8S9S: Human ER membrane protein complex (EMC) in GDN

Name: PDB 8S9S: Structure of the human ER membrane protein complex (EMC) in GDN
Published: 2023-05-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: membrane protein

Structure of the human ER membrane protein complex (EMC) in GDN. Determined by electron microscopy at 3.6 Å resolution. Released 17 May 2023.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 9
Atoms: 18,012
Mol. weight: 307.49 kDa
Ligands: PCW, NAG
Released: 17 May 2023

Explore 8S9S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8S9S contains 93 α-helices and 114 β-strands across 9 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 1: 23 helices, 77 β-strands

Element	Residues	Length	Sheet
β-strand	32-34	3	1
β-strand	42-44	3	2
β-strand	53-57	5	2
β-strand	63-67	5	2
β-strand	73-77	5	2
α-helix	83-85	3
β-strand	87-93	7	3
β-strand	96-101	6	3
β-strand	106-111	6	3
β-strand	116-122	7	3
β-strand	128-135	8	4
β-strand	140-147	8	4
β-strand	150-155	6	4
β-strand	161-165	5	4
β-strand	174-181	8	5
β-strand	185-191	7	5
β-strand	197-203	7	5
β-strand	209-215	7	5
α-helix	223-226	4
β-strand	228-230	3	6
β-strand	234-239	6	6
β-strand	244-248	5	6
β-strand	257	1	6
β-strand	260	1	6
α-helix	262-264	3
β-strand	275-277	3	7
α-helix	286-288	3
β-strand	290-294	5	7
β-strand	299-306	8	7
β-strand	309-317	9	7
β-strand	322-326	5	8
β-strand	331-338	8	8
β-strand	372-379	8	8
β-strand	385	1	8
α-helix	386	1
β-strand	391-394	4	8
β-strand	402-411	10	9
β-strand	417-425	9	9
β-strand	430-434	5	9
β-strand	441-445	5	9
α-helix	447-450	4
β-strand	452-458	7	10
α-helix	459-463	5
α-helix	464-467	4
α-helix	468-470	3
α-helix	480-499	20
β-strand	535-540	6	10
β-strand	544-549	6	10
β-strand	555-560	6	10
β-strand	569	1	11
β-strand	572-576	5	11
β-strand	586-592	7	11
β-strand	599-604	6	11
α-helix	610	1
β-strand	611	1	11
α-helix	612	1
α-helix	615-617	3
β-strand	623-632	10	12
β-strand	638-644	7	12
β-strand	648	1	13
β-strand	649-652	4	12
α-helix	656-664	9
α-helix	666-668	3
β-strand	669-675	7	14
β-strand	680-684	5	14
β-strand	691	1	13
β-strand	694-699	6	14
β-strand	705-709	5	15
α-helix	712-714	3
β-strand	723-727	5	16
β-strand	730-733	4	16
β-strand	734	1	17
β-strand	740	1	18
β-strand	743-747	5	15
β-strand	756-762	7	15
β-strand	763	1	18
β-strand	769-776	8	15
β-strand	779-786	8	17
β-strand	791-797	7	17
β-strand	802-804	3	17
β-strand	807-811	5	17
β-strand	821-822	2	19
α-helix	830-831	2
β-strand	832-836	5	17
β-strand	839	1	17
β-strand	846	1	20
β-strand	849	1	20
α-helix	858-859	2
β-strand	860-864	5	20
β-strand	870-874	5	20
α-helix	875-878	4
α-helix	888-893	6
α-helix	895-898	4
β-strand	901	1	17
α-helix	906-908	3
β-strand	909	1	20
β-strand	919-925	7	1
β-strand	933-939	7	1
β-strand	942-947	6	1
α-helix	962-992	31

Chain 10: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	51-59	9	14
β-strand	69-77	9	14
β-strand	82-87	6	14
α-helix	88-90	3
α-helix	92-103	12
β-strand	107-113	7	14
β-strand	127-133	7	14
α-helix	134-138	5
β-strand	143-150	8	28
β-strand	156-163	8	28
α-helix	175-179	5
β-strand	182-188	7	28
α-helix	189-191	3
β-strand	192	1	15
α-helix	193-196	4
α-helix	199-209	11

Chain 2: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	12-24	13
α-helix	30-43	14
α-helix	51-66	16
α-helix	70-82	13
α-helix	87-98	12
α-helix	103-116	14
α-helix	122-133	12
α-helix	137-148	12
α-helix	155-168	14
α-helix	171-184	14
α-helix	189-202	14
α-helix	205-221	17
α-helix	226-241	16
α-helix	247-274	28
α-helix	280-289	10

Chain 3: 17 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	11-12	2
α-helix	13-17	5
α-helix	18-38	21
α-helix	41-43	3
α-helix	46-64	19
α-helix	65-67	3
α-helix	70-80	11
α-helix	105-115	11
α-helix	119-131	13
β-strand	138-139	2	21
α-helix	146-148	3
α-helix	149-152	4
β-strand	165-166	2	21
α-helix	168-177	10
α-helix	180-186	7
α-helix	215-227	13
α-helix	233-235	3
α-helix	237-242	6
α-helix	245-247	3

Chain 4: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	43-44	2
α-helix	68-90	23
α-helix	92-95	4
α-helix	98-107	10
α-helix	111-114	4
α-helix	116-122	7
α-helix	128-154	27
α-helix	162-167	6
α-helix	169-171	3
β-strand	172-173	2	19
β-strand	176-181	6	14

Chain 5: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	5-34	30
α-helix	43-63	21
β-strand	71	1	22
α-helix	81-84	4
α-helix	88-90	3
α-helix	96-100	5

Chain 6: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	14	1	22
α-helix	16-44	29
α-helix	49-70	22
α-helix	74-76	3
α-helix	82-86	5
α-helix	89-104	16
α-helix	105-109	5

Chain 7: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	45-50	6	23
β-strand	53	1	24
β-strand	56	1	24
α-helix	58-61	4
α-helix	62-64	3
β-strand	66-69	4	25
β-strand	74-77	4	25
β-strand	78	1	23
β-strand	79	1	3
β-strand	84-89	6	23
β-strand	92-99	8	25
β-strand	108-112	5	25
β-strand	118-122	5	25
β-strand	133-134	2	25
β-strand	138-139	2	23
α-helix	157-161	5
α-helix	164-177	14

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ER membrane protein complex subunit 1	1	protein	993	Homo sapiens	Q8N766 (AlphaFold model)
ER membrane protein complex subunit 2	2	protein	297	Homo sapiens	Q15006 (AlphaFold model)
ER membrane protein complex subunit 3	3	protein	261	Homo sapiens	Q9P0I2 (AlphaFold model)
ER membrane protein complex subunit 4	4	protein	183	Homo sapiens	Q5J8M3 (AlphaFold model)
Membrane magnesium transporter 1	5	protein	131	Homo sapiens	Q8N4V1
ER membrane protein complex subunit 6	6	protein	110	Homo sapiens	Q9BV81
ER membrane protein complex subunit 7	7	protein	242	Homo sapiens	Q9NPA0
ER membrane protein complex subunit 8	8	protein	210	Homo sapiens	O43402
ER membrane protein complex subunit 10	10	protein	262	Homo sapiens	Q5UCC4

Sequence of entity 1 (1), FASTA

>8S9S_1 ER membrane protein complex subunit 1 (chains 1)
MAAEWASRFWLWATLLIPAAAVYEDQVGKFDWRQQYVGKVKFASLEFSPGSKKLVVATEK
NVIAALNSRTGEILWRHVDKGTAEGAVDAMLLHGQDVITVSNGGRIMRSWETNIGGLNWE
ITLDSGSFQALGLVGLQESVRYIAVLKKTTLALHHLSSGHLKWVEHLPESDSIHYQMVYS
YGSGVVWALGVVPFSHVNIVKFNVEDGEIVQQVRVSTPWLQHLSGACGVVDEAVLVCPDP
SSRSLQTLALETEWELRQIPLQSLDLEFGSGFQPRVLPTQPNPVDASRAQFFLHLSPSHY
ALLQYHYGTLSLLKNFPQTALVSFATTGEKTVAAVMACRNEVQKSSSSEDGSMGSFSEKS
SSKDSLACFNQTYTINLYLVETGRRLLDTTITFSLEQSGTRPERLYIQVFLKKDDSVGYR
ALVQTEDHLLLFLQQLAGKVVLWSREESLAEVVCLEMVDLPLTGAQAELEGEFGKKADGL
LGMFLKRLSSQLILLQAWTSHLWKMFYDARKPRSQIKNEINIDTLARDEFNLQKMMVMVT
ASGKLFGIESSSGTILWKQYLPNVKPDSSFKLMVQRTTAHFPHPPQCTLLVKDKESGMSS
LYVFNPIFGKWSQVAPPVLKRPILQSLLLPVMDQDYAKVLLLIDDEYKVTAFPATRNVLR
QLHELAPSIFFYLVDAEQGRLCGYRLRKDLTTELSWELTIPPEVQRIVKVKGKRSSEHVH
SQGRVMGDRSVLYKSLNPNLLAVVTESTDAHHERTFIGIFLIDGVTGRIIHSSVQKKAKG
PVHIVHSENWVVYQYWNTKARRNEFTVLELYEGTEQYNATAFSSLDRPQLPQVLQQSYIF
PSSISAMEATITERGITSRHLLIGLPSGAILSLPKALLDPRRPEIPTEQSREENLIPYSP
DVQIHAERFINYNQTVSRMRGIYTAPSGLESTCLVVAYGLDIYQTRVYPSKQFDVLKDDY
DYVLISSVLFGLVFATMITKRLAQVKLLNRAWR

Sequence of entity 2 (2), FASTA

>8S9S_2 ER membrane protein complex subunit 2 (chains 2)
MAKVSELYDVTWEEMRDKMRKWREENSRNSEQIVEVGEELINEYASKLGDDIWIIYEQVM
IAALDYGRDDLALFCLQELRRQFPGSHRVKRLTGMRFEAMERYDDAIQLYDRILQEDPTN
TAARKRKIAIRKAQGKNVEAIRELNEYLEQFVGDQEAWHELAELYINEHDYAKAAFCLEE
LMMTNPHNHLYCQQYAEVKYTQGGLENLELSRKYFAQALKLNNRNMRALFGLYMSASHIA
SNPKASAKTKKDNMKYASWAASQINRAYQFAGRSKKETKYSLKAVEDMLETLQITQS

Sequence of entity 3 (3), FASTA

>8S9S_3 ER membrane protein complex subunit 3 (chains 3)
MAGPELLLDSNIRLWVVLPIVIITFFVGMIRHYVSILLQSDKKLTQEQVSDSQVLIRSRV
LRENGKYIPKQSFLTRKYYFNNPEDGFFKKTKRKVVPPSPMTDPTMLTDMMKGNVTNVLP
MILIGGWINMTFSGFVTTKVPFPLTLRFKPMLQQGIELLTLDASWVSSASWYFLNVFGLR
SIYSLILGQDNAADQSRMMQEQMTGAAMAMPADTNKAFKTEWEALELTDHQWALDDVEEE
LMAKDLHFEGMFKKELQTSIF

Sequence of entity 4 (4), FASTA

>8S9S_4 ER membrane protein complex subunit 4 (chains 4)
MTAQGGLVANRGRRFKWAIELSGPGGGSRGRSDRGSGQGDSLYPVGYLDKQVPDTSVQET
DRILVEKRCWDIALGPLKQIPMNLFIMYMAGNTISIFPTMMVCMMAWRPIQALMAISATF
KMLESSSQKFLQGLVYLIGNLMGLALAVYKCQSMGLLPTHASDWLAFIEPPERMEFSGGG
LLL

Sequence of entity 5 (5), FASTA

>8S9S_5 Membrane magnesium transporter 1 (chains 5)
MAPSLWKGLVGIGLFALAHAAFSAAQHRSYMRLTEKEDESLPIDIVLQTLLAFAVTCYGI
VHIAGEFKDMDATSELKNKTFDTLRNHPSFYVFNHRGRVLFRPSDTANSSNQDALSSNTS
LKLRKLESLRR

Sequence of entity 6 (6), FASTA

>8S9S_6 ER membrane protein complex subunit 6 (chains 6)
MAAVVAKREGPPFISEAAVRGNAAVLDYCRTSVSALSGATAGILGLTGLYGFIFYLLASV
LLSLLLILKAGRRWNKYFKSRRPLFTGGLIGGLFTYVLFWTFLYGMVHVY

Sequence of entity 7 (7), FASTA

>8S9S_7 ER membrane protein complex subunit 7 (chains 7)
MAAALWGFFPVLLLLLLSGDVQSSEVPGAAAEGSGGSGVGIGDRFKIEGRAVVPGVKPQD
WISAARVLVDGEEHVGFLKTDGSFVVHDIPSGSYVVEVVSPAYRFDPVRVDITSKGKMRA
RYVNYIKTSEVVRLPYPLQMKSSGPPSYFIKRESWGWTDFLMNPMVMMMVLPLLIFVLLP
KVVNTSDPDMRREMEQSMNMLNSNHELPDVSEFMTRLFSSKSSGKSSSGSSKTGKSGAGK
RR

Sequence of entity 8 (8), FASTA

>8S9S_8 ER membrane protein complex subunit 8 (chains 8)
MPGVKLTTQAYCKMVLHGAKYPHCAVNGLLVAEKQKPRKEHLPLGGPGAHHTLFVDCIPL
FHGTLALAPMLEVALTLIDSWCKDHSYVIAGYYQANERVKDASPNQVAEKVASRIAEGFS
DTALIMVDNTKFTMDCVAPTIHVYEHHENRWRCRDPHHDYCEDWPEAQRISASLLDSRSY
ETLVDFDNHLDDIRNDWTNPEINKAVLHLC

Sequence of entity 9 (10), FASTA

>8S9S_9 ER membrane protein complex subunit 10 (chains 10)
MAAASAGATRLLLLLLMAVAAPSRARGSGCRAGTGARGAGAEGREGEACGTVGLLLEHSF
EIDDSANFRKRGSLLWNQQDGTLSLSQRQLSEEERGRLRDVAALNGLYRVRIPRRPGALD
GLEAGGYVSSFVPACSLVESHLSDQLTLHVDVAGNVVGVSVVTHPGGCRGHEVEDVDLEL
FNTSVQLQPPTTAPGPETAAFIERLEMEQAQKAKNPQEQKSFFAKYWMYIIPVVLFLMMS
GAPDTGGQGGGGGGGGGGGSGR

Ligands and cofactors

ID	Name	Formula	Copies
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	6
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

A selectivity filter in the ER membrane protein complex limits protein misinsertion at the ER. Pleiner, T., Hazu, M., Pinton Tomaleri, G. et al. J Cell Biol (2023) 222. DOI 10.1083/jcb.202212007 · PubMed

Other PDB entries of the same protein (UniProt Q8N766 (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
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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