187	-	expression tag
Gln 188	-	expression tag
Phe 189	-	expression tag
Glu 190	-	expression tag
Lys 191	-	expression tag
Gly 192	-	expression tag
Gly 193	-	expression tag
Gly 194	-	expression tag
Ser 195	-	expression tag
Gly 196	-	expression tag
Gly 197	-	expression tag
Gly 198	-	expression tag
Ser 199	-	expression tag
Gly 200	-	expression tag
Gly 201	-	expression tag
Ser 202	-	expression tag
Ala 203	-	expression tag
Trp 204	-	expression tag
Ser 205	-	expression tag
His 206	-	expression tag
Pro 207	-	expression tag
Gln 208	-	expression tag
Phe 209	-	expression tag
Glu 210	-	expression tag
Lys 211	-	expression tag

B: 2312 - 2778 (UniProt: Q7Z7M0)

PDB	External Database	Details
Gly 2779	-	expression tag
Thr 2780	-	expression tag
Glu 2781	-	expression tag
Thr 2782	-	expression tag
Ser 2783	-	expression tag
Gln 2784	-	expression tag
Val 2785	-	expression tag
Ala 2786	-	expression tag
Pro 2787	-	expression tag
Ala 2788	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	4
	Total formula weight	146781.1
Non-Polymers*	Number of molecules	4
	Total formula weight	815.9
All*	Total formula weight	147597.0

*Water molecules are not included.