6Z3W: Human ER membrane protein complex

Name: PDB 6Z3W: Human ER membrane protein complex
Published: 2020-07-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: membrane protein

Human ER membrane protein complex. Determined by electron microscopy at 6.4 Å resolution. Released 15 Jul 2020.

Method: Electron microscopy
Resolution: 6.4 Å
Organism: Homo sapiens
Chains: 9
Atoms: 9,412
Mol. weight: 275.33 kDa
Released: 15 Jul 2020

Explore 6Z3W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Z3W contains 54 α-helices and 85 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 A: 6 helices, 60 β-strands

Element	Residues	Length	Sheet
β-strand	57	1	1
β-strand	63	1	1
β-strand	64-65	2	2
β-strand	72-73	2	2
β-strand	77	1	3
β-strand	96	1	4
β-strand	100-101	2	5
β-strand	106-107	2	5
β-strand	110	1	6
β-strand	111	1	4
β-strand	117	1	6
β-strand	132	1	7
β-strand	143-146	4	7
β-strand	150-154	5	7
β-strand	161-166	6	7
β-strand	174-179	6	8
β-strand	186-192	7	8
β-strand	196-202	7	8
β-strand	209-211	3	8
β-strand	214-216	3	8
α-helix	220-226	7
β-strand	228-229	2	9
α-helix	234	1
β-strand	235-236	2	9
β-strand	245-248	4	9
β-strand	256-259	4	9
β-strand	306	1	10
β-strand	309	1	10
β-strand	323-325	3	11
β-strand	327	1	12
β-strand	329	1	12
β-strand	332-334	3	11
β-strand	372-376	5	13
β-strand	390-394	5	13
β-strand	409-411	3	14
β-strand	417-419	3	14
β-strand	432	1	3
β-strand	452-454	3	15
α-helix	483-509	27
β-strand	537-540	4	15
β-strand	545-547	3	15
β-strand	557-559	3	15
β-strand	571-575	5	16
α-helix	584-585	2
β-strand	586-593	8	16
β-strand	597-604	8	16
β-strand	614-615	2	16
β-strand	625-629	5	17
β-strand	639-643	5	17
β-strand	650-652	3	17
α-helix	657-664	8
β-strand	669-675	7	18
β-strand	680-686	7	18
β-strand	709	1	19
β-strand	741-746	6	19
β-strand	757-762	6	19
β-strand	771-775	5	19
β-strand	783	1	20
β-strand	786	1	21
β-strand	791	1	21
β-strand	793-795	3	20
β-strand	804-806	3	20
β-strand	838-839	2	20
β-strand	862-863	2	22
β-strand	871-872	2	22
α-helix	963-992	30

Chain B: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	13-24	12
α-helix	31-48	18
α-helix	49-53	5
α-helix	57-65	9
α-helix	69-82	14
α-helix	87-99	13
α-helix	103-116	14
α-helix	121-131	11
α-helix	137-150	14
α-helix	156-167	12
α-helix	171-184	14
α-helix	189-202	14
α-helix	205-221	17
α-helix	226-234	9
α-helix	235-240	6
α-helix	247-272	26

Chain C: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	13-17	5
α-helix	19-39	21
α-helix	47-64	18
α-helix	70-81	12
α-helix	85-90	6
α-helix	112-130	19
α-helix	170-187	18
α-helix	211-259	49

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	59-85	27
α-helix	99-119	21
α-helix	129-147	19

Chain E: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	3-28	26
α-helix	29-33	5
α-helix	43-62	20

Chain F: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	4-6	3
α-helix	16-44	29
α-helix	50-68	19
α-helix	82-85	4
α-helix	90-103	14

Chain G: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	47	1	23
β-strand	67-68	2	24
β-strand	86	1	23
β-strand	92-98	7	24
β-strand	106-112	7	24
β-strand	118-121	4	24
α-helix	163-178	16

Chain H: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
β-strand	27-30	4	25
β-strand	46-50	5	25
α-helix	57-66	10
α-helix	67-71	5
α-helix	72	1
β-strand	80	1	25
α-helix	95-107	13
β-strand	114-115	2	26
α-helix	119-121	3
β-strand	131-132	2	26
β-strand	135-136	2	27
β-strand	139-140	2	27
α-helix	153-166	14
α-helix	168-170	3
α-helix	175-180	6

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,ER membrane protein complex subunit 1,ER membrane protein…	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	131	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 9	H	protein	208	Homo sapiens	Q9Y3B6
ER membrane protein complex subunit 10	I	protein	262	Homo sapiens	Q5UCC4

Sequence of entity 1 (A), FASTA

>6Z3W_1 ER membrane protein complex subunit 1,ER membrane protein complex subunit 1,ER membrane protein complex subunit 1,ER membrane protein complex subunit 1 (chains A)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XGMFLKRLSSQLILLQAWTSHLWKMFYDARXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXY
DYVLISSVLFGLVFATMITKRLAQVKLLNRAWR

Sequence of entity 2 (B), FASTA

>6Z3W_2 ER membrane protein complex subunit 2 (chains B)
MAKVSELYDVTWEEMRDKMRKWREENSRNSEQIVEVGEELINEYASKLGDDIWIIYEQVM
IAALDYGRDDLALFCLQELRRQFPGSHRVKRLTGMRFEAMERYDDAIQLYDRILQEDPTN
TAARKRKIAIRKAQGKNVEAIRELNEYLEQFVGDQEAWHELAELYINEHDYAKAAFCLEE
LMMTNPHNHLYCQQYAEVKYTQGGLENLELSRKYFAQALKLNNRNMRALFGLYMSASHIA
SNPKASAKTKKDNMKYASWAASQINRAYQFAGRSKKETKYSLKAVEDMLETLQITQS

Sequence of entity 3 (C), FASTA

>6Z3W_3 ER membrane protein complex subunit 3 (chains C)
MAGPELLLDSNIRLWVVLPIVIITFFVGMIRHYVSILLQSDKKLTQEQVSDSQVLIRSRV
LRENGKYIPKQSFLTRKYYFNNPEDGFFKKTKRKVVPPSPMTDPTMLTDMMKGNVTNVLP
MILIGGWINMTFSGFVTTKVPFPLTLRFKPMLQQGIELLTLDASWVSSASWYFLNVFGLR
SIYSLILGQDNAADQSRMMQEQMTGAAMAMPADTNKAFKTEWEALELTDHQWALDDVEEE
LMAKDLHFEGMFKKELQTSIF

Sequence of entity 4 (D), FASTA

>6Z3W_4 ER membrane protein complex subunit 4 (chains D)
MTAQGGLVANRGRRFKWAIELSGPGGGSRGRSDRGSGQGDSLYPVGYLDKQVPDTSVQET
DRILVEKRCWDIALGPLKQIPMNLFIMYMAGNTISIFPTMMVCMMAWRPIQALMAISATF
KMLESSSQKFLQGLVYLIGNLMGLALAVYKCQSMGLLPTHASDWLAFIEPPERMEFSGGG
LLL

Sequence of entity 5 (E), FASTA

>6Z3W_5 Membrane magnesium transporter 1 (chains E)
MAPSLWKGLVGIGLFALAHAAFSAAQHRSYMRLTEKEDESLPIDIVLQTLLAFAVTCYGI
VHIAGEFKDMDATSELKNKTFDTLRNHPSFYVFNHRGRVLFRPSDTANSSNQDALSSNTS
LKLRKLESLRR

Sequence of entity 6 (F), FASTA

>6Z3W_6 ER membrane protein complex subunit 6 (chains F)
MAAVVAKREGPPFISEAAVRGNAAVLDYCRTSVSALSGATAGILGLTGLYGFIFYLLASV
LLSLLLILKAGRRWNKYFKSRRPLFTGGLIGGLFTYVLFWTFLYGMVHVY

Sequence of entity 7 (G), FASTA

>6Z3W_7 ER membrane protein complex subunit 7 (chains G)
MAAALWGFFPVLLLLLLSGDVQSSEVPGAAAEGSGGSGVGIGDRFKIEGRAVVPGVKPQD
WISAARVLVDGEEHVGFLKTDGSFVVHDIPSGSYVVEVVSPAYRFDPVRVDITSKGKMRA
RYVNYIKTSEVVRLPYPLQMKSSGPPSYFIKRESWGWTDFLMNPMVMMMVLPLLIFVLLP
KVVNTSDPDMRREMEQSMNMLNSNHELPDVSEFMTRLFSSKSSGKSSSGSSKTGKSGAGK
RR

Sequence of entity 8 (H), FASTA

>6Z3W_8 ER membrane protein complex subunit 9 (chains H)
MGEVEISALAYVKMCLHAARYPHAAVNGLFLAPAPRSGECLCLTDCVPLFHSHLALSVML
EVALNQVDVWGAQAGLVVAGYYHANAAVNDQSPGPLALKIAGRIAEFFPDAVLIMLDNQK
LVPQPRVPPVIVLENQGLRWVPKDKNLVMWRDWEESRQMVGALLEDRAHQHLVDFDCHLD
DIRQDWTNQRLNTQITQWVGPTNGNGNA

Sequence of entity 9 (I), FASTA

>6Z3W_9 ER membrane protein complex subunit 10 (chains I)
MAAASAGATRLLLLLLMAVAAPSRARGSGCRAGTGARGAGAEGREGEACGTVGLLLEHSF
EIDDSANFRKRGSLLWNQQDGTLSLSQRQLSEEERGRLRDVAALNGLYRVRIPRRPGALD
GLEAGGYVSSFVPACSLVESHLSDQLTLHVDVAGNVVGVSVVTHPGGCRGHEVEDVDLEL
FNTSVQLQPPTTAPGPETAAFIERLEMEQAQKAKNPQEQKSFFAKYWMYIIPVVLFLMMS
GAPDTGGQGGGGGGGGGGGSGR

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 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
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…
9C7V 6.6 Å, Structure of the human BOS:human EMC complex in GDN

Browse structure collections

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