7B2M: Complement C4b

Cryo-EM structure of complement C4b in complex with nanobody E3. Determined by electron microscopy at 3.39 Å resolution. Released 2 Mar 2022.

Method: Electron microscopy
Resolution: 3.39 Å
Organisms: Homo sapiens, Lama glama
Chains: 4
Atoms: 11,664
Mol. weight: 204.52 kDa
Ligands: NAG
Released: 2 Mar 2022

Explore 7B2M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7B2M contains 38 α-helices and 116 β-strands across 4 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: 17 helices, 54 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	1
β-strand	30-32	3	2
β-strand	37-44	8	1
β-strand	55-60	6	3
α-helix	61-63	3
β-strand	66-67	2	3
β-strand	72-73	2	3
β-strand	83-87	5	1
α-helix	91-97	7
β-strand	108-113	6	3
α-helix	115-119	5
β-strand	127-132	6	3
β-strand	133-135	3	2
β-strand	140-145	6	4
β-strand	149-150	2	5
α-helix	154	1
β-strand	155-163	9	4
β-strand	169	1	4
β-strand	173-179	7	6
β-strand	185-192	8	6
β-strand	197-203	7	4
α-helix	208-209	2
β-strand	211-212	2	5
β-strand	214-219	6	6
β-strand	227-229	3	6
β-strand	232-233	2	5
β-strand	241-247	7	7
β-strand	251-253	3	8
β-strand	262-270	9	7
α-helix	274	1
β-strand	275	1	7
α-helix	276	1
β-strand	278-287	10	8
β-strand	293-295	3	8
β-strand	301-304	4	8
β-strand	310-314	5	7
α-helix	316-326	11
β-strand	337-346	10	8
β-strand	352-356	5	8
β-strand	361-363	3	8
β-strand	367-370	4	9
β-strand	384-392	9	9
β-strand	397	1	9
β-strand	403-410	8	10
β-strand	419-423	5	10
β-strand	430-435	6	9
α-helix	436	1
β-strand	443-450	8	10
β-strand	456-463	8	10
α-helix	464-466	3
α-helix	470-471	2
β-strand	472-476	5	11
α-helix	483-484	2
β-strand	488-496	9	11
β-strand	504-510	7	12
β-strand	515-522	8	12
β-strand	527-532	6	11
β-strand	540-541	2	13
β-strand	542-549	8	12
β-strand	552-556	5	12
β-strand	560-561	2	13
β-strand	572-574	3	14
β-strand	581	1	15
α-helix	582	1
β-strand	586-605	20	14
α-helix	606-610	5
α-helix	621-629	9
α-helix	643-650	8
β-strand	652-655	4	1
β-strand	660	1	1
α-helix	662-664	3

Chain B: 16 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	766	1	16
β-strand	774-775	2	17
β-strand	781	1	14
β-strand	785-798	14	14
β-strand	805-814	10	14
β-strand	818-821	4	14
β-strand	825-828	4	14
β-strand	829	1	15
β-strand	833-836	4	18
β-strand	843-844	2	19
β-strand	849-851	3	20
β-strand	854-857	4	18
β-strand	863-869	7	17
β-strand	875-876	2	21
β-strand	885-889	5	17
β-strand	893-895	3	18
β-strand	899-901	3	20
β-strand	902-903	2	21
β-strand	908-917	10	17
β-strand	918	1	16
β-strand	924-932	9	17
β-strand	933-934	2	19
α-helix	935	1
β-strand	938-945	8	6
β-strand	959-960	2	22
α-helix	961-963	3
β-strand	968	1	6
β-strand	974-981	8	6
α-helix	997-1002	6
α-helix	1013-1031	19
α-helix	1039-1057	19
α-helix	1073-1074	2
α-helix	1076-1089	14
α-helix	1097-1110	14
β-strand	1111	1	23
β-strand	1117	1	23
α-helix	1127-1129	3
α-helix	1138-1151	14
α-helix	1162-1184	23
α-helix	1190-1202	13
α-helix	1207-1220	14
α-helix	1259-1274	16
α-helix	1282-1293	12
α-helix	1303-1319	17
β-strand	1329-1335	7	22
β-strand	1338-1341	4	22
β-strand	1344	1	22
β-strand	1355-1359	5	6
β-strand	1366-1370	5	22
β-strand	1377-1386	10	6
β-strand	1397-1405	9	24
β-strand	1409	1	25

Chain C: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	1466-1474	9	24
β-strand	1484-1486	3	26
β-strand	1489	1	26
α-helix	1490-1491	2
β-strand	1494-1496	3	24
α-helix	1498-1506	9
β-strand	1512-1518	7	26
β-strand	1521-1526	6	26
β-strand	1535-1536	2	24
β-strand	1539-1542	4	24
β-strand	1546	1	25
β-strand	1552-1555	4	27
β-strand	1556-1558	3	26
β-strand	1567-1570	4	27
β-strand	1581-1583	3	28
β-strand	1588-1590	3	28

Chain D: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	29
β-strand	12	1	30
β-strand	22-24	3	29
β-strand	33-39	7	31
α-helix	44-45	2
β-strand	46-51	6	31
β-strand	57-59	3	31
α-helix	61-63	3
β-strand	70-72	3	29
β-strand	77-79	3	29
α-helix	87-89	3
β-strand	91-99	9	31
β-strand	103-106	4	31
β-strand	110-112	3	31
β-strand	114	1	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C4 beta chain	A	protein	656	Homo sapiens	P0C0L4 (AlphaFold model)
Complement C4 alpha chain	B	protein	767	Homo sapiens	P0C0L4 (AlphaFold model)
Complement C4 gamma chain	C	protein	291	Homo sapiens	P0C0L4 (AlphaFold model)
Anti-C4b nanobody E3	D	protein	135	Lama glama

Sequence of entity 1 (A), FASTA

>7B2M_1 Complement C4 beta chain (chains A)
KPRLLLFSPSVVHLGVPLSVGVQLQDVPRGQVVKGSVFLRNPSRNNVPCSPKVDFTLSSE
RDFALLSLQVPLKDAKSCGLHQLLRGPEVQLVAHSPWLKDSLSRTTNIQGINLLFSSRRG
HLFLQTDQPIYNPGQRVRYRVFALDQKMRPSTDTITVMVENSHGLRVRKKEVYMPSSIFQ
DDFVIPDISEPGTWKISARFSDGLESNSSTQFEVKKYVLPNFEVKITPGKPYILTVPGHL
DEMQLDIQARYIYGKPVQGVAYVRFGLLDEDGKKTFFRGLESQTKLVNGQSHISLSKAEF
QDALEKLNMGITDLQGLRLYVAAAIIESPGGEMEEAELTSWYFVSSPFSLDLSKTKRHLV
PGAPFLLQALVREMSGSPASGIPVKVSATVSSPGSVPEVQDIQQNTDGSGQVSIPIIIPQ
TISELQLSVSAGSPHPAIARLTVAAPPSGGPGFLSIERPDSRPPRVGDTLNLNLRAVGSG
ATFSHYYYMILSRGQIVFMNREPKRTLTSVSVFVDHHLAPSFYFVAFYYHGDHPVANSLR
VDVQAGACEGKLELSVDGAKQYRNGESVKLHLETDSLALVALGALDTALYAAGSKSHKPL
NMGKVFEAMNSYDLGCGPGGGDSALQVFQAAGLAFSDGDQWTLSRKRLSCPKEKTT

Sequence of entity 2 (B), FASTA

>7B2M_2 Complement C4 alpha chain (chains B)
NVNFQKAINEKLGQYASPTAKRCCQDGVTRLPMMRSCEQRAARVQQPDCREPFLSCCQFA
ESLRKKSRDKGQAGLQRALEILQEEDLIDEDDIPVRSFFPENWLWRVETVDRFQILTLWL
PDSLTTWEIHGLSLSKTKGLCVATPVQLRVFREFHLHLRLPMSVRRFEQLELRPVLYNYL
DKNLTVSVHVSPVEGLCLAGGGGLAQQVLVPAGSARPVAFSVVPTAAAAVSLKVVARGSF
EFPVGDAVSKVLQIEKEGAIHREELVYELNPLDHRGRTLEIPGNSDPNMIPDGDFNSYVR
VTASDPLDTLGSEGALSPGGVASLLRLPRGCGEQTMIYLAPTLAASRYLDKTEQWSTLPP
ETKDHAVDLIQKGYMRIQQFRKADGSYAAWLSRDSSTWLTAFVLKVLSLAQEQVGGSPEK
LQETSNWLLSQQQADGSFQDPCPVLDRSMQGGLVGNDETVALTAFVTIALHHGLAVFQDE
GAEPLKQRVEASISKANSFLGEKASAGLLGAHAAAITAYALSLTKAPVDLLGVAHNNLMA
MAQETGDNLYWGSVTGSQSNAVSPTPAPRNPSDPMPQAPALWIETTAYALLHLLLHEGKA
EMADQASAWLTRQGSFQGGFRSTQDTVIALDALSAYWIASHTTEERGLNVTLSSTGRNGF
KSHALQLNNRQIRGLEEELQFSLGSKINVKVGGNSKGTLKVLRTYNVLDMKNTTCQDLQI
EVTVKGHVEYTMEANEDYEDYEYDELPAKDDPDAPLQPVTPLQLFEG

Sequence of entity 3 (C), FASTA

>7B2M_3 Complement C4 gamma chain (chains C)
EAPKVVEEQESRVHYTVCIWRNGKVGLSGMAIADVTLLSGFHALRADLEKLTSLSDRYVS
HFETEGPHVLLYFDSVPTSRECVGFEAVQEVPVGLVQPASATLYDYYNPERRCSVFYGAP
SKSRLLATLCSAEVCQCAEGKCPRQRRALERGLQDEDGYRMKFACYYPRVEYGFQVKVLR
EDSRAAFRLFETKITQVLHFTKDVKAAANQMRNFLVRASCRLRLEPGKEYLIMGLDGATY
DLEGHPQYLLDSNSWIEEMPSERLCRSTRQRAACAQLNDFLQEYGTQGCQV

Sequence of entity 4 (D), FASTA

>7B2M_4 Anti-C4b nanobody E3 (chains D)
EVQLVESGGGLVQAGGSLRLSCAASGSDFSANAVGWYRQAPGKQRVVVASISSTGNTKYS
NSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCWLFRFGIENYWGQGTQVTVSSHGSG
LVPRGSGGGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Multifaceted Activities of Seven Nanobodies against Complement C4b. De la O Becerra, K.I., Oosterheert, W., van den Bos, R.M. et al. J Immunol (2022) 208:2207-2219. DOI 10.4049/jimmunol.2100647 · PubMed

Other PDB entries of the same protein (UniProt P0C0L4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1HZF 2.3 Å, C4ADG fragment of human complement factor C4A
6YSQ 3.3 Å, The hC4Nb8 complement inhibitory nanobody in complex with C4b
7B2P 3.43 Å, Cryo-EM structure of complement C4b in complex with nanobody B5
5JTW 3.5 Å, Crystal structure of complement C4b re-refined using iMDFF
9QJ5 3.5 Å, Structure of the Complement classical and lectin pathway proconvertase, C4b2
9QK2 3.5 Å, Structure of the Complement classical and lectin pathway C3 convertase in complex with…
5JPN 3.6 Å, Structure of human complement C4 rebuilt using iMDFF
5JPM 3.75 Å, Structure of the complex of human complement C4 with MASP-2 rebuilt using iMDFF
7B2Q 3.76 Å, Cryo-EM structure of complement C4b in complex with nanobody B12
9QJ4 3.9 Å, Structure of the Complement classical and lectin pathway proconvertase, C4b2
9QPY 4.3 Å, Structure of the Complement classical and lectin pathway C3 convertase

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