6YSQ: The hC4Nb8 complement inhibitory nanobody

The hC4Nb8 complement inhibitory nanobody in complex with C4b. Determined by X-ray diffraction at 3.3 Å resolution. Released 24 Jun 2020.

Method: X-ray diffraction
Resolution: 3.3 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 8
Atoms: 26,297
Mol. weight: 392.43 kDa
Released: 24 Jun 2020

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

Secondary structure: helices and β-sheets

6YSQ contains 88 α-helices and 251 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: 18 helices, 56 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	1
β-strand	30-32	3	2
α-helix	36	1
β-strand	37-44	8	1
β-strand	52-60	9	2
β-strand	63	1	3
β-strand	65	1	3
β-strand	66-67	2	2
β-strand	72-76	5	2
β-strand	82-87	6	1
α-helix	91-97	7
β-strand	107-113	7	2
β-strand	127-135	9	2
β-strand	140-145	6	4
β-strand	149-150	2	5
β-strand	155-163	9	4
β-strand	169	1	4
β-strand	174-179	6	5
β-strand	185-191	7	5
β-strand	197-203	7	4
α-helix	208-209	2
β-strand	211-219	9	5
β-strand	228-233	6	5
β-strand	241-247	7	6
β-strand	252-253	2	7
β-strand	254	1	8
β-strand	259	1	8
β-strand	262-270	9	6
α-helix	274	1
β-strand	275	1	6
α-helix	276	1
β-strand	278-287	10	9
β-strand	293-295	3	9
α-helix	296	1
β-strand	301-304	4	9
β-strand	306	1	6
β-strand	309-314	6	6
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	1	9
β-strand	362-363	2	7
β-strand	367-370	4	10
α-helix	378-379	2
β-strand	384-392	9	10
β-strand	397	1	10
β-strand	402-409	8	11
β-strand	417-424	8	11
β-strand	430-435	6	10
β-strand	443-450	8	11
β-strand	456-463	8	11
α-helix	464-466	3
β-strand	472-476	5	12
α-helix	482-483	2
β-strand	488-496	9	12
β-strand	504-511	8	13
β-strand	514-522	9	13
β-strand	527-532	6	12
α-helix	535-537	3
β-strand	540-549	10	13
β-strand	552-561	10	13
β-strand	571-574	4	14
β-strand	581	1	15
β-strand	586-605	20	14
α-helix	608-611	4
α-helix	615-617	3
α-helix	622-628	7
α-helix	629-631	3
α-helix	644-650	7
β-strand	652-654	3	1
β-strand	655	1	16
β-strand	660	1	16
α-helix	661-664	4

Chain B: 15 helices, 56 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	33
β-strand	30-32	3	34
α-helix	36	1
β-strand	37-44	8	33
β-strand	52-60	9	34
β-strand	63	1	35
β-strand	65	1	35
β-strand	66-67	2	34
β-strand	72-76	5	34
β-strand	82-87	6	33
α-helix	91-97	7
β-strand	107-113	7	34
β-strand	127-135	9	34
β-strand	140-145	6	36
β-strand	149-150	2	37
β-strand	155-163	9	36
β-strand	169	1	36
β-strand	174-179	6	37
β-strand	185-191	7	37
β-strand	197-203	7	36
α-helix	208-209	2
β-strand	211-219	9	37
β-strand	228-233	6	37
β-strand	241-247	7	38
β-strand	252-253	2	39
β-strand	254	1	40
β-strand	259	1	40
β-strand	262-270	9	38
β-strand	275	1	38
β-strand	278-287	10	41
β-strand	293-295	3	41
α-helix	296	1
β-strand	301-304	4	41
β-strand	306	1	38
β-strand	309-314	6	38
α-helix	316-325	10
α-helix	330-332	3
β-strand	337-346	10	41
β-strand	352-355	4	41
β-strand	361	1	41
β-strand	362-363	2	39
β-strand	367-370	4	42
α-helix	378-379	2
β-strand	384-392	9	42
β-strand	397	1	42
β-strand	402-409	8	43
β-strand	413	1	2
β-strand	417-424	8	43
β-strand	430-435	6	42
β-strand	443-450	8	43
β-strand	456-463	8	43
α-helix	464-466	3
β-strand	472-476	5	44
α-helix	482-483	2
β-strand	488-496	9	44
β-strand	504-511	8	45
β-strand	514-522	9	45
β-strand	527-532	6	44
α-helix	535-537	3
β-strand	540-549	10	45
β-strand	552-561	10	45
β-strand	571-575	5	46
β-strand	581	1	47
β-strand	586-605	20	46
α-helix	608-611	4
α-helix	615-617	3
α-helix	622-628	7
α-helix	644-650	7
β-strand	652-655	4	33
β-strand	660	1	33
α-helix	661-664	4

Chain C: 19 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	766	1	17
α-helix	773	1
β-strand	774-775	2	18
β-strand	781-782	2	14
β-strand	786-798	13	14
β-strand	805-814	10	14
β-strand	818-821	4	14
α-helix	823-824	2
β-strand	825-828	4	14
β-strand	829	1	15
β-strand	833-837	5	19
α-helix	838-840	3
β-strand	843-844	2	20
β-strand	849-851	3	21
β-strand	853-857	5	19
β-strand	863-869	7	18
β-strand	875-876	2	22
α-helix	878-880	3
β-strand	884-889	6	18
β-strand	894-896	3	19
β-strand	899-901	3	21
β-strand	902-903	2	22
β-strand	908-917	10	18
β-strand	918	1	17
β-strand	924-932	9	18
β-strand	933-934	2	20
α-helix	935	1
β-strand	938-948	11	5
β-strand	957-960	4	23
β-strand	973-981	9	5
α-helix	1001-1003	3
α-helix	1011-1030	20
α-helix	1040-1053	14
α-helix	1073-1074	2
α-helix	1076-1088	13
α-helix	1097-1101	5
α-helix	1103-1109	7
β-strand	1111	1	24
β-strand	1117	1	24
α-helix	1137-1151	15
α-helix	1162-1183	22
α-helix	1190-1202	13
α-helix	1207-1219	13
β-strand	1223-1224	2	25
β-strand	1227-1228	2	25
α-helix	1261-1275	15
α-helix	1282-1292	11
α-helix	1303-1318	16
β-strand	1326-1335	10	23
β-strand	1338-1347	10	23
β-strand	1354-1356	3	5
β-strand	1366-1370	5	23
β-strand	1376-1386	11	5
β-strand	1397-1404	8	26
β-strand	1409	1	27

Chain D: 20 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	766	1	48
α-helix	773	1
β-strand	774-775	2	49
β-strand	781-782	2	46
β-strand	786-798	13	46
β-strand	805-814	10	46
β-strand	818-821	4	46
α-helix	823-824	2
β-strand	825-828	4	46
β-strand	829	1	47
β-strand	833-837	5	50
β-strand	843-844	2	51
β-strand	849-851	3	52
β-strand	853-857	5	50
β-strand	863-869	7	49
β-strand	875-876	2	53
α-helix	878-880	3
β-strand	885-889	5	49
β-strand	894-896	3	50
β-strand	899-901	3	52
β-strand	902-903	2	53
β-strand	908-917	10	49
β-strand	918	1	48
β-strand	924-932	9	49
β-strand	933-934	2	51
α-helix	935	1
β-strand	938-948	11	37
β-strand	957-960	4	54
β-strand	973-981	9	37
α-helix	1001-1003	3
α-helix	1011-1030	20
α-helix	1040-1056	17
α-helix	1073-1074	2
α-helix	1076-1088	13
α-helix	1097-1101	5
α-helix	1103-1107	5
β-strand	1111	1	55
β-strand	1117	1	55
α-helix	1130-1132	3
α-helix	1137-1151	15
α-helix	1152-1154	3
α-helix	1162-1183	22
α-helix	1190-1202	13
α-helix	1207-1219	13
α-helix	1259-1275	17
α-helix	1282-1292	11
α-helix	1303-1318	16
β-strand	1326-1335	10	54
β-strand	1338-1347	10	54
β-strand	1354-1356	3	37
β-strand	1366-1370	5	54
β-strand	1376-1386	11	37
β-strand	1397	1	56
β-strand	1400-1404	5	57
β-strand	1409	1	58

Chain E: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	1465-1474	10	26
β-strand	1484-1489	6	28
β-strand	1494-1496	3	26
α-helix	1498-1501	4
α-helix	1502-1504	3
β-strand	1512-1517	6	28
β-strand	1521-1526	6	28
β-strand	1534-1536	3	26
β-strand	1539-1542	4	26
β-strand	1546	1	27
β-strand	1552	1	29
β-strand	1554-1558	5	28
β-strand	1565-1567	3	28
β-strand	1570	1	29
α-helix	1579-1580	2
β-strand	1581-1584	4	30
β-strand	1587-1590	4	30
β-strand	1599	1	31
α-helix	1613-1618	6
β-strand	1625-1634	10	31
β-strand	1640-1652	13	31
β-strand	1664-1670	7	31
β-strand	1682-1687	6	31
β-strand	1693	1	32
β-strand	1699	1	32
β-strand	1701-1702	2	31
β-strand	1708-1711	4	31
α-helix	1712-1714	3
α-helix	1715-1718	4
α-helix	1724-1739	16

Chain F: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	1465-1472	8	57
β-strand	1474	1	56
β-strand	1484-1489	6	59
β-strand	1494-1496	3	57
α-helix	1498-1501	4
α-helix	1502-1504	3
β-strand	1512-1517	6	59
β-strand	1521-1526	6	59
β-strand	1534-1542	9	57
β-strand	1546	1	58
β-strand	1552-1558	7	59
β-strand	1565-1570	6	59
α-helix	1579-1580	2
β-strand	1581-1584	4	60
β-strand	1587-1590	4	60
β-strand	1599	1	61
α-helix	1613-1618	6
β-strand	1625-1634	10	61
β-strand	1640-1652	13	61
β-strand	1664-1670	7	61
β-strand	1682-1687	6	61
β-strand	1693	1	62
β-strand	1699	1	62
β-strand	1701-1702	2	61
β-strand	1708-1711	4	61
α-helix	1712-1714	3
α-helix	1715-1718	4
α-helix	1724-1739	16

Chain G: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	63
β-strand	11-13	3	64
β-strand	18-24	7	63
β-strand	33-39	7	65
β-strand	45-51	7	65
β-strand	58-60	3	65
β-strand	68-73	6	63
β-strand	78-83	6	63
α-helix	88-90	3
β-strand	92-99	8	65
β-strand	113-114	2	65
β-strand	118-120	3	65
β-strand	121-123	3	64

Chain H: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	66
β-strand	11-12	2	67
β-strand	18-25	8	66
β-strand	33-39	7	68
β-strand	45-51	7	68
β-strand	58-60	3	68
β-strand	69-73	5	66
β-strand	78-83	6	66
α-helix	88-90	3
β-strand	92-99	8	68
β-strand	113-114	2	68
β-strand	118-120	3	68
β-strand	121-122	2	67

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C4 beta chain	A, B	protein	656	Homo sapiens	P0C0L5 (AlphaFold model)
Complement C4-A alpha chain	C, D	protein	690	Homo sapiens	P0C0L4 (AlphaFold model)
Complement C4 gamma chain	E, F	protein	291	Homo sapiens	P0C0L5 (AlphaFold model)
hC4Nb8 nanobody	G, H	protein	132	Escherichia coli

Sequence of entity 1 (A, B), FASTA

>6YSQ_1 Complement C4 beta chain (chains A, B)
KPRLLLFSPSVVHLGVPLSVGVQLQDVPRGQVVKGSVFLRNPSRNNVPCSPKVDFTLSSE
RDFALLSLQVPLKDAKSCGLHQLLRGPEVQLVAHSPWLKDSLSRTTNIQGINLLFSSRRG
HLFLQTDQPIYNPGQRVRYRVFALDQKMRPSTDTITVMVENSHGLRVRKKEVYMPSSIFQ
DDFVIPDISEPGTWKISARFSDGLESNSSTQFEVKKYVLPNFEVKITPGKPYILTVPGHL
DEMQLDIQARYIYGKPVQGVAYVRFGLLDEDGKKTFFRGLESQTKLVNGQSHISLSKAEF
QDALEKLNMGITDLQGLRLYVAAAIIESPGGEMEEAELTSWYFVSSPFSLDLSKTKRHLV
PGAPFLLQALVREMSGSPASGIPVKVSATVSSPGSVPEVQDIQQNTDGSGQVSIPIIIPQ
TISELQLSVSAGSPHPAIARLTVAAPPSGGPGFLSIERPDSRPPRVGDTLNLNLRAVGSG
ATFSHYYYMILSRGQIVFMNREPKRTLTSVSVFVDHHLAPSFYFVAFYYHGDHPVANSLR
VDVQAGACEGKLELSVDGAKQYRNGESVKLHLETDSLALVALGALDTALYAAGSKSHKPL
NMGKVFEAMNSYDLGCGPGGGDSALQVFQAAGLAFSDGDQWTLSRKRLSCPKEKTT

Sequence of entity 2 (C, D), FASTA

>6YSQ_2 Complement C4-A alpha chain (chains C, D)
ALEILQEEDLIDEDDIPVRSFFPENWLWRVETVDRFQILTLWLPDSLTTWEIHGLSLSKT
KGLCVATPVQLRVFREFHLHLRLPMSVRRFEQLELRPVLYNYLDKNLTVSVHVSPVEGLC
LAGGGGLAQQVLVPAGSARPVAFSVVPTAAAAVSLKVVARGSFEFPVGDAVSKVLQIEKE
GAIHREELVYELNPLDHRGRTLEIPGNSDPNMIPDGDFNSYVRVTASDPLDTLGSEGALS
PGGVASLLRLPRGCGEETMIYLAPTLAASRYLDKTEQWSTLPPETKDHAVDLIQKGYMRI
QQFRKADGSYAAWLSRDSSTWLTAFVLKVLSLAQEQVGGSPEKLQETSNWLLSQQQADGS
FQDPCPVLDRSMQGGLVGNDETVALTAFVTIALHHGLAVFQDEGAEPLKQRVEASISKAN
SFLGEKASAGLLGAHAAAITAYALSLTKAPVDLLGVAHNNLMAMAQETGDNLYWGSVTGS
QSNAVSPTPAPRNPSDPMPQAPALWIETTAYALLHLLLHEGKAEMADQASAWLTRQGSFQ
GGFRSTQDTVIALDALSAYWIASHTTEERGLNVTLSSTGRNGFKSHALQLNNRQIRGLEE
ELQFSLGSKINVKVGGNSKGTLKVLRTYNVLDMKNTTCQDLQIEVTVKGHVEYTMEANED
YEDYEYDELPAKDDPDAPLQPVTPLQLFEG

Sequence of entity 3 (E, F), FASTA

>6YSQ_3 Complement C4 gamma chain (chains E, F)
EAPKVVEEQESRVHYTVCIWRNGKVGLSGMAIADVTLLSGFHALRADLEKLTSLSDRYVS
HFETEGPHVLLYFDSVPTSRECVGFEAVQEVPVGLVQPASATLYDYYNPERRCSVFYGAP
SKSRLLATLCSAEVCQCAEGKCPRQRRALERGLQDEDGYRMKFACYYPRVEYGFQVKVLR
EDSRAAFRLFETKITQVLHFTKDVKAAANQMRNFLVRASCRLRLEPGKEYLIMGLDGATY
DLEGHPQYLLDSNSWIEEMPSERLCRSTRQRAACAQLNDFLNEFGTQGCQV

Sequence of entity 4 (G, H), FASTA

>6YSQ_4 hC4Nb8 nanobody (chains G, H)
QVQLVESGGGLVQTGDSLRLSCAASGRTFSRYAMGWFRQAPGKERELVAAINWSGGSTYY
ADFAKGRFTISRDNAKNMLYLRMSSLKPEDTAVYYCAAGGPEVEITRANEYDYWGQGTQV
TVSSLEHHHHHH

Primary citation

An Ultrahigh-Affinity Complement C4b-Specific Nanobody Inhibits In Vivo Assembly of the Classical Pathway Proconvertase. Zarantonello, A., Presumey, J., Simoni, L. et al. J Immunol (2020) 205:1678-1694. DOI 10.4049/jimmunol.2000528 · PubMed

Other PDB entries of the same protein (UniProt P0C0L5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9U60 2.9 Å, C3 convertases zymogen C4b2 in loading state
9U5Z 3.1 Å, C3 convertases zymogen C4b2 in activation state
9U61 3.1 Å, CP/MBL pathways C3 convertase C4b2a and C3 complex

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