7ADP: ER membrane protein complex subunit 1

Name: PDB 7ADP: Cryo-EM structure of human ER membrane protein complex in GDN detergent
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 GDN detergent. Determined by electron microscopy at 3.6 Å resolution. Released 2 Dec 2020.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 8
Atoms: 15,026
Mol. weight: 276.51 kDa
Ligands: NAG
Released: 2 Dec 2020

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

Secondary structure: helices and β-sheets

7ADP contains 63 α-helices and 98 β-strands across 8 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: 12 helices, 73 β-strands

Element	Residues	Length	Sheet
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
α-helix	83-85	3
β-strand	87	1	5
β-strand	91-92	2	6
β-strand	97-98	2	6
β-strand	99	1	7
β-strand	101	1	5
β-strand	106-109	4	7
β-strand	119-122	4	7
β-strand	130-131	2	8
β-strand	143	1	9
β-strand	145-146	2	8
β-strand	150-154	5	9
β-strand	161-166	6	9
β-strand	177-179	3	10
β-strand	185-191	7	10
β-strand	197-203	7	10
β-strand	210	1	10
β-strand	214-215	2	10
β-strand	235-239	5	11
α-helix	241-243	3
β-strand	244-248	5	11
β-strand	258-260	3	11
β-strand	275-277	3	12
α-helix	286-288	3
β-strand	291-296	6	12
β-strand	299-305	7	12
β-strand	310-316	7	12
β-strand	319-326	8	13
β-strand	331-338	8	13
β-strand	373-379	7	13
α-helix	384	1
β-strand	385-392	8	13
β-strand	406-409	4	14
β-strand	419-423	5	14
β-strand	429-434	6	14
β-strand	441-446	6	14
α-helix	448-450	3
β-strand	452-457	6	15
α-helix	482-501	20
β-strand	536-540	5	15
β-strand	544-545	2	16
β-strand	548	1	15
β-strand	559-560	2	16
β-strand	570-576	7	17
β-strand	586-592	7	17
β-strand	599-604	6	17
β-strand	611	1	17
α-helix	616-618	3
β-strand	625-627	3	18
β-strand	641-643	3	18
β-strand	649-650	2	18
α-helix	656-665	10
α-helix	666-668	3
β-strand	669-675	7	19
β-strand	680-685	6	19
β-strand	696-699	4	19
β-strand	706-712	7	20
β-strand	723	1	21
β-strand	733-734	2	21
β-strand	740-746	7	20
β-strand	756-763	8	20
β-strand	769-776	8	20
β-strand	778	1	21
α-helix	780-782	3
β-strand	783-786	4	21
β-strand	790-797	8	21
β-strand	802-813	12	21
β-strand	832-836	5	21
β-strand	839	1	21
β-strand	845-849	5	22
β-strand	860-864	5	22
β-strand	870-874	5	22
α-helix	875-878	4
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	962-991	30

Chain B: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	14-24	11
α-helix	32-43	12
α-helix	45-48	4
α-helix	55-58	4
α-helix	60-66	7
α-helix	71-82	12
α-helix	89-99	11
α-helix	103-116	14
α-helix	122-134	13
α-helix	137-150	14
α-helix	155-167	13
α-helix	174-181	8
α-helix	189-200	12
α-helix	205-222	18
α-helix	227-239	13
α-helix	247-271	25
α-helix	282-291	10

Chain C: 11 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	47-63	17
α-helix	70-81	12
α-helix	122-131	10
β-strand	139	1	23
α-helix	146-148	3
α-helix	149-152	4
β-strand	165	1	23
α-helix	169-186	18
α-helix	215-226	12
α-helix	237-242	6

Chain D: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	161-165	5
α-helix	168-173	6
β-strand	176-179	4	19

Chain E: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	5-33	29
α-helix	44-64	21
β-strand	71	1	24
α-helix	72-75	4
α-helix	76-78	3
α-helix	81-85	5
α-helix	88-90	3
α-helix	96-99	4

Chain F: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	14	1	24
α-helix	18-43	26
α-helix	49-70	22
α-helix	82-85	4
α-helix	90-108	19

Chain H: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	25
α-helix	8-20	13
β-strand	26-31	6	26
β-strand	53-54	2	25
β-strand	56-62	7	26
α-helix	68-84	17
β-strand	89-95	7	26
α-helix	106-119	14
β-strand	123-126	4	26
β-strand	144-145	2	26
β-strand	152-153	2	26
α-helix	166-176	11
α-helix	180-182	3
α-helix	186-191	6
α-helix	200-205	6

Chain I: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	52-54	3	27
β-strand	57-59	3	19
β-strand	69-70	2	19
β-strand	72-77	6	27
β-strand	82-87	6	27
α-helix	92-103	12
β-strand	107-112	6	19
β-strand	128-133	6	19
α-helix	135-138	4
β-strand	144-150	7	28
β-strand	156-163	8	28
β-strand	184-185	2	28
β-strand	188	1	28
α-helix	190	1
β-strand	191-192	2	20

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 8	H	protein	210	Homo sapiens	O43402
ER membrane protein complex subunit 10	I	protein	263	Homo sapiens	Q5UCC4

Sequence of entity 1 (A), FASTA

>7ADP_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

>7ADP_2 ER membrane protein complex subunit 2 (chains B)
MAKVSELYDVTWEEMRDKMRKWREENSRNSEQIVEVGEELINEYASKLGDDIWIIYEQVM
IAALDYGRDDLALFCLQELRRQFPGSHRVKRLTGMRFEAMERYDDAIQLYDRILQEDPTN
TAARKRKIAIRKAQGKNVEAIRELNEYLEQFVGDQEAWHELAELYINEHDYAKAAFCLEE
LMMTNPHNHLYCQQYAEVKYTQGGLENLELSRKYFAQALKLNNRNMRALFGLYMSASHIA
SNPKASAKTKKDNMKYASWAASQINRAYQFAGRSKKETKYSLKAVEDMLETLQITQS

Sequence of entity 3 (C), FASTA

>7ADP_3 ER membrane protein complex subunit 3 (chains C)
MAGPELLLDSNIRLWVVLPIVIITFFVGMIRHYVSILLQSDKKLTQEQVSDSQVLIRSRV
LRENGKYIPKQSFLTRKYYFNNPEDGFFKKTKRKVVPPSPMTDPTMLTDMMKGNVTNVLP
MILIGGWINMTFSGFVTTKVPFPLTLRFKPMLQQGIELLTLDASWVSSASWYFLNVFGLR
SIYSLILGQDNAADQSRMMQEQMTGAAMAMPADTNKAFKTEWEALELTDHQWALDDVEEE
LMAKDLHFEGMFKKELQTSIF

Sequence of entity 4 (D), FASTA

>7ADP_4 ER membrane protein complex subunit 4 (chains D)
MTAQGGLVANRGRRFKWAIELSGPGGGSRGRSDRGSGQGDSLYPVGYLDKQVPDTSVQET
DRILVEKRCWDIALGPLKQIPMNLFIMYMAGNTISIFPTMMVCMMAWRPIQALMAISATF
KMLESSSQKFLQGLVYLIGNLMGLALAVYKCQSMGLLPTHASDWLAFIEPPERMEFSGGG
LLL

Sequence of entity 5 (E), FASTA

>7ADP_5 Membrane magnesium transporter 1 (chains E)
MAPSLWKGLVGIGLFALAHAAFSAAQHRSYMRLTEKEDESLPIDIVLQTLLAFAVTCYGI
VHIAGEFKDMDATSELKNKTFDTLRNHPSFYVFNHRGRVLFRPSDTANSSNQDALSSNTS
LKLRKLESLRRDYKDDDDK

Sequence of entity 6 (F), FASTA

>7ADP_6 ER membrane protein complex subunit 6 (chains F)
MAAVVAKREGPPFISEAAVRGNAAVLDYCRTSVSALSGATAGILGLTGLYGFIFYLLASV
LLSLLLILKAGRRWNKYFKSRRPLFTGGLIGGLFTYVLFWTFLYGMVHVY

Sequence of entity 7 (H), FASTA

>7ADP_7 ER membrane protein complex subunit 8 (chains H)
MPGVKLTTQAYCKMVLHGAKYPHCAVNGLLVAEKQKPRKEHLPLGGPGAHHTLFVDCIPL
FHGTLALAPMLEVALTLIDSWCKDHSYVIAGYYQANERVKDASPNQVAEKVASRIAEGFS
DTALIMVDNTKFTMDCVAPTIHVYEHHENRWRCRDPHHDYCEDWPEAQRISASLLDSRSY
ETLVDFDNHLDDIRNDWTNPEINKAVLHLC

Sequence of entity 8 (I), FASTA

>7ADP_8 ER membrane protein complex subunit 10 (chains I)
MAAAASAGATRLLLLLLMAVAAPSRARGSGCRAGTGARGAGAEGREGEACGTVGLLLEHS
FEIDDSANFRKRGSLLWNQQDGTLSLSQRQLSEEERGRLRDVAALNGLYRVRIPRRPGAL
DGLEAGGYVSSFVPACSLVESHLSDQLTLHVDVAGNVVGVSVVTHPGGCRGHEVEDVDLE
LFNTSVQLQPPTTAPGPETAAFIERLEMEQAQKAKNPQEQKSFFAKYWMYIIPVVLFLMM
SGAPDTGGQGGGGGGGGGGGSGR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

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
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
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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