7ADO: ER membrane protein complex subunit 1

Name: PDB 7ADO: Cryo-EM structure of human ER membrane protein complex in lipid nanodiscs
Published: 2020-12-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: membrane protein

Cryo-EM structure of human ER membrane protein complex in lipid nanodiscs. Determined by electron microscopy at 3.39 Å resolution. Released 2 Dec 2020.

Method: Electron microscopy
Resolution: 3.39 Å
Organism: Homo sapiens
Chains: 10
Atoms: 16,845
Mol. weight: 308.54 kDa
Ligands: PCW, NAG
Released: 2 Dec 2020

Explore 7ADO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ADO contains 72 α-helices and 102 β-strands across 10 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: 15 helices, 67 β-strands

Element	Residues	Length	Sheet
α-helix	24-29	6
β-strand	32	1	1
β-strand	35	1	2
β-strand	40-44	5	3
β-strand	53	1	4
β-strand	55-58	4	3
β-strand	63-64	2	3
β-strand	67	1	4
β-strand	87-92	6	5
β-strand	97-101	5	5
β-strand	106-109	4	5
β-strand	119-122	4	5
β-strand	130-134	5	6
β-strand	142-146	5	6
β-strand	150-155	6	6
β-strand	161-166	6	6
β-strand	175-179	5	7
β-strand	185-192	8	7
β-strand	196-203	8	7
β-strand	209-216	8	7
β-strand	235-239	5	8
β-strand	244-248	5	8
β-strand	257-260	4	8
β-strand	275-277	3	9
α-helix	286-288	3
β-strand	290-296	7	9
β-strand	299-305	7	9
β-strand	310-316	7	9
β-strand	322-326	5	10
β-strand	331-338	8	10
β-strand	372-379	8	10
α-helix	384	1
β-strand	385-394	10	10
β-strand	405-409	5	11
β-strand	419-424	6	11
β-strand	430-433	4	11
β-strand	441-445	5	11
α-helix	447-450	4
β-strand	452-457	6	12
α-helix	464-472	9
α-helix	481-501	21
β-strand	536-540	5	12
β-strand	544-547	4	13
β-strand	548	1	12
β-strand	557-560	4	13
β-strand	570-576	7	14
β-strand	586-592	7	14
β-strand	599-605	7	14
β-strand	610-611	2	14
α-helix	615-619	5
β-strand	625-627	3	15
β-strand	641-643	3	15
β-strand	649-651	3	15
α-helix	656-665	10
α-helix	666-668	3
β-strand	669-675	7	16
β-strand	680-685	6	16
β-strand	693-699	7	16
β-strand	706-712	7	17
β-strand	723-725	3	18
β-strand	731-734	4	18
β-strand	740-746	7	17
β-strand	756-763	8	17
β-strand	769-776	8	17
β-strand	778	1	18
α-helix	781-782	2
β-strand	783-787	5	18
β-strand	790-797	8	18
β-strand	802-813	12	18
β-strand	832-840	9	18
β-strand	845-849	5	19
β-strand	860-864	5	19
β-strand	870-874	5	19
α-helix	875-877	3
α-helix	888-893	6
β-strand	921-926	6	1
β-strand	933-938	6	1
β-strand	941	1	2
β-strand	943-947	5	1
α-helix	962-966	5
α-helix	969-981	13
α-helix	984-991	8

Chain B: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	14-24	11
α-helix	32-40	9
α-helix	44-48	5
α-helix	52-66	15
α-helix	70-82	13
α-helix	88-99	12
α-helix	103-115	13
α-helix	122-133	12
α-helix	138-148	11
α-helix	155-167	13
α-helix	173-183	11
α-helix	189-202	14
α-helix	205-222	18
α-helix	227-239	13
α-helix	247-272	26
α-helix	281-291	11

Chain C: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	13-17	5
α-helix	18-38	21
α-helix	46-64	19
α-helix	70-81	12
α-helix	87-89	3
α-helix	115-131	17
β-strand	138-139	2	20
α-helix	149-151	3
β-strand	165-166	2	20
α-helix	168-178	11
α-helix	180-182	3
α-helix	184-186	3
α-helix	214-226	13
α-helix	237-241	5

Chain D: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	141-155	15
α-helix	161-164	4
α-helix	169-171	3
β-strand	176-181	6	16

Chain E: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	5-34	30
α-helix	43-63	21
α-helix	72-76	5
α-helix	81-84	4
α-helix	88-90	3
β-strand	95	1	21
α-helix	96-99	4

Chain F: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	18-43	26
α-helix	49-69	21
α-helix	71-73	3
α-helix	82-85	4
α-helix	91-107	17

Chain G: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	47-49	3	22
α-helix	58-64	7
β-strand	67	1	23
β-strand	68	1	24
β-strand	76	1	23
β-strand	77	1	22
β-strand	84-86	3	22
β-strand	93-96	4	25
β-strand	97	1	24
β-strand	108-111	4	25
β-strand	120	1	25
β-strand	134	1	25

Chain H: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	26
α-helix	8-20	13
β-strand	25-32	8	27
β-strand	53	1	26
β-strand	56-63	8	27
α-helix	68-82	15
α-helix	83-85	3
β-strand	88-95	8	27
β-strand	98	1	21
α-helix	106-115	10
β-strand	123-126	4	27
β-strand	127	1	28
β-strand	141	1	28
β-strand	144-145	2	29
β-strand	152-153	2	29
α-helix	166-176	11
α-helix	180-182	3
α-helix	186-189	4
α-helix	200-208	9

2 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	A	protein	993	Homo sapiens	Q8N766 (AlphaFold model)
ER membrane protein complex subunit 2	B	protein	297	Homo sapiens	Q15006 (AlphaFold model)
ER membrane protein complex subunit 3	C	protein	261	Homo sapiens	Q9P0I2 (AlphaFold model)
ER membrane protein complex subunit 4	D	protein	183	Homo sapiens	Q5J8M3 (AlphaFold model)
Membrane magnesium transporter 1	E	protein	139	Homo sapiens	Q8N4V1
ER membrane protein complex subunit 6	F	protein	110	Homo sapiens	Q9BV81
ER membrane protein complex subunit 7	G	protein	242	Homo sapiens	Q9NPA0
ER membrane protein complex subunit 8	H	protein	210	Homo sapiens	O43402
ER membrane protein complex subunit 10	I	protein	263	Homo sapiens	Q5UCC4
Unassigned helix	K	protein	16	Homo sapiens

Sequence of entity 1 (A), FASTA

>7ADO_1 ER membrane protein complex subunit 1 (chains A)
MAAEWASRFWLWATLLIPAAAVYEDQVGKFDWRQQYVGKVKFASLEFSPGSKKLVVATEK
NVIAALNSRTGEILWRHVDKGTAEGAVDAMLLHGQDVITVSNGGRIMRSWETNIGGLNWE
ITLDSGSFQALGLVGLQESVRYIAVLKKTTLALHHLSSGHLKWVEHLPESDSIHYQMVYS
YGSGVVWALGVVPFSHVNIVKFNVEDGEIVQQVRVSTPWLQHLSGACGVVDEAVLVCPDP
SSRSLQTLALETEWELRQIPLQSLDLEFGSGFQPRVLPTQPNPVDASRAQFFLHLSPSHY
ALLQYHYGTLSLLKNFPQTALVSFATTGEKTVAAVMACRNEVQKSSSSEDGSMGSFSEKS
SSKDSLACFNQTYTINLYLVETGRRLLDTTITFSLEQSGTRPERLYIQVFLKKDDSVGYR
ALVQTEDHLLLFLQQLAGKVVLWSREESLAEVVCLEMVDLPLTGAQAELEGEFGKKADGL
LGMFLKRLSSQLILLQAWTSHLWKMFYDARKPRSQIKNEINIDTLARDEFNLQKMMVMVT
ASGKLFGIESSSGTILWKQYLPNVKPDSSFKLMVQRTTAHFPHPPQCTLLVKDKESGMSS
LYVFNPIFGKWSQVAPPVLKRPILQSLLLPVMDQDYAKVLLLIDDEYKVTAFPATRNVLR
QLHELAPSIFFYLVDAEQGRLCGYRLRKDLTTELSWELTIPPEVQRIVKVKGKRSSEHVH
SQGRVMGDRSVLYKSLNPNLLAVVTESTDAHHERTFIGIFLIDGVTGRIIHSSVQKKAKG
PVHIVHSENWVVYQYWNTKARRNEFTVLELYEGTEQYNATAFSSLDRPQLPQVLQQSYIF
PSSISAMEATITERGITSRHLLIGLPSGAILSLPKALLDPRRPEIPTEQSREENLIPYSP
DVQIHAERFINYNQTVSRMRGIYTAPSGLESTCLVVAYGLDIYQTRVYPSKQFDVLKDDY
DYVLISSVLFGLVFATMITKRLAQVKLLNRAWR

Sequence of entity 2 (B), FASTA

>7ADO_2 ER membrane protein complex subunit 2 (chains B)
MAKVSELYDVTWEEMRDKMRKWREENSRNSEQIVEVGEELINEYASKLGDDIWIIYEQVM
IAALDYGRDDLALFCLQELRRQFPGSHRVKRLTGMRFEAMERYDDAIQLYDRILQEDPTN
TAARKRKIAIRKAQGKNVEAIRELNEYLEQFVGDQEAWHELAELYINEHDYAKAAFCLEE
LMMTNPHNHLYCQQYAEVKYTQGGLENLELSRKYFAQALKLNNRNMRALFGLYMSASHIA
SNPKASAKTKKDNMKYASWAASQINRAYQFAGRSKKETKYSLKAVEDMLETLQITQS

Sequence of entity 3 (C), FASTA

>7ADO_3 ER membrane protein complex subunit 3 (chains C)
MAGPELLLDSNIRLWVVLPIVIITFFVGMIRHYVSILLQSDKKLTQEQVSDSQVLIRSRV
LRENGKYIPKQSFLTRKYYFNNPEDGFFKKTKRKVVPPSPMTDPTMLTDMMKGNVTNVLP
MILIGGWINMTFSGFVTTKVPFPLTLRFKPMLQQGIELLTLDASWVSSASWYFLNVFGLR
SIYSLILGQDNAADQSRMMQEQMTGAAMAMPADTNKAFKTEWEALELTDHQWALDDVEEE
LMAKDLHFEGMFKKELQTSIF

Sequence of entity 4 (D), FASTA

>7ADO_4 ER membrane protein complex subunit 4 (chains D)
MTAQGGLVANRGRRFKWAIELSGPGGGSRGRSDRGSGQGDSLYPVGYLDKQVPDTSVQET
DRILVEKRCWDIALGPLKQIPMNLFIMYMAGNTISIFPTMMVCMMAWRPIQALMAISATF
KMLESSSQKFLQGLVYLIGNLMGLALAVYKCQSMGLLPTHASDWLAFIEPPERMEFSGGG
LLL

Sequence of entity 5 (E), FASTA

>7ADO_5 Membrane magnesium transporter 1 (chains E)
MAPSLWKGLVGIGLFALAHAAFSAAQHRSYMRLTEKEDESLPIDIVLQTLLAFAVTCYGI
VHIAGEFKDMDATSELKNKTFDTLRNHPSFYVFNHRGRVLFRPSDTANSSNQDALSSNTS
LKLRKLESLRRDYKDDDDK

Sequence of entity 6 (F), FASTA

>7ADO_6 ER membrane protein complex subunit 6 (chains F)
MAAVVAKREGPPFISEAAVRGNAAVLDYCRTSVSALSGATAGILGLTGLYGFIFYLLASV
LLSLLLILKAGRRWNKYFKSRRPLFTGGLIGGLFTYVLFWTFLYGMVHVY

Sequence of entity 7 (G), FASTA

>7ADO_7 ER membrane protein complex subunit 7 (chains G)
MAAALWGFFPVLLLLLLSGDVQSSEVPGAAAEGSGGSGVGIGDRFKIEGRAVVPGVKPQD
WISAARVLVDGEEHVGFLKTDGSFVVHDIPSGSYVVEVVSPAYRFDPVRVDITSKGKMRA
RYVNYIKTSEVVRLPYPLQMKSSGPPSYFIKRESWGWTDFLMNPMVMMMVLPLLIFVLLP
KVVNTSDPDMRREMEQSMNMLNSNHELPDVSEFMTRLFSSKSSGKSSSGSSKTGKSGAGK
RR

Sequence of entity 8 (H), FASTA

>7ADO_8 ER membrane protein complex subunit 8 (chains H)
MPGVKLTTQAYCKMVLHGAKYPHCAVNGLLVAEKQKPRKEHLPLGGPGAHHTLFVDCIPL
FHGTLALAPMLEVALTLIDSWCKDHSYVIAGYYQANERVKDASPNQVAEKVASRIAEGFS
DTALIMVDNTKFTMDCVAPTIHVYEHHENRWRCRDPHHDYCEDWPEAQRISASLLDSRSY
ETLVDFDNHLDDIRNDWTNPEINKAVLHLC

Sequence of entity 9 (I), FASTA

>7ADO_9 ER membrane protein complex subunit 10 (chains I)
MAAAASAGATRLLLLLLMAVAAPSRARGSGCRAGTGARGAGAEGREGEACGTVGLLLEHS
FEIDDSANFRKRGSLLWNQQDGTLSLSQRQLSEEERGRLRDVAALNGLYRVRIPRRPGAL
DGLEAGGYVSSFVPACSLVESHLSDQLTLHVDVAGNVVGVSVVTHPGGCRGHEVEDVDLE
LFNTSVQLQPPTTAPGPETAAFIERLEMEQAQKAKNPQEQKSFFAKYWMYIIPVVLFLMM
SGAPDTGGQGGGGGGGGGGGSGR

Sequence of entity 10 (K), FASTA

>7ADO_10 Unassigned helix (chains K)
XXXXXXXXXXXXXXXX

Ligands and cofactors

ID	Name	Formula	Copies
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	5
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients. Miller-Vedam, L.E., Brauning, B., Popova, K.D. et al. Elife (2020) 9. DOI 10.7554/eLife.62611 · 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
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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