8DE6: Oligomeric C9

Oligomeric C9 in complex with aE11 Fab. Determined by electron microscopy at 3.2 Å resolution. Released 25 Jan 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Mus musculus, Homo sapiens
Chains: 7
Atoms: 13,243
Mol. weight: 251.67 kDa
Ligands: CA, BMA, NAG
Released: 25 Jan 2023

Explore 8DE6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DE6 contains 52 α-helices and 131 β-strands across 7 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: 14 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	6
β-strand	23-24	2	7
α-helix	25-27	3
α-helix	32-34	3
β-strand	39-43	5	8
β-strand	46-48	3	7
β-strand	50	1	9
β-strand	51	1	6
α-helix	55-57	3
β-strand	62-66	5	8
β-strand	84-85	2	10
β-strand	91-92	2	10
α-helix	94-96	3
α-helix	110-112	3
β-strand	127-128	2	11
β-strand	138-139	2	12
β-strand	146	1	12
β-strand	151	1	13
β-strand	162-165	4	11
β-strand	170-173	4	11
β-strand	178-199	22	14
β-strand	234	1	14
β-strand	237-256	20	14
β-strand	263	1	13
α-helix	265-272	8
α-helix	280-290	11
β-strand	293-295	3	12
β-strand	297-317	21	14
β-strand	349-364	16	14
α-helix	370-380	11
α-helix	386-395	10
α-helix	396-398	3
β-strand	401-404	4	14
β-strand	407-409	3	12
α-helix	410-413	4
α-helix	421-437	17
α-helix	441-443	3
α-helix	445-446	2
β-strand	452-455	4	15
β-strand	459	1	9
β-strand	460-463	4	15
β-strand	468	1	16
β-strand	476	1	16

Chain B: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	22-24	3	17
β-strand	30-31	2	18
β-strand	37-44	8	17
α-helix	48-50	3
β-strand	53-58	6	19
β-strand	65-70	6	19
β-strand	76-78	3	19
α-helix	80-82	3
β-strand	86-91	6	17
β-strand	96-101	6	17
β-strand	110-116	7	19
β-strand	130	1	19
β-strand	134-136	3	19
β-strand	137-138	2	18

Chain C: 15 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	22
β-strand	23-24	2	23
α-helix	25-27	3
α-helix	32-34	3
β-strand	39-43	5	24
β-strand	46-48	3	23
β-strand	50-51	2	22
α-helix	55-57	3
β-strand	62-66	5	24
β-strand	84-85	2	25
β-strand	91-92	2	25
α-helix	94-96	3
α-helix	110-112	3
β-strand	127-128	2	26
α-helix	130-133	4
β-strand	138-139	2	27
β-strand	146	1	27
β-strand	151	1	28
β-strand	164-165	2	29
β-strand	170-171	2	29
β-strand	172-173	2	26
β-strand	178-187	10	14
β-strand	190-199	10	14
β-strand	234-256	23	14
β-strand	263	1	28
α-helix	265-272	8
α-helix	280-290	11
β-strand	293-295	3	27
β-strand	297-317	21	14
β-strand	350-364	15	14
α-helix	370-380	11
α-helix	386-395	10
α-helix	396-398	3
β-strand	401-404	4	14
β-strand	407-409	3	27
α-helix	410-413	4
α-helix	421-437	17
α-helix	441-443	3
α-helix	445-446	2
β-strand	452-455	4	22
β-strand	459-463	5	22
β-strand	468	1	30
β-strand	476	1	30

Chain E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	1
β-strand	30-31	2	2
β-strand	39-44	6	1
α-helix	48-50	3
β-strand	53-58	6	3
β-strand	65-70	6	3
β-strand	76-78	3	3
β-strand	88-91	4	1
β-strand	96-99	4	1
α-helix	106-108	3
β-strand	110-116	7	3
β-strand	134-136	3	3
β-strand	137-138	2	2

Chain F: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	4
β-strand	29-32	4	5
β-strand	38-43	6	4
β-strand	52-58	7	5
β-strand	62-68	7	5
β-strand	73	1	5
α-helix	74	1
β-strand	81-86	6	4
β-strand	89-94	6	4
β-strand	104-109	6	5
α-helix	115	1
β-strand	117	1	5
β-strand	121-125	5	5

Chain G: 15 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	31
β-strand	23-24	2	32
α-helix	25-27	3
α-helix	32-34	3
β-strand	39-43	5	33
β-strand	46-48	3	32
β-strand	50	1	34
β-strand	51	1	31
α-helix	55-57	3
β-strand	62-66	5	33
β-strand	84-85	2	35
β-strand	91-92	2	35
α-helix	94-96	3
α-helix	110-112	3
β-strand	127-128	2	36
α-helix	131-133	3
β-strand	138-139	2	37
β-strand	146	1	37
β-strand	151	1	38
β-strand	162-165	4	36
β-strand	170-173	4	36
β-strand	178-201	24	14
β-strand	234	1	14
β-strand	237-256	20	14
β-strand	263	1	38
α-helix	265-272	8
α-helix	280-290	11
β-strand	293-295	3	37
β-strand	297-317	21	14
β-strand	350-364	15	14
α-helix	370-380	11
α-helix	386-395	10
α-helix	396-398	3
β-strand	401-404	4	14
β-strand	407-409	3	37
α-helix	410-413	4
α-helix	421-437	17
α-helix	441-443	3
α-helix	445-446	2
β-strand	452-455	4	39
β-strand	459	1	34
β-strand	460-463	4	39
β-strand	468	1	40
β-strand	476	1	40

Chain I: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	20
β-strand	29-32	4	21
β-strand	38-43	6	20
β-strand	52-58	7	21
β-strand	62-68	7	21
β-strand	72-73	2	21
β-strand	82-86	5	20
β-strand	89-94	6	20
α-helix	99-101	3
β-strand	104-105	2	21
β-strand	107-109	3	21
α-helix	115	1
β-strand	121-125	5	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
aE11 Fab VH	B, E	protein	140	Mus musculus
aE11 Fab VL	F, I	protein	126	Mus musculus
Complement component C9	A, C, G	protein	564	Homo sapiens	P02748 (AlphaFold model)

Sequence of entity 1 (B, E), FASTA

>8DE6_1 aE11 Fab VH (chains B, E)
MAVLALLFCLVTFPSCILSQVQLKESGPGLVAPSQSLSITCTVSGFSLTVYGVNWIRQPP
GKGLEWLGMIWGDGSTDYNSALKSRLSITKDNSKSQVFLKMNSLQTDDTARYYCARDRSY
GGSSAWFGYWGQGTLVTVSA

Sequence of entity 2 (F, I), FASTA

>8DE6_2 aE11 Fab VL (chains F, I)
MSSAQFLGLLLLCFQGTRCDIQMTQTTSSLSASLGDRVTISCRASHDISNYLNWYQQKPD
GTLKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDVATYFCQQGNYLPYTFGGG
TKLEIK

Sequence of entity 3 (A, C, G), FASTA

>8DE6_3 Complement component C9 (chains A, C, G)
METDTLLLWVLLLWVPGSTGDAAQPAQYTTSYDPELTESSGSASHIDCRMSPWSEWSQCD
PCLRQMFRSRSIEVFGQFNGKRCTDAVGDRRQCVPTEPCEDAEDDCGNDFQCSTGRCIKM
RLRCNGDNDCGDFSDEDDCESEPRPPCRDRVVEESELARTAGYGINILGMDPLSTPFDNE
FYNGLCNRDRDGNTLTYYRRPWNVASLIYETKGEKNFRTEHYEEQIEAFKSIIQEKTSNF
NAAISLKFTPTETNKAEQCCEETASSISLHGKGSFRFSYSKNETYQLFLSYSSKKEKMFL
HVKGEIHLGRFVMRNRDVVLTTTFVDDIKALPTTYEKGEYFAFLETYGTHYSSSGSLGGL
YELIYVLDKASMKRKGVELKDIKRCLGYHLDVSLAFSEISVGAEFNKDDCVKRGEGRAVN
ITSENLIDDVVSLIRGGTRKYAFELKEKLLRGTVIDVTDFVNWASSINDAPVLISQKLSP
IYNLVPVKMKNAHLKKQNLERAIEDYINEFSVRKCHTCQNGGTVILMDGKCLCACPFKFE
GIACEISKQKISEGLPALEFPNEK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3
BMA	beta-D-mannopyranose	C6 H12 O6	6
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

The neoepitope of the complement C5b-9 Membrane Attack Complex is formed by proximity of adjacent ancillary regions of C9. Bayly-Jones, C., Ho, B.H.T., Lau, C. et al. Commun Biol (2023) 6:42-42. DOI 10.1038/s42003-023-04431-y · PubMed

Other PDB entries of the same protein (UniProt P02748 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7NYD 3.27 Å, cryoEM structure of 2C9-sMAC
8B0G 3.3 Å, 2C9, C5b9-CD59 structure
8B0H 3.3 Å, 2C9, C5b9-CD59 cryoEM structure
7NYC 3.54 Å, cryoEM structure of 3C9-sMAC
6DLW 3.9 Å, Complement component polyC9
6H03 5.6 Å, Open conformation of the membrane attack complex
6H04 5.6 Å, Closed conformation of the Membrane Attack Complex
5FMW 6.7 Å, The poly-C9 component of the Complement Membrane Attack Complex

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