7B2P: Complement C4b

Cryo-EM structure of complement C4b in complex with nanobody B5. Determined by electron microscopy at 3.43 Å resolution. Released 2 Mar 2022.

Method: Electron microscopy
Resolution: 3.43 Å
Organisms: Homo sapiens, Lama glama
Chains: 4
Atoms: 11,690
Mol. weight: 205.29 kDa
Ligands: NAG
Released: 2 Mar 2022

Explore 7B2P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7B2P contains 36 α-helices and 112 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: 15 helices, 56 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	52	1	3
β-strand	55-60	6	4
α-helix	61-63	3
β-strand	66-67	2	4
β-strand	76	1	3
β-strand	83-87	5	1
α-helix	91-96	6
β-strand	108-113	6	4
α-helix	116-119	4
β-strand	127-132	6	4
β-strand	133-135	3	2
β-strand	140-145	6	5
β-strand	149-150	2	6
β-strand	155-163	9	5
β-strand	169	1	5
β-strand	174-179	6	7
β-strand	185-191	7	7
β-strand	197-203	7	5
α-helix	208-209	2
β-strand	211-212	2	6
β-strand	214-219	6	7
β-strand	227-229	3	7
β-strand	232-233	2	6
β-strand	241-247	7	8
β-strand	251-252	2	9
β-strand	262-270	9	8
α-helix	274	1
β-strand	275	1	8
α-helix	276	1
β-strand	278-287	10	9
β-strand	293-295	3	9
β-strand	301-304	4	9
β-strand	306	1	8
β-strand	309-314	6	8
α-helix	316-325	10
α-helix	330-332	3
β-strand	337-346	10	9
β-strand	352-357	6	9
β-strand	361-362	2	9
β-strand	367-370	4	10
β-strand	386-392	7	10
β-strand	397	1	10
β-strand	403-409	7	11
β-strand	418-423	6	11
β-strand	430-433	4	10
β-strand	443-450	8	11
β-strand	456-463	8	11
α-helix	464-466	3
β-strand	473-476	4	12
α-helix	482-484	3
β-strand	488-495	8	12
β-strand	504-510	7	13
β-strand	515-522	8	13
β-strand	528-532	5	12
β-strand	540-549	10	13
β-strand	552-556	5	13
β-strand	559-561	3	13
β-strand	572-574	3	14
β-strand	581	1	15
α-helix	582	1
β-strand	586-592	7	14
β-strand	597-605	9	16
α-helix	606-610	5
α-helix	621-629	9
α-helix	643-649	7
β-strand	652-655	4	1
β-strand	660	1	1
α-helix	662-664	3

Chain B: 18 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	775	1	17
β-strand	781-783	3	16
β-strand	786-789	4	16
β-strand	792-798	7	14
β-strand	805-813	9	16
β-strand	820-821	2	16
β-strand	825-828	4	16
β-strand	829	1	15
β-strand	835-836	2	18
β-strand	849-851	3	19
α-helix	853	1
β-strand	854-857	4	18
β-strand	863-869	7	17
β-strand	875-877	3	19
β-strand	885-889	5	17
β-strand	893-896	4	18
β-strand	899-903	5	19
β-strand	908-916	9	17
β-strand	925-932	8	17
α-helix	933-935	3
β-strand	938-948	11	7
β-strand	959-960	2	20
α-helix	961-963	3
β-strand	968	1	7
β-strand	975-980	6	7
α-helix	997-1001	5
α-helix	1005-1007	3
α-helix	1013-1031	19
α-helix	1039-1057	19
α-helix	1073-1074	2
α-helix	1076-1089	14
α-helix	1097-1109	13
β-strand	1111	1	21
β-strand	1117	1	21
α-helix	1126-1129	4
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	20
β-strand	1338-1344	7	20
β-strand	1356-1359	4	7
β-strand	1366-1369	4	20
β-strand	1376-1386	11	7
β-strand	1397-1405	9	22
β-strand	1409	1	23

Chain C: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	1466-1474	9	22
β-strand	1484-1486	3	24
β-strand	1489	1	24
α-helix	1490-1491	2
β-strand	1494-1496	3	22
α-helix	1499-1506	8
β-strand	1515-1518	4	24
β-strand	1521-1526	6	24
β-strand	1534-1542	9	22
β-strand	1546	1	23
β-strand	1552-1555	4	25
β-strand	1556-1558	3	24
β-strand	1567-1570	4	25
β-strand	1581-1583	3	26
β-strand	1588-1590	3	26

Chain D: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	27
β-strand	19-24	6	27
α-helix	29-31	3
β-strand	33-39	7	28
β-strand	45-51	7	28
β-strand	68-73	6	27
β-strand	78-83	6	27
β-strand	92-94	3	28
β-strand	97-99	3	28
β-strand	100	1	14
β-strand	104-106	3	14
β-strand	110-111	2	28
β-strand	115-117	3	28

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)
Nanobody B5	D	protein	140	Lama glama

Sequence of entity 1 (A), FASTA

>7B2P_1 Complement C4 beta chain (chains A)
KPRLLLFSPSVVHLGVPLSVGVQLQDVPRGQVVKGSVFLRNPSRNNVPCSPKVDFTLSSE
RDFALLSLQVPLKDAKSCGLHQLLRGPEVQLVAHSPWLKDSLSRTTNIQGINLLFSSRRG
HLFLQTDQPIYNPGQRVRYRVFALDQKMRPSTDTITVMVENSHGLRVRKKEVYMPSSIFQ
DDFVIPDISEPGTWKISARFSDGLESNSSTQFEVKKYVLPNFEVKITPGKPYILTVPGHL
DEMQLDIQARYIYGKPVQGVAYVRFGLLDEDGKKTFFRGLESQTKLVNGQSHISLSKAEF
QDALEKLNMGITDLQGLRLYVAAAIIESPGGEMEEAELTSWYFVSSPFSLDLSKTKRHLV
PGAPFLLQALVREMSGSPASGIPVKVSATVSSPGSVPEVQDIQQNTDGSGQVSIPIIIPQ
TISELQLSVSAGSPHPAIARLTVAAPPSGGPGFLSIERPDSRPPRVGDTLNLNLRAVGSG
ATFSHYYYMILSRGQIVFMNREPKRTLTSVSVFVDHHLAPSFYFVAFYYHGDHPVANSLR
VDVQAGACEGKLELSVDGAKQYRNGESVKLHLETDSLALVALGALDTALYAAGSKSHKPL
NMGKVFEAMNSYDLGCGPGGGDSALQVFQAAGLAFSDGDQWTLSRKRLSCPKEKTT

Sequence of entity 2 (B), FASTA

>7B2P_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

>7B2P_3 Complement C4 gamma chain (chains C)
EAPKVVEEQESRVHYTVCIWRNGKVGLSGMAIADVTLLSGFHALRADLEKLTSLSDRYVS
HFETEGPHVLLYFDSVPTSRECVGFEAVQEVPVGLVQPASATLYDYYNPERRCSVFYGAP
SKSRLLATLCSAEVCQCAEGKCPRQRRALERGLQDEDGYRMKFACYYPRVEYGFQVKVLR
EDSRAAFRLFETKITQVLHFTKDVKAAANQMRNFLVRASCRLRLEPGKEYLIMGLDGATY
DLEGHPQYLLDSNSWIEEMPSERLCRSTRQRAACAQLNDFLQEYGTQGCQV

Sequence of entity 4 (D), FASTA

>7B2P_4 Nanobody B5 (chains D)
EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYHMSWVRQAPGKGLEWISVINDSGDLTRY
ADSVKGRFTISRDNAKNTLYLQMNSLQPEDTAVYSCLKSSDFYSYSNADSRGQGTQVTVS
SHGSGLVPRGSGGGHHHHHH

Ligands and cofactors

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

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
7B2M 3.39 Å, Cryo-EM structure of complement C4b in complex with nanobody E3
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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