6Y4L: ER membrane protein complex subunit 2

Crystal structure of human ER membrane protein complex subunits EMC2 and EMC9. Determined by X-ray diffraction at 2.2 Å resolution. Released 27 May 2020.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,606
Mol. weight: 57.28 kDa
Ligands: PE4
Released: 27 May 2020

Explore 6Y4L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Y4L contains 25 α-helices and 9 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	13-25	13
α-helix	30-43	14
α-helix	45-48	4
α-helix	49-51	3
α-helix	52-66	15
α-helix	69-82	14
α-helix	87-99	13
α-helix	103-116	14
α-helix	121-133	13
α-helix	137-150	14
α-helix	155-167	13
α-helix	171-184	14
α-helix	189-202	14
α-helix	205-221	17
α-helix	226-240	15
α-helix	247-279	33

Chain B: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
α-helix	7	1
α-helix	8-20	13
β-strand	26-32	7	2
β-strand	43	1	1
β-strand	45-48	4	2
α-helix	58-73	16
β-strand	77-84	8	2
α-helix	95-107	13
β-strand	112-116	5	2
β-strand	130-136	7	2
β-strand	139-142	4	2
α-helix	143-144	2
α-helix	145-147	3
β-strand	148-150	3	1
α-helix	153-165	13
α-helix	168-171	4
α-helix	175-180	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ER membrane protein complex subunit 2	A	protein	275	Homo sapiens	Q15006 (AlphaFold model)
ER membrane protein complex subunit 9	B	protein	212	Homo sapiens	Q9Y3B6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6Y4L_1 ER membrane protein complex subunit 2 (chains A)
MTWEEMRDKMRKWREENSRNSEQIVEVGEELINEYASKLGDDIWIIYEQVMIAALDYGRD
DLALFCLQELRRQFPGSHRVKRLTGMRFEAMERYDDAIQLYDRILQEDPTNTAARKRKIA
IRKAQGKNVEAIRELNEYLEQFVGDQEAWHELAELYINEHDYAKAAFCLEELMMTNPHNH
LYCQQYAEVKYTQGGLENLELSRKYFAQALKLNNRNMRALFGLYMSASHIASNPKASAKT
KKDNMKYASWAASQINRAYQFAGRSAAALEHHHHH

Sequence of entity 2 (B), FASTA

>6Y4L_2 ER membrane protein complex subunit 9 (chains B)
MGEVEISALAYVKMCLHAARYPHAAVNGLFLAPAPRSGECLCLTDCVPLFHSHLALSVML
EVALNQVDVWGAQAGLVVAGYYHANAAVNDQSPGPLALKIAGRIAEFFPDAVLIMLDNQK
LVPQPRVPPVIVLENQGLRWVPKDKNLVMWRDWEESRQMVGALLEDRAHQHLVDFDCHLD
DIRQDWTNQRLNTQITQWVGAAALEHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PE4	2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-etha…	C16 H34 O8	1

Water and common crystallization additives (PEG, EDO, SO4) are not listed.

Primary citation

The architecture of EMC reveals a path for membrane protein insertion. O'Donnell, J.P., Phillips, B.P., Yagita, Y. et al. Elife (2020) 9. DOI 10.7554/eLife.57887 · PubMed

Other PDB entries of the same protein (UniProt Q15006 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8J0O 3.32 Å, cryo-EM structure of human EMC and VDAC
7ADO 3.39 Å, Cryo-EM structure of human ER membrane protein complex in lipid nanodiscs
6WW7 3.4 Å, Structure of the human ER membrane protein complex in a lipid nanodisc
8EOI 3.4 Å, Structure of a human EMC:human Cav1.2 channel complex in GDN detergent
8J0N 3.47 Å, cryo-EM structure of human EMC
7ADP 3.6 Å, Cryo-EM structure of human ER membrane protein complex in GDN detergent
8S9S 3.6 Å, Structure of the human ER membrane protein complex (EMC) in GDN
9ZZ6 4.16 Å, The ER membrane protein complex acts as a chaperone to promote voltage-gated calcium…
6Z3W 6.4 Å, Human ER membrane protein complex
9C7V 6.6 Å, Structure of the human BOS:human EMC complex in GDN

Browse structure collections

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